Path to genome folder specified as: /gscratch/srlab/sr320/data/geoduck/v01/ Using 28 threads for the top and bottom strand indexing processes each, so using 56 cores in total Aligner to be used: >> Bowtie 2 << (default) Writing bisulfite genomes out into a single MFA (multi FastA) file Bismark Genome Preparation - Step I: Preparing folders Path to Bowtie 2 specified as: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ Bisulfite Genome Indexer version v0.21.0 (last modified: 05 Feb 2019) Created Bisulfite Genome folder /gscratch/srlab/sr320/data/geoduck/v01/Bisulfite_Genome/ Created Bisulfite Genome folder /gscratch/srlab/sr320/data/geoduck/v01/Bisulfite_Genome/CT_conversion/ Created Bisulfite Genome folder /gscratch/srlab/sr320/data/geoduck/v01/Bisulfite_Genome/GA_conversion/ Step I - Prepare genome folders - completed Bismark Genome Preparation - Step II: Bisulfite converting reference genome conversions performed: chromosome C->T G->A Scaffold_01 12767429 12765526 Scaffold_02 10088811 10062918 Scaffold_03 8199278 8194496 Scaffold_04 9161562 9161987 Scaffold_05 9498414 9497714 Scaffold_06 8458182 8463483 Scaffold_07 6054340 6047203 Scaffold_08 8517146 8506733 Scaffold_09 5420328 5445998 Scaffold_10 7547438 7543051 Scaffold_11 7053984 7054209 Scaffold_12 7145712 7105651 Scaffold_13 6273846 6290785 Scaffold_14 6515251 6527291 Scaffold_15 6625508 6624214 Scaffold_16 4528254 4550625 Scaffold_17 4780809 4787183 Scaffold_18 3756408 3758031 Total number of conversions performed: C->T: 132392700 G->A: 132387098 Step II - Genome bisulfite conversions - completed Bismark Genome Preparation - Step III: Launching the Bowtie 2 indexer Please be aware that this process can - depending on genome size - take several hours! Preparing indexing of CT converted genome in /gscratch/srlab/sr320/data/geoduck/v01/Bisulfite_Genome/CT_conversion/ Parent process: Starting to index C->T converted genome with the following command: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2-build -f genome_mfa.CT_conversion.fa BS_CT --threads 28 Settings: Output files: "BS_CT.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 112 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: genome_mfa.CT_conversion.fa Building a SMALL index Reading reference sizes Preparing indexing of GA converted genome in /gscratch/srlab/sr320/data/geoduck/v01/Bisulfite_Genome/GA_conversion/ Child process: Starting to index G->A converted genome with the following command: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2-build -f genome_mfa.GA_conversion.fa BS_GA --threads 28 Settings: Output files: "BS_GA.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 112 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: genome_mfa.GA_conversion.fa Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:08 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time reading reference sizes: 00:00:08 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:04 bmax according to bmaxDivN setting: 6998760 Using parameters --bmax 5249070 --dcv 1024 Doing ahead-of-time memory usage test Time to join reference sequences: 00:00:05 bmax according to bmaxDivN setting: 6998760 Using parameters --bmax 5249070 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 5249070 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Passed! Constructing with these parameters: --bmax 5249070 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:06 Allocating rank array Ranking v-sort output V-Sorting samples time: 00:00:07 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:04 Invoking Larsson-Sadakane on ranks Ranking v-sort output time: 00:00:05 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:07 Sanity-checking and returning Building samples Reserving space for 300 sample suffixes Generating random suffixes QSorting 300 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 300 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Invoking Larsson-Sadakane on ranks time: 00:00:06 Sanity-checking and returning Building samples Reserving space for 300 sample suffixes Generating random suffixes QSorting 300 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 300 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 40, merged 136; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 41, merged 134; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 21, merged 23; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 18, merged 24; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 13, merged 10; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 14, merged 12; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 7, merged 8; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 6, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 5; iterating... Avg bucket size: 3.8805e+06 (target: 5249069) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 202 Reserving size (5249070) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: Getting block 2 of 202 Reserving size (5249070) for bucket 2 Getting block 3 of 202 Getting block 4 of 202 Getting block 5 of 202 Getting block 6 of 202 Getting block 7 of 202 Getting block 8 of 202 Getting block 9 of 202 Getting block 10 of 202 Getting block 11 of 202 Getting block 12 of 202 Getting block 13 of 202 Getting block 14 of 202 Getting block 15 of 202 Getting block 16 of 202 Getting block 17 of 202 Getting block 18 of 202 Reserving size (5249070) for bucket 3 Calculating Z arrays for bucket 2 Reserving size (5249070) for bucket 4 Reserving size (5249070) for bucket 5 Reserving size (5249070) for bucket 6 Reserving size (5249070) for bucket 7 Reserving size (5249070) for bucket 8 Reserving size (5249070) for bucket 9 Reserving size (5249070) for bucket 10 Getting block 19 of 202 Getting block 20 of 202 Getting block 21 of 202 Reserving size (5249070) for bucket 11 Reserving size (5249070) for bucket 12 Reserving size (5249070) for bucket 13 Getting block 22 of 202 Reserving size (5249070) for bucket 14 Reserving size (5249070) for bucket 15 Reserving size (5249070) for bucket 16 Reserving size (5249070) for bucket 17 Getting block 23 of 202 Getting block 24 of 202 Getting block 25 of 202 Reserving size (5249070) for bucket 18 Getting block 26 of 202 Calculating Z arrays for bucket 3 Getting block 27 of 202 Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 9 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 6 Reserving size (5249070) for bucket 19 Reserving size (5249070) for bucket 20 Reserving size (5249070) for bucket 21 Calculating Z arrays for bucket 11 Calculating Z arrays for bucket 13 Reserving size (5249070) for bucket 22 Calculating Z arrays for bucket 17 Calculating Z arrays for bucket 14 Calculating Z arrays for bucket 15 Reserving size (5249070) for bucket 23 Calculating Z arrays for bucket 12 Reserving size (5249070) for bucket 24 Calculating Z arrays for bucket 16 Reserving size (5249070) for bucket 25 Calculating Z arrays for bucket 18 Reserving size (5249070) for bucket 26 Reserving size (5249070) for bucket 27 Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 10: Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 20 Entering block accumulator loop for bucket 6: Calculating Z arrays for bucket 21 Entering block accumulator loop for bucket 11: Calculating Z arrays for bucket 22 Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 14: Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 24 Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 12: Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 16: Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 18: Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 27: bucket 16: 10% bucket 1: 10% bucket 4: 10% bucket 3: 10% bucket 7: 10% bucket 6: 10% bucket 5: 10% bucket 10: 10% bucket 8: 10% bucket 9: 10% bucket 2: 10% bucket 11: 10% bucket 15: 10% bucket 12: 10% bucket 13: 10% bucket 17: 10% bucket 14: 10% bucket 18: 10% bucket 20: 10% bucket 19: 10% bucket 21: 10% bucket 24: 10% bucket 25: 10% bucket 23: 10% bucket 27: 10% bucket 26: 10% bucket 22: 10% bucket 16: 20% bucket 1: 20% bucket 4: 20% bucket 10: 20% bucket 17: 20% bucket 15: 20% bucket 20: 20% bucket 5: 20% bucket 21: 20% bucket 2: 20% bucket 7: 20% bucket 3: 20% bucket 26: 20% bucket 6: 20% bucket 9: 20% bucket 24: 20% bucket 8: 20% bucket 18: 20% bucket 11: 20% bucket 19: 20% bucket 14: 20% bucket 12: 20% bucket 22: 20% bucket 27: 20% bucket 23: 20% bucket 13: 20% bucket 1: 30% bucket 25: 20% Splitting and merging Splitting and merging time: 00:00:00 Split 4, merged 4; iterating... Avg bucket size: 3.86138e+06 (target: 5249069) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 203 Getting block 2 of 203 Reserving size (5249070) for bucket 1 Reserving size (5249070) for bucket 2 Getting block 3 of 203 Getting block 4 of 203 Getting block 5 of 203 Getting block 6 of 203 Getting block 7 of 203 Getting block 8 of 203 Getting block 9 of 203 Getting block 10 of 203 Getting block 11 of 203 Getting block 12 of 203 Getting block 13 of 203 Getting block 14 of 203 Getting block 15 of 203 Getting block 16 of 203 Getting block 17 of 203 Getting block 18 of 203 Getting block 19 of 203 Getting block 20 of 203 Getting block 22 of 203 Getting block 21 of 203 Getting block 23 of 203 Getting block 24 of 203 Getting block 25 of 203 Calculating Z arrays for bucket 1 Calculating Z arrays for bucket 2 Reserving size (5249070) for bucket 3 Getting block 26 of 203 Reserving size (5249070) for bucket 4 Reserving size (5249070) for bucket 5 Reserving size (5249070) for bucket 6 Reserving size (5249070) for bucket 7 Reserving size (5249070) for bucket 8 Reserving size (5249070) for bucket 9 Reserving size (5249070) for bucket 10 Reserving size (5249070) for bucket 11 Reserving size (5249070) for bucket 12 Reserving size (5249070) for bucket 13 Reserving size (5249070) for bucket 14 Reserving size (5249070) for bucket 15 Reserving size (5249070) for bucket 16 Getting block 27 of 203 Reserving size (5249070) for bucket 17 Reserving size (5249070) for bucket 18 Reserving size (5249070) for bucket 19 Reserving size (5249070) for bucket 20 Reserving size (5249070) for bucket 22 Reserving size (5249070) for bucket 21 Reserving size (5249070) for bucket 23 Reserving size (5249070) for bucket 24 Reserving size (5249070) for bucket 25 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 2: Reserving size (5249070) for bucket 26 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 9 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 14 Calculating Z arrays for bucket 16 Calculating Z arrays for bucket 15 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 13 Calculating Z arrays for bucket 12 Calculating Z arrays for bucket 11 Reserving size (5249070) for bucket 27 Calculating Z arrays for bucket 17 Calculating Z arrays for bucket 18 Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 3: Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 10: Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 12: Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 27: bucket 16: 30% bucket 7: 30% bucket 10: 30% bucket 18: 30% bucket 19: 30% bucket 5: 30% bucket 15: 30% bucket 4: 30% bucket 20: 30% bucket 23: 30% bucket 17: 30% bucket 3: 30% bucket 2: 30% bucket 14: 30% bucket 8: 30% bucket 21: 30% bucket 6: 30% bucket 9: 30% bucket 26: 30% bucket 3: 10% bucket 12: 30% bucket 27: 10% bucket 24: 30% bucket 1: 10% bucket 22: 30% bucket 1: 40% bucket 2: 10% bucket 4: 10% bucket 6: 10% bucket 5: 10% bucket 13: 30% bucket 9: 10% bucket 27: 30% bucket 11: 30% bucket 12: 10% bucket 8: 10% bucket 7: 10% bucket 10: 10% bucket 11: 10% bucket 14: 10% bucket 16: 10% bucket 15: 10% bucket 20: 10% bucket 17: 10% bucket 21: 10% bucket 22: 10% bucket 24: 10% bucket 18: 10% bucket 25: 30% bucket 23: 10% bucket 25: 10% bucket 26: 10% bucket 13: 10% bucket 16: 40% bucket 19: 10% bucket 18: 40% bucket 7: 40% bucket 10: 40% bucket 19: 40% bucket 3: 20% bucket 5: 40% bucket 27: 20% bucket 11: 20% bucket 4: 40% bucket 15: 40% bucket 2: 40% bucket 3: 40% bucket 1: 20% bucket 23: 40% bucket 20: 40% bucket 6: 40% bucket 8: 40% bucket 2: 20% bucket 17: 40% bucket 14: 40% bucket 4: 20% bucket 9: 40% bucket 9: 20% bucket 21: 40% bucket 13: 20% bucket 5: 20% bucket 6: 20% bucket 12: 20% bucket 1: 50% bucket 7: 20% bucket 12: 40% bucket 8: 20% bucket 10: 20% bucket 23: 20% bucket 14: 20% bucket 26: 40% bucket 24: 40% bucket 15: 20% bucket 16: 20% bucket 22: 40% bucket 20: 20% bucket 13: 40% bucket 17: 20% bucket 11: 40% bucket 21: 20% bucket 18: 20% bucket 22: 20% bucket 24: 20% bucket 27: 40% bucket 25: 20% bucket 19: 20% bucket 26: 20% bucket 25: 40% bucket 18: 50% bucket 16: 50% bucket 3: 30% bucket 11: 30% bucket 5: 30% bucket 7: 50% bucket 9: 50% bucket 10: 50% bucket 5: 50% bucket 1: 30% bucket 8: 50% bucket 27: 30% bucket 19: 50% bucket 2: 30% bucket 4: 50% bucket 10: 30% bucket 2: 50% bucket 3: 50% bucket 4: 30% bucket 9: 30% bucket 15: 50% bucket 6: 50% bucket 6: 30% bucket 12: 30% bucket 7: 30% bucket 13: 30% bucket 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70% bucket 26: 50% bucket 16: 60% bucket 8: 80% bucket 24: 70% bucket 22: 70% bucket 9: 60% bucket 10: 60% bucket 7: 60% bucket 26: 70% bucket 7: 80% bucket 6: 60% bucket 15: 60% bucket 21: 60% bucket 14: 60% bucket 12: 60% bucket 5: 80% bucket 27: 70% bucket 2: 80% bucket 16: 80% bucket 27: 60% bucket 25: 60% bucket 4: 80% bucket 13: 60% bucket 18: 80% bucket 8: 60% bucket 9: 80% bucket 25: 70% bucket 20: 60% bucket 3: 80% bucket 19: 80% bucket 1: 70% bucket 14: 80% bucket 20: 80% bucket 19: 60% bucket 3: 70% bucket 1: 90% bucket 2: 70% bucket 6: 80% bucket 4: 70% bucket 11: 70% bucket 23: 80% bucket 5: 70% bucket 18: 60% bucket 17: 60% bucket 15: 80% bucket 24: 60% bucket 10: 90% bucket 23: 60% bucket 22: 60% bucket 17: 80% bucket 12: 80% bucket 7: 70% bucket 21: 80% bucket 16: 70% bucket 9: 70% bucket 8: 90% bucket 6: 70% bucket 10: 70% bucket 11: 80% bucket 26: 60% bucket 6: 90% bucket 13: 80% bucket 21: 70% bucket 15: 70% bucket 12: 70% bucket 14: 70% bucket 7: 90% bucket 24: 80% bucket 22: 80% bucket 8: 70% bucket 16: 90% bucket 2: 90% bucket 13: 70% bucket 5: 90% bucket 27: 70% bucket 1: 80% bucket 4: 90% bucket 26: 80% bucket 25: 70% bucket 2: 80% bucket 19: 70% bucket 3: 80% bucket 20: 70% bucket 9: 90% bucket 27: 80% bucket 11: 80% bucket 3: 90% bucket 4: 80% bucket 18: 70% bucket 18: 90% bucket 25: 80% bucket 1: 100% Sorting block of length 5050263 for bucket 1 (Using difference cover) bucket 17: 70% bucket 5: 80% bucket 19: 90% bucket 14: 90% bucket 20: 90% bucket 6: 100% Sorting block of length 4614355 for bucket 6 (Using difference cover) bucket 8: 100% Sorting block of length 3300857 for bucket 8 (Using difference cover) bucket 23: 90% bucket 24: 70% bucket 22: 70% bucket 11: 90% bucket 15: 90% bucket 7: 80% bucket 23: 70% bucket 10: 100% Sorting block of length 5173127 for bucket 10 (Using difference cover) bucket 12: 90% bucket 9: 80% bucket 17: 90% bucket 18: 80% bucket 16: 80% bucket 6: 80% bucket 10: 80% bucket 21: 90% bucket 15: 80% bucket 1: 90% bucket 12: 80% bucket 21: 80% bucket 14: 80% bucket 8: 80% bucket 26: 70% bucket 13: 90% bucket 2: 90% bucket 13: 80% bucket 7: 100% Sorting block of length 3545429 for bucket 7 (Using difference cover) bucket 2: 100% Sorting block of length 4511536 for bucket 2 (Using difference cover) bucket 3: 90% bucket 5: 100% Sorting block of length 4999726 for bucket 5 (Using difference cover) bucket 27: 80% bucket 4: 100% Sorting block of length 4211089 for bucket 4 (Using difference cover) bucket 4: 90% bucket 24: 90% bucket 19: 80% bucket 16: 100% Sorting block of length 3798043 for bucket 16 (Using difference cover) bucket 11: 90% bucket 22: 90% bucket 20: 80% bucket 25: 80% bucket 5: 90% bucket 3: 100% Sorting block of length 2688603 for bucket 3 (Using difference cover) bucket 9: 100% Sorting block of length 3732256 for bucket 9 (Using difference cover) bucket 18: 90% bucket 26: 90% bucket 17: 80% bucket 14: 100% Sorting block of length 3972937 for bucket 14 (Using difference cover) bucket 27: 90% bucket 18: 100% Sorting block of length 4841486 for bucket 18 (Using difference cover) bucket 25: 90% bucket 23: 80% bucket 19: 100% Sorting block of length 3263920 for bucket 19 (Using difference cover) bucket 7: 90% bucket 12: 100% Sorting block of length 4791159 for bucket 12 (Using difference cover) bucket 20: 100% Sorting block of length 4494626 for bucket 20 (Using difference cover) bucket 24: 80% bucket 10: 90% bucket 9: 90% bucket 22: 80% bucket 11: 100% Sorting block of length 4236701 for bucket 11 (Using difference cover) bucket 6: 90% bucket 1: 100% Sorting block of length 4564657 for bucket 1 (Using difference cover) bucket 16: 90% bucket 15: 100% Sorting block of length 4541931 for bucket 15 (Using difference cover) bucket 23: 100% Sorting block of length 5057285 for bucket 23 (Using difference cover) bucket 5: 100% Sorting block of length 4315998 for bucket 5 (Using difference cover) bucket 12: 90% bucket 17: 100% Sorting block of length 3110985 for bucket 17 (Using difference cover) bucket 2: 100% bucket 15: 90% Sorting block of length 4625056 for bucket 2 (Using difference cover) bucket 8: 90% bucket 14: 90% bucket 21: 90% bucket 3: 100% Sorting block of length 4213684 for bucket 3 (Using difference cover) bucket 13: 90% bucket 4: 100% Sorting block of length 4120580 for bucket 4 (Using difference cover) bucket 26: 80% bucket 21: 100% Sorting block of length 3777395 for bucket 21 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3300858 for bucket 8 bucket 13: 100% Sorting block of length 3531043 for bucket 13 (Using difference cover) bucket 27: 90% bucket 11: 100% Sorting block of length 4315595 for bucket 11 (Using difference cover) Getting block 28 of 202 Reserving size (5249070) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 19: 90% bucket 20: 90% bucket 25: 90% bucket 18: 100% Sorting block of length 2376257 for bucket 18 (Using difference cover) bucket 24: 100% Sorting block of length 1252216 for bucket 24 (Using difference cover) bucket 10: 100% Sorting block of length 5148591 for bucket 10 (Using difference cover) bucket 17: 90% bucket 22: 100% Sorting block of length 1608469 for bucket 22 (Using difference cover) bucket 7: 100% Sorting block of length 1137970 for bucket 7 (Using difference cover) bucket 26: 100% Sorting block of length 2892660 for bucket 26 (Using difference cover) bucket 9: 100% Sorting block of length 1283383 for bucket 9 (Using difference cover) bucket 23: 90% Sorting block time: 00:00:02 Returning block of 2688604 for bucket 3 Sorting block time: 00:00:03 Returning block of 5050264 for bucket 1 bucket 6: 100% Sorting block of length 4369477 for bucket 6 (Using difference cover) bucket 25: 100% Sorting block of length 4039829 for bucket 25 (Using difference cover) bucket 27: 100% Sorting block of length 4808034 for bucket 27 (Using difference cover) bucket 27: 100% Sorting block of length 4531174 for bucket 27 (Using difference cover) Getting block 29 of 202 Reserving size (5249070) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: Sorting block time: 00:00:02 Returning block of 3972938 for bucket 14 bucket 24: 90% bucket 22: 90% bucket 26: 90% bucket 16: 100% Sorting block of length 1938611 for bucket 16 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3545430 for bucket 7 bucket 14: 100% Sorting block of length 4752110 for bucket 14 (Using difference cover) Getting block 30 of 202 Reserving size (5249070) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 12: 100% Sorting block of length 1534873 for bucket 12 (Using difference cover) Getting block 31 of 202 Reserving size (5249070) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: bucket 15: 100% Sorting block of length 4133567 for bucket 15 (Using difference cover) bucket 8: 100% Sorting block of length 4920594 for bucket 8 (Using difference cover) Getting block 32 of 202 Reserving size (5249070) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: Sorting block time: 00:00:04 Returning block of 4614356 for bucket 6 bucket 13: 100% Sorting block of length 4736534 for bucket 13 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3798044 for bucket 16 bucket 21: 100% Sorting block of length 3646177 for bucket 21 (Using difference cover) Getting block 33 of 202 Reserving size (5249070) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: Getting block 34 of 202 Reserving size (5249070) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: Sorting block time: 00:00:03 Returning block of 4211090 for bucket 4 Sorting block time: 00:00:03 Returning block of 3732257 for bucket 9 Sorting block time: 00:00:01 Returning block of 1283384 for bucket 9 Sorting block time: 00:00:01 Returning block of 1252217 for bucket 24 Sorting block time: 00:00:04 Returning block of 5173128 for bucket 10 Sorting block time: 00:00:01 Returning block of 1137971 for bucket 7 Getting block 28 of 203 Reserving size (5249070) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: Getting block 35 of 202 Reserving size (5249070) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: Getting block 29 of 203 Reserving size (5249070) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: Getting block 36 of 202 Reserving size (5249070) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Sorting block time: 00:00:01 Returning block of 1608470 for bucket 22 bucket 19: 100% Sorting block of length 2995574 for bucket 19 (Using difference cover) Getting block 37 of 202 Reserving size (5249070) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: bucket 20: 100% Sorting block of length 2505673 for bucket 20 (Using difference cover) Getting block 38 of 202 Reserving size (5249070) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: Sorting block time: 00:00:03 Returning block of 4511537 for bucket 2 bucket 26: 100% Sorting block of length 2074552 for bucket 26 (Using difference cover) Getting block 39 of 202 Reserving size (5249070) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Sorting block time: 00:00:02 Returning block of 3110986 for bucket 17 bucket 25: 100% Sorting block of length 4834032 for bucket 25 (Using difference cover) Getting block 40 of 202 Reserving size (5249070) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: Getting block 41 of 202 Reserving size (5249070) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: Sorting block time: 00:00:03 Returning block of 3263921 for bucket 19 bucket 28: 10% bucket 17: 100% Sorting block of length 4834187 for bucket 17 (Using difference cover) bucket 23: 100% Sorting block of length 4780589 for bucket 23 (Using difference cover) Getting block 42 of 202 Reserving size (5249070) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: Sorting block time: 00:00:04 Returning block of 4999727 for bucket 5 Sorting block time: 00:00:02 Returning block of 2376258 for bucket 18 Sorting block time: 00:00:02 Returning block of 1534874 for bucket 12 Getting block 30 of 203 Reserving size (5249070) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: Getting block 31 of 203 Reserving size (5249070) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: Sorting block time: 00:00:03 Returning block of 3531044 for bucket 13 bucket 29: 10% Sorting block time: 00:00:03 Returning block of 4541932 for bucket 15 bucket 22: 100% Sorting block of length 2944920 for bucket 22 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4564658 for bucket 1 bucket 24: 100% Sorting block of length 1101739 for bucket 24 (Using difference cover) Getting block 43 of 202 Reserving size (5249070) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: Getting block 44 of 202 Reserving size (5249070) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: Getting block 45 of 202 Reserving size (5249070) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Getting block 32 of 203 Reserving size (5249070) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: Sorting block time: 00:00:03 Returning block of 4120581 for bucket 4 Sorting block time: 00:00:03 Returning block of 4213685 for bucket 3 Sorting block time: 00:00:04 Returning block of 4791160 for bucket 12 Sorting block time: 00:00:04 Returning block of 4494627 for bucket 20 Sorting block time: 00:00:04 Returning block of 4841487 for bucket 18 Sorting block time: 00:00:03 Returning block of 4236702 for bucket 11 Sorting block time: 00:00:02 Returning block of 1938612 for bucket 16 Sorting block time: 00:00:03 Returning block of 4315999 for bucket 5 Sorting block time: 00:00:02 Returning block of 2892661 for bucket 26 Getting block 33 of 203 Reserving size (5249070) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: Getting block 34 of 203 Reserving size (5249070) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: Getting block 46 of 202 Reserving size (5249070) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: Getting block 47 of 202 Reserving size (5249070) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: Sorting block time: 00:00:03 Returning block of 3777396 for bucket 21 Getting block 35 of 203 Reserving size (5249070) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: Sorting block time: 00:00:03 Returning block of 5057286 for bucket 23 Getting block 36 of 203 Reserving size (5249070) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Getting block 48 of 202 Reserving size (5249070) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Getting block 49 of 202 Reserving size (5249070) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: Getting block 50 of 202 Reserving size (5249070) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: Getting block 51 of 202 Reserving size (5249070) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: Sorting block time: 00:00:04 Returning block of 4625057 for bucket 2 bucket 28: 10% Sorting block time: 00:00:04 Returning block of 4315596 for bucket 11 Getting block 52 of 202 Reserving size (5249070) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: Sorting block time: 00:00:01 Returning block of 1101740 for bucket 24 Getting block 37 of 203 Reserving size (5249070) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: bucket 31: 10% Sorting block time: 00:00:02 Returning block of 2074553 for bucket 26 Getting block 38 of 203 Reserving size (5249070) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: Getting block 39 of 203 Reserving size (5249070) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Getting block 40 of 203 Reserving size (5249070) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: bucket 29: 10% bucket 32: 10% bucket 30: 10% Sorting block time: 00:00:02 Returning block of 2505674 for bucket 20 bucket 31: 10% Getting block 41 of 203 Reserving size (5249070) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: Sorting block time: 00:00:03 Returning block of 4808035 for bucket 27 Getting block 53 of 202 Reserving size (5249070) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: Sorting block time: 00:00:03 Returning block of 4039830 for bucket 25 Sorting block time: 00:00:02 Returning block of 2995575 for bucket 19 Sorting block time: 00:00:03 Returning block of 4531175 for bucket 27 Sorting block time: 00:00:04 Returning block of 4369478 for bucket 6 Getting block 42 of 203 Reserving size (5249070) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: Getting block 54 of 202 Reserving size (5249070) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: Sorting block time: 00:00:04 Returning block of 4133568 for bucket 15 Getting block 43 of 203 Reserving size (5249070) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: Sorting block time: 00:00:04 Returning block of 5148592 for bucket 10 bucket 37: 10% bucket 34: 10% Getting block 44 of 203 Reserving size (5249070) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: bucket 40: 10% Sorting block time: 00:00:04 Returning block of 4752111 for bucket 14 bucket 35: 10% Getting block 45 of 203 Reserving size (5249070) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Sorting block time: 00:00:02 Returning block of 2944921 for bucket 22 Sorting block time: 00:00:03 Returning block of 3646178 for bucket 21 bucket 33: 10% Getting block 46 of 203 Reserving size (5249070) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: Getting block 47 of 203 Reserving size (5249070) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 39: 10% bucket 36: 10% Getting block 48 of 203 Reserving size (5249070) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Getting block 49 of 203 Reserving size (5249070) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: Sorting block time: 00:00:03 Returning block of 4920595 for bucket 8 bucket 28: 20% bucket 38: 10% Sorting block time: 00:00:03 Returning block of 4736535 for bucket 13 Getting block 50 of 203 Reserving size (5249070) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 30: 10% Getting block 51 of 203 Reserving size (5249070) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 32: 20% bucket 42: 10% bucket 41: 10% Sorting block time: 00:00:04 Returning block of 4834188 for bucket 17 bucket 29: 20% Sorting block time: 00:00:03 Returning block of 4780590 for bucket 23 bucket 28: 20% Sorting block time: 00:00:04 Returning block of 4834033 for bucket 25 bucket 32: 10% bucket 35: 10% bucket 46: 10% Getting block 52 of 203 Reserving size (5249070) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 43: 10% bucket 37: 10% Getting block 53 of 203 Reserving size (5249070) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: Getting block 54 of 203 Reserving size (5249070) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 33: 10% bucket 38: 10% bucket 31: 20% bucket 36: 10% bucket 44: 10% bucket 49: 10% bucket 34: 10% bucket 48: 10% bucket 51: 10% bucket 30: 20% bucket 52: 10% bucket 44: 10% bucket 31: 20% bucket 29: 20% bucket 45: 10% bucket 47: 10% bucket 41: 10% bucket 37: 20% bucket 34: 20% bucket 50: 10% bucket 39: 20% bucket 45: 10% bucket 47: 10% bucket 39: 10% bucket 40: 20% bucket 40: 10% bucket 46: 10% bucket 35: 20% bucket 53: 10% bucket 42: 10% bucket 32: 30% bucket 43: 10% bucket 28: 30% bucket 54: 10% bucket 28: 30% bucket 36: 20% bucket 33: 20% bucket 33: 20% bucket 38: 20% bucket 45: 20% bucket 38: 20% bucket 30: 20% bucket 48: 10% bucket 29: 30% bucket 31: 30% bucket 49: 10% bucket 36: 20% bucket 37: 20% bucket 35: 20% bucket 42: 20% bucket 30: 30% bucket 41: 20% bucket 51: 10% bucket 37: 30% bucket 32: 20% bucket 46: 20% bucket 44: 20% bucket 50: 10% bucket 44: 20% bucket 48: 20% bucket 47: 20% bucket 31: 30% bucket 29: 30% bucket 41: 20% bucket 45: 20% bucket 43: 20% bucket 52: 10% bucket 54: 10% bucket 49: 20% bucket 53: 10% bucket 34: 30% bucket 34: 20% bucket 51: 20% bucket 50: 20% bucket 28: 40% bucket 38: 30% bucket 46: 20% bucket 40: 30% bucket 53: 20% bucket 35: 30% bucket 28: 40% bucket 39: 30% bucket 40: 20% bucket 42: 20% bucket 52: 20% bucket 33: 30% bucket 47: 20% bucket 36: 30% bucket 36: 30% bucket 39: 20% bucket 43: 20% bucket 32: 40% bucket 33: 30% bucket 37: 30% bucket 29: 40% bucket 38: 30% bucket 30: 30% bucket 29: 40% bucket 45: 30% bucket 37: 40% bucket 31: 40% bucket 31: 40% bucket 44: 30% bucket 32: 30% bucket 54: 20% bucket 48: 20% bucket 28: 50% bucket 45: 30% bucket 51: 20% bucket 50: 20% bucket 41: 30% bucket 35: 30% bucket 42: 30% bucket 30: 40% bucket 36: 40% bucket 49: 20% bucket 44: 30% bucket 41: 30% bucket 53: 20% bucket 39: 40% bucket 38: 40% bucket 34: 30% bucket 40: 40% bucket 34: 40% bucket 47: 30% bucket 52: 20% bucket 46: 30% bucket 48: 30% bucket 53: 30% bucket 46: 30% bucket 33: 40% bucket 43: 30% bucket 54: 20% bucket 51: 30% bucket 49: 30% bucket 35: 40% bucket 31: 50% bucket 52: 30% bucket 36: 40% bucket 50: 30% bucket 32: 50% bucket 28: 50% bucket 29: 50% bucket 33: 40% bucket 36: 50% bucket 42: 30% bucket 29: 50% bucket 38: 40% bucket 31: 50% bucket 37: 40% bucket 47: 30% bucket 40: 30% bucket 37: 50% bucket 43: 30% bucket 45: 40% bucket 41: 40% bucket 30: 50% bucket 44: 40% bucket 30: 40% bucket 28: 60% bucket 45: 40% bucket 38: 50% bucket 39: 50% bucket 34: 50% bucket 50: 30% bucket 39: 30% bucket 54: 30% bucket 35: 40% bucket 44: 40% bucket 32: 40% bucket 51: 30% bucket 41: 40% bucket 33: 50% bucket 52: 30% bucket 40: 50% bucket 36: 60% bucket 42: 40% bucket 47: 40% bucket 49: 30% bucket 46: 40% bucket 36: 50% bucket 46: 40% bucket 35: 50% bucket 31: 60% bucket 53: 40% bucket 48: 30% bucket 34: 40% bucket 37: 50% bucket 44: 50% bucket 41: 50% bucket 29: 60% bucket 43: 40% bucket 52: 40% bucket 50: 40% bucket 31: 60% bucket 28: 60% bucket 38: 60% bucket 32: 60% bucket 48: 40% bucket 51: 40% bucket 33: 50% bucket 54: 30% bucket 53: 30% bucket 49: 40% bucket 47: 40% bucket 28: 70% bucket 45: 50% bucket 37: 60% bucket 38: 50% bucket 51: 40% bucket 42: 40% bucket 45: 50% bucket 39: 60% bucket 34: 60% bucket 30: 60% bucket 43: 40% bucket 29: 60% bucket 40: 40% bucket 33: 60% bucket 30: 50% bucket 40: 60% bucket 39: 40% bucket 44: 50% bucket 31: 70% bucket 46: 50% bucket 32: 50% bucket 29: 70% bucket 35: 50% bucket 38: 70% bucket 50: 40% bucket 36: 60% bucket 37: 60% bucket 28: 70% bucket 52: 40% bucket 41: 50% bucket 41: 60% bucket 36: 70% bucket 49: 40% bucket 54: 40% bucket 44: 60% bucket 34: 50% bucket 46: 50% bucket 35: 60% bucket 47: 50% bucket 42: 50% bucket 28: 80% bucket 32: 70% bucket 52: 50% bucket 42: 50% bucket 45: 60% bucket 34: 70% bucket 43: 50% bucket 31: 70% bucket 53: 50% bucket 33: 60% bucket 51: 50% bucket 48: 40% bucket 29: 70% bucket 37: 70% bucket 50: 50% bucket 39: 70% bucket 38: 60% bucket 49: 50% bucket 33: 70% bucket 54: 40% bucket 45: 60% bucket 43: 50% bucket 48: 50% bucket 30: 70% bucket 53: 40% bucket 30: 60% bucket 31: 80% bucket 38: 80% bucket 36: 70% bucket 40: 70% bucket 29: 80% bucket 40: 50% bucket 32: 60% bucket 44: 70% bucket 35: 60% bucket 47: 50% bucket 28: 80% bucket 46: 60% bucket 39: 50% bucket 51: 50% bucket 42: 60% bucket 37: 70% bucket 41: 70% bucket 44: 60% bucket 36: 80% bucket 28: 90% bucket 41: 60% bucket 50: 50% bucket 34: 60% bucket 46: 60% bucket 32: 80% bucket 54: 50% bucket 35: 70% bucket 39: 80% bucket 29: 80% bucket 47: 60% bucket 44: 80% bucket 31: 90% bucket 45: 70% bucket 33: 80% bucket 42: 60% bucket 38: 90% bucket 52: 50% bucket 36: 80% bucket 29: 90% bucket 43: 60% bucket 30: 70% bucket 43: 60% bucket 53: 60% bucket 37: 80% bucket 38: 70% bucket 32: 70% bucket 34: 80% bucket 53: 50% bucket 54: 50% bucket 31: 80% bucket 52: 60% bucket 48: 50% bucket 45: 70% bucket 49: 50% bucket 35: 70% bucket 33: 70% bucket 46: 70% bucket 50: 60% bucket 40: 60% bucket 50: 60% bucket 30: 80% bucket 51: 60% bucket 49: 60% bucket 48: 60% bucket 41: 80% bucket 33: 90% bucket 28: 100% Sorting block of length 4889372 for bucket 28 (Using difference cover) bucket 37: 80% bucket 47: 60% bucket 39: 60% bucket 28: 90% bucket 40: 80% bucket 44: 90% bucket 31: 100% Sorting block of length 5194322 for bucket 31 (Using difference cover) bucket 42: 70% bucket 51: 60% bucket 45: 80% bucket 39: 90% bucket 38: 100% Sorting block of length 5081006 for bucket 38 (Using difference cover) bucket 34: 70% bucket 29: 90% bucket 36: 90% bucket 32: 90% bucket 36: 90% bucket 44: 70% bucket 29: 100% Sorting block of length 4523437 for bucket 29 (Using difference cover) bucket 37: 90% bucket 35: 80% bucket 41: 70% bucket 43: 70% bucket 30: 80% bucket 32: 80% bucket 47: 70% bucket 52: 60% bucket 46: 80% bucket 38: 80% bucket 34: 90% bucket 41: 90% bucket 44: 100% Sorting block of length 4883242 for bucket 44 (Using difference cover) bucket 53: 70% bucket 46: 70% bucket 48: 60% bucket 33: 100% Sorting block of length 2056833 for bucket 33 (Using difference cover) bucket 40: 70% bucket 54: 60% bucket 37: 90% bucket 35: 80% bucket 42: 70% bucket 54: 60% bucket 43: 70% bucket 50: 70% bucket 53: 60% bucket 31: 90% bucket 45: 90% bucket 33: 80% bucket 49: 60% bucket 45: 80% bucket 51: 70% bucket 42: 80% bucket 50: 70% bucket 39: 70% bucket 48: 70% bucket 30: 90% bucket 52: 70% bucket 51: 70% bucket 49: 70% bucket 39: 100% Sorting block of length 4707774 for bucket 39 (Using difference cover) bucket 36: 100% Sorting block of length 4923718 for bucket 36 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4889373 for bucket 28 bucket 47: 70% Sorting block time: 00:00:03 Returning block of 5194323 for bucket 31 Getting block 55 of 203 Reserving size (5249070) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 34: 80% bucket 40: 90% bucket 32: 90% Sorting block time: 00:00:01 Returning block of 2056834 for bucket 33 bucket 37: 100% Sorting block of length 3223621 for bucket 37 (Using difference cover) Getting block 56 of 203 Reserving size (5249070) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 29: 100% Sorting block of length 2725250 for bucket 29 (Using difference cover) Getting block 57 of 203 Reserving size (5249070) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 28: 100% Sorting block of length 3811910 for bucket 28 (Using difference cover) bucket 46: 90% bucket 36: 100% Sorting block of length 3081366 for bucket 36 (Using difference cover) bucket 30: 90% bucket 44: 80% Sorting block time: 00:00:03 Returning block of 4523438 for bucket 29 bucket 41: 100% Sorting block of length 1253096 for bucket 41 (Using difference cover) Getting block 58 of 203 Reserving size (5249070) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: Sorting block time: 00:00:04 Returning block of 5081007 for bucket 38 bucket 32: 100% Sorting block of length 4066335 for bucket 32 (Using difference cover) bucket 38: 90% bucket 52: 70% bucket 35: 90% Getting block 59 of 203 Reserving size (5249070) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 37: 100% Sorting block of length 3089624 for bucket 37 (Using difference cover) bucket 43: 80% Sorting block time: 00:00:01 Returning block of 2725251 for bucket 29 bucket 41: 80% bucket 42: 90% bucket 45: 100% Sorting block of length 4911415 for bucket 45 (Using difference cover) bucket 48: 70% Sorting block time: 00:00:01 Returning block of 1253097 for bucket 41 Getting block 55 of 202 Reserving size (5249070) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 40: 80% Getting block 60 of 203 Reserving size (5249070) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 34: 100% Sorting block of length 5124966 for bucket 34 (Using difference cover) bucket 47: 80% bucket 35: 90% bucket 53: 80% bucket 30: 100% Sorting block of length 4693921 for bucket 30 (Using difference cover) bucket 54: 70% bucket 31: 100% Sorting block of length 4376362 for bucket 31 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3223622 for bucket 37 Sorting block time: 00:00:04 Returning block of 4883243 for bucket 44 bucket 50: 80% bucket 49: 70% bucket 43: 80% Getting block 56 of 202 Reserving size (5249070) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 46: 80% bucket 39: 80% bucket 42: 80% Getting block 61 of 203 Reserving size (5249070) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: bucket 53: 70% bucket 54: 70% bucket 51: 80% bucket 46: 100% Sorting block of length 4355650 for bucket 46 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3811911 for bucket 28 bucket 40: 100% Sorting block of length 4344360 for bucket 40 (Using difference cover) bucket 33: 90% bucket 45: 90% bucket 50: 80% bucket 55: 10% Getting block 57 of 202 Reserving size (5249070) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 48: 80% bucket 34: 90% bucket 32: 100% Sorting block of length 4961074 for bucket 32 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4707775 for bucket 39 Sorting block time: 00:00:03 Returning block of 3081367 for bucket 36 bucket 52: 80% bucket 56: 10% Getting block 58 of 202 Reserving size (5249070) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: Getting block 59 of 202 Reserving size (5249070) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 47: 80% bucket 57: 10% bucket 30: 100% Sorting block of length 1892749 for bucket 30 (Using difference cover) bucket 58: 10% bucket 49: 80% bucket 51: 80% Sorting block time: 00:00:03 Returning block of 4923719 for bucket 36 Sorting block time: 00:00:02 Returning block of 3089625 for bucket 37 Sorting block time: 00:00:02 Returning block of 4066336 for bucket 32 bucket 43: 90% Getting block 62 of 203 Reserving size (5249070) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: Getting block 63 of 203 Reserving size (5249070) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 59: 10% Getting block 60 of 202 Reserving size (5249070) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 38: 100% Sorting block of length 5033196 for bucket 38 (Using difference cover) bucket 44: 90% bucket 52: 80% Sorting block time: 00:00:03 Returning block of 4911416 for bucket 45 bucket 40: 90% bucket 43: 90% bucket 60: 10% Getting block 64 of 203 Reserving size (5249070) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 42: 100% Sorting block of length 970552 for bucket 42 (Using difference cover) bucket 35: 100% Sorting block of length 2791464 for bucket 35 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4693922 for bucket 30 Sorting block time: 00:00:01 Returning block of 1892750 for bucket 30 bucket 48: 80% bucket 35: 100% Sorting block of length 4896634 for bucket 35 (Using difference cover) Getting block 65 of 203 Reserving size (5249070) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: Getting block 61 of 202 Reserving size (5249070) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: bucket 55: 10% Sorting block time: 00:00:02 Returning block of 4376363 for bucket 31 Sorting block time: 00:00:03 Returning block of 4344361 for bucket 40 bucket 53: 90% bucket 41: 90% bucket 39: 90% bucket 45: 100% Sorting block of length 5015543 for bucket 45 (Using difference cover) Getting block 62 of 202 Reserving size (5249070) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 55: 20% Sorting block time: 00:00:04 Returning block of 5124967 for bucket 34 bucket 56: 10% Sorting block time: 00:00:01 Returning block of 970553 for bucket 42 bucket 54: 80% bucket 61: 10% Getting block 66 of 203 Reserving size (5249070) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: bucket 50: 90% bucket 49: 80% Getting block 63 of 202 Reserving size (5249070) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 53: 80% bucket 56: 20% bucket 48: 90% bucket 54: 80% bucket 42: 90% bucket 47: 90% Getting block 64 of 202 Reserving size (5249070) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 50: 90% bucket 57: 20% bucket 33: 100% Sorting block of length 3041596 for bucket 33 (Using difference cover) bucket 34: 100% Sorting block of length 7868628 for bucket 34 (Using difference cover) bucket 46: 90% Sorting block time: 00:00:03 Returning block of 4355651 for bucket 46 bucket 59: 10% bucket 51: 90% bucket 58: 20% bucket 57: 10% Getting block 67 of 203 Reserving size (5249070) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: bucket 58: 10% bucket 60: 10% bucket 47: 90% bucket 52: 90% bucket 43: 100% Sorting block of length 4228344 for bucket 43 (Using difference cover) bucket 62: 10% bucket 59: 20% bucket 49: 90% bucket 51: 90% bucket 64: 10% bucket 43: 100% Sorting block of length 4340011 for bucket 43 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2791465 for bucket 35 Sorting block time: 00:00:04 Returning block of 4961075 for bucket 32 bucket 63: 10% bucket 44: 100% Sorting block of length 1729010 for bucket 44 (Using difference cover) bucket 40: 100% Sorting block of length 5525809 for bucket 40 (Using difference cover) Getting block 65 of 202 Reserving size (5249070) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: Getting block 68 of 203 Reserving size (5249070) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 60: 20% bucket 52: 90% Sorting block time: 00:00:03 Returning block of 5033197 for bucket 38 bucket 61: 10% bucket 48: 90% bucket 55: 30% bucket 56: 20% Getting block 66 of 202 Reserving size (5249070) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: bucket 61: 20% bucket 39: 100% Sorting block of length 3341374 for bucket 39 (Using difference cover) bucket 55: 20% bucket 65: 10% bucket 56: 30% Sorting block time: 00:00:01 Returning block of 1729011 for bucket 44 Getting block 67 of 202 Reserving size (5249070) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: bucket 41: 100% Sorting block of length 3305982 for bucket 41 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3041597 for bucket 33 bucket 57: 30% bucket 58: 20% Getting block 68 of 202 Reserving size (5249070) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 53: 100% Sorting block of length 3983289 for bucket 53 (Using difference cover) bucket 54: 90% bucket 62: 10% bucket 42: 100% Sorting block of length 4910263 for bucket 42 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4896635 for bucket 35 bucket 48: 100% Sorting block of length 3540500 for bucket 48 (Using difference cover) bucket 64: 10% bucket 66: 10% bucket 50: 100% Sorting block of length 3550581 for bucket 50 (Using difference cover) bucket 54: 90% Sorting block time: 00:00:03 Returning block of 5015544 for bucket 45 bucket 49: 90% bucket 46: 100% Sorting block of length 3561212 for bucket 46 (Using difference cover) bucket 47: 100% Sorting block of length 2456686 for bucket 47 (Using difference cover) bucket 58: 30% Getting block 69 of 203 Reserving size (5249070) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: bucket 53: 90% bucket 51: 100% Sorting block of length 4114541 for bucket 51 (Using difference cover) bucket 59: 20% bucket 57: 20% bucket 63: 20% bucket 63: 10% Getting block 69 of 202 Reserving size (5249070) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: bucket 50: 100% Sorting block of length 4475397 for bucket 50 (Using difference cover) bucket 59: 30% bucket 67: 10% bucket 47: 100% Sorting block of length 4131295 for bucket 47 (Using difference cover) bucket 60: 30% bucket 52: 100% Sorting block of length 5106915 for bucket 52 (Using difference cover) bucket 60: 20% bucket 64: 20% bucket 51: 100% Sorting block of length 970978 for bucket 51 (Using difference cover) bucket 62: 20% bucket 61: 20% bucket 49: 100% Sorting block of length 2295591 for bucket 49 (Using difference cover) bucket 61: 30% Sorting block time: 00:00:03 Returning block of 4228345 for bucket 43 bucket 55: 30% bucket 55: 40% bucket 65: 10% bucket 48: 100% Sorting block of length 2831684 for bucket 48 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3341375 for bucket 39 bucket 56: 30% Getting block 70 of 202 Reserving size (5249070) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: Sorting block time: 00:00:04 Returning block of 4340012 for bucket 43 bucket 58: 30% Getting block 70 of 203 Reserving size (5249070) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: Sorting block time: 00:00:01 Returning block of 970979 for bucket 51 Getting block 71 of 202 Reserving size (5249070) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: Getting block 71 of 203 Reserving size (5249070) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: Sorting block time: 00:00:02 Returning block of 3983290 for bucket 53 bucket 56: 40% bucket 57: 40% Getting block 72 of 202 Reserving size (5249070) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 52: 100% Sorting block of length 3455400 for bucket 52 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3305983 for bucket 41 Sorting block time: 00:00:02 Returning block of 2456687 for bucket 47 bucket 68: 10% Getting block 73 of 202 Reserving size (5249070) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: bucket 64: 20% Getting block 74 of 202 Reserving size (5249070) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: bucket 54: 100% Sorting block of length 2423068 for bucket 54 (Using difference cover) bucket 65: 20% bucket 66: 10% bucket 69: 10% bucket 59: 40% Sorting block time: 00:00:03 Returning block of 3550582 for bucket 50 Sorting block time: 00:00:03 Returning block of 3561213 for bucket 46 bucket 60: 40% bucket 58: 40% Sorting block time: 00:00:05 Returning block of 5525810 for bucket 40 Sorting block time: 00:00:03 Returning block of 3540501 for bucket 48 Getting block 75 of 202 Reserving size (5249070) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 63: 20% Getting block 72 of 203 Reserving size (5249070) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: Getting block 76 of 202 Reserving size (5249070) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 54: 100% Sorting block of length 4416821 for bucket 54 (Using difference cover) bucket 57: 30% bucket 49: 100% Sorting block of length 4637858 for bucket 49 (Using difference cover) Getting block 73 of 203 Reserving size (5249070) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: Sorting block time: 00:00:02 Returning block of 2295592 for bucket 49 Sorting block time: 00:00:06 Returning block of 7868629 for bucket 34 bucket 62: 20% bucket 63: 30% Getting block 77 of 202 Reserving size (5249070) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 67: 10% bucket 68: 10% Sorting block time: 00:00:03 Returning block of 4475398 for bucket 50 bucket 53: 100% Sorting block of length 3901511 for bucket 53 (Using difference cover) bucket 69: 10% Sorting block time: 00:00:03 Returning block of 4114542 for bucket 51 bucket 61: 30% Getting block 78 of 202 Reserving size (5249070) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 59: 30% bucket 64: 30% bucket 67: 20% Getting block 74 of 203 Reserving size (5249070) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: bucket 55: 50% Sorting block time: 00:00:04 Returning block of 4910264 for bucket 42 Sorting block time: 00:00:03 Returning block of 4131296 for bucket 47 Sorting block time: 00:00:02 Returning block of 2831685 for bucket 48 Getting block 75 of 203 Reserving size (5249070) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 60: 30% bucket 66: 20% Getting block 76 of 203 Reserving size (5249070) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 62: 30% Getting block 77 of 203 Reserving size (5249070) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: Getting block 79 of 202 Reserving size (5249070) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 61: 40% Sorting block time: 00:00:03 Returning block of 5106916 for bucket 52 bucket 71: 10% bucket 58: 40% bucket 57: 50% bucket 55: 40% bucket 56: 40% Sorting block time: 00:00:01 Returning block of 2423069 for bucket 54 Getting block 80 of 202 Reserving size (5249070) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 56: 50% Getting block 78 of 203 Reserving size (5249070) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 71: 10% bucket 70: 10% bucket 70: 10% bucket 72: 10% bucket 59: 50% bucket 65: 20% Sorting block time: 00:00:03 Returning block of 3455401 for bucket 52 bucket 64: 30% Getting block 79 of 203 Reserving size (5249070) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 73: 10% bucket 55: 60% bucket 60: 50% bucket 73: 10% bucket 63: 30% bucket 66: 20% bucket 58: 50% bucket 68: 20% bucket 65: 30% bucket 74: 10% bucket 72: 10% Sorting block time: 00:00:03 Returning block of 3901512 for bucket 53 bucket 63: 40% bucket 74: 10% bucket 57: 40% Sorting block time: 00:00:03 Returning block of 4637859 for bucket 49 bucket 69: 20% Getting block 80 of 203 Reserving size (5249070) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 69: 20% bucket 77: 10% Sorting block time: 00:00:03 Returning block of 4416822 for bucket 54 Getting block 81 of 203 Reserving size (5249070) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 61: 40% bucket 67: 30% bucket 75: 10% Getting block 81 of 202 Reserving size (5249070) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 58: 50% bucket 61: 50% bucket 67: 20% bucket 76: 10% bucket 62: 40% bucket 68: 20% bucket 76: 10% bucket 60: 40% bucket 64: 40% bucket 75: 10% bucket 66: 30% bucket 56: 60% bucket 62: 30% bucket 77: 10% bucket 59: 40% bucket 71: 20% bucket 79: 10% bucket 78: 10% bucket 78: 10% bucket 80: 10% bucket 70: 20% bucket 73: 20% bucket 72: 20% bucket 55: 50% bucket 59: 60% bucket 55: 70% bucket 57: 60% bucket 79: 10% bucket 64: 40% bucket 56: 50% bucket 72: 20% bucket 65: 30% bucket 70: 20% bucket 60: 60% bucket 71: 20% bucket 74: 20% bucket 58: 60% bucket 57: 50% bucket 63: 40% bucket 73: 20% bucket 63: 50% bucket 80: 10% bucket 68: 30% bucket 58: 60% bucket 74: 20% bucket 81: 10% bucket 66: 30% bucket 69: 30% bucket 69: 30% bucket 77: 20% bucket 61: 50% bucket 65: 40% bucket 76: 20% bucket 62: 50% bucket 60: 50% bucket 62: 40% bucket 67: 40% bucket 67: 30% bucket 64: 50% bucket 77: 20% bucket 75: 20% bucket 81: 10% bucket 59: 50% bucket 73: 30% bucket 76: 20% bucket 70: 30% bucket 61: 60% bucket 71: 30% bucket 55: 60% bucket 80: 20% bucket 75: 20% bucket 59: 70% bucket 78: 20% bucket 68: 30% bucket 56: 70% bucket 55: 80% bucket 78: 20% bucket 79: 20% bucket 66: 40% bucket 57: 70% bucket 72: 30% bucket 60: 70% bucket 57: 60% bucket 79: 20% bucket 65: 40% bucket 63: 50% bucket 58: 70% bucket 56: 60% bucket 64: 50% bucket 70: 30% bucket 74: 30% bucket 72: 30% bucket 80: 20% bucket 63: 60% bucket 71: 30% bucket 81: 20% bucket 60: 60% bucket 62: 60% bucket 66: 40% bucket 55: 70% bucket 62: 50% bucket 69: 40% bucket 59: 60% bucket 77: 30% bucket 57: 70% bucket 69: 40% bucket 76: 30% bucket 65: 50% bucket 74: 30% bucket 77: 30% bucket 73: 40% bucket 73: 30% bucket 58: 70% bucket 70: 40% bucket 68: 40% bucket 61: 60% bucket 71: 40% bucket 67: 50% bucket 61: 70% bucket 56: 80% bucket 64: 60% bucket 67: 40% bucket 59: 80% bucket 76: 30% bucket 55: 90% bucket 81: 20% bucket 75: 30% bucket 63: 60% bucket 58: 80% bucket 78: 30% bucket 78: 30% bucket 75: 30% bucket 79: 30% bucket 79: 30% bucket 80: 30% bucket 56: 70% bucket 64: 60% bucket 80: 30% bucket 68: 40% bucket 72: 40% bucket 74: 40% bucket 60: 70% bucket 63: 70% bucket 65: 50% bucket 70: 40% bucket 60: 80% bucket 57: 80% bucket 55: 80% bucket 61: 70% bucket 81: 30% bucket 72: 40% bucket 66: 50% bucket 58: 80% bucket 77: 40% bucket 71: 40% bucket 57: 80% bucket 59: 70% bucket 70: 50% bucket 62: 60% bucket 66: 50% bucket 55: 100% Sorting block of length 3497908 for bucket 55 (Using difference cover) bucket 69: 50% bucket 73: 50% bucket 65: 60% bucket 62: 70% bucket 64: 70% bucket 73: 40% bucket 71: 50% bucket 76: 40% bucket 58: 90% bucket 77: 40% bucket 68: 50% bucket 56: 90% bucket 59: 90% bucket 76: 40% bucket 78: 40% bucket 79: 40% bucket 64: 70% bucket 67: 50% bucket 74: 40% bucket 63: 70% bucket 75: 40% bucket 69: 50% bucket 81: 30% bucket 80: 40% bucket 67: 60% bucket 79: 40% bucket 61: 80% bucket 75: 40% bucket 60: 90% bucket 78: 40% bucket 56: 80% bucket 60: 80% bucket 72: 50% bucket 74: 50% bucket 57: 90% bucket 58: 90% bucket 80: 40% bucket 68: 50% bucket 55: 90% Sorting block time: 00:00:03 Returning block of 3497909 for bucket 55 bucket 81: 40% bucket 62: 80% bucket 63: 80% Getting block 82 of 203 Reserving size (5249070) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 57: 90% bucket 70: 60% bucket 65: 60% bucket 72: 50% bucket 77: 50% bucket 64: 80% bucket 73: 60% bucket 61: 80% bucket 62: 70% bucket 70: 50% bucket 71: 60% bucket 59: 80% bucket 66: 60% bucket 56: 100% Sorting block of length 3797586 for bucket 56 (Using difference cover) bucket 71: 50% bucket 58: 100% Sorting block of length 4667280 for bucket 58 (Using difference cover) bucket 66: 60% bucket 79: 50% bucket 76: 50% bucket 69: 60% bucket 77: 50% bucket 59: 100% Sorting block of length 5194804 for bucket 59 (Using difference cover) bucket 78: 50% bucket 55: 100% Sorting block of length 4318759 for bucket 55 (Using difference cover) bucket 64: 80% bucket 78: 50% bucket 73: 50% bucket 63: 80% bucket 80: 50% bucket 65: 70% bucket 72: 60% bucket 67: 70% bucket 58: 100% Sorting block of length 4040089 for bucket 58 (Using difference cover) bucket 76: 50% bucket 74: 60% bucket 75: 50% bucket 74: 50% bucket 68: 60% bucket 60: 90% bucket 61: 90% bucket 69: 60% bucket 67: 60% bucket 60: 100% Sorting block of length 1436360 for bucket 60 (Using difference cover) bucket 79: 50% bucket 70: 70% bucket 56: 90% bucket 63: 90% bucket 57: 100% Sorting block of length 4767532 for bucket 57 (Using difference cover) bucket 75: 50% bucket 81: 50% bucket 81: 40% bucket 72: 60% bucket 68: 60% bucket 82: 10% bucket 61: 90% bucket 64: 90% bucket 77: 60% bucket 73: 70% Sorting block time: 00:00:02 Returning block of 3797587 for bucket 56 bucket 80: 50% bucket 62: 90% Sorting block time: 00:00:01 Returning block of 1436361 for bucket 60 Getting block 83 of 203 Reserving size (5249070) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: Getting block 84 of 203 Reserving size (5249070) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 65: 70% bucket 71: 70% bucket 57: 100% Sorting block of length 882169 for bucket 57 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4667281 for bucket 58 bucket 62: 80% Getting block 82 of 202 Reserving size (5249070) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 79: 60% Sorting block time: 00:00:03 Returning block of 4318760 for bucket 55 Sorting block time: 00:00:01 Returning block of 882170 for bucket 57 Getting block 83 of 202 Reserving size (5249070) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: Getting block 84 of 202 Reserving size (5249070) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 70: 60% bucket 60: 100% Sorting block of length 4218095 for bucket 60 (Using difference cover) bucket 76: 60% Sorting block time: 00:00:03 Returning block of 5194805 for bucket 59 bucket 66: 70% bucket 80: 60% bucket 59: 90% bucket 61: 100% Sorting block of length 4813045 for bucket 61 (Using difference cover) Getting block 85 of 203 Reserving size (5249070) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 78: 60% Sorting block time: 00:00:03 Returning block of 4040090 for bucket 58 bucket 71: 60% Getting block 86 of 203 Reserving size (5249070) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 64: 90% bucket 69: 70% bucket 63: 90% Sorting block time: 00:00:03 Returning block of 4767533 for bucket 57 bucket 77: 60% bucket 61: 100% Sorting block of length 4911200 for bucket 61 (Using difference cover) bucket 66: 70% bucket 73: 60% bucket 56: 100% Sorting block of length 4952604 for bucket 56 (Using difference cover) bucket 67: 80% bucket 78: 60% bucket 76: 60% Getting block 87 of 203 Reserving size (5249070) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 82: 20% bucket 74: 60% bucket 69: 70% bucket 72: 70% bucket 67: 70% bucket 74: 70% bucket 68: 70% bucket 72: 70% bucket 75: 60% bucket 81: 60% bucket 79: 60% bucket 65: 80% bucket 63: 100% Sorting block of length 4354744 for bucket 63 (Using difference cover) bucket 64: 100% Sorting block of length 4374831 for bucket 64 (Using difference cover) bucket 62: 100% Sorting block of length 2168726 for bucket 62 (Using difference cover) bucket 81: 50% bucket 68: 70% bucket 70: 80% bucket 75: 60% bucket 83: 10% Sorting block time: 00:00:02 Returning block of 4218096 for bucket 60 bucket 73: 80% bucket 84: 10% bucket 85: 10% bucket 71: 80% Getting block 85 of 202 Reserving size (5249070) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 77: 70% bucket 80: 60% bucket 86: 10% bucket 59: 100% Sorting block of length 4779944 for bucket 59 (Using difference cover) bucket 76: 70% bucket 82: 10% bucket 65: 80% bucket 62: 90% bucket 66: 80% Sorting block time: 00:00:01 Returning block of 2168727 for bucket 62 bucket 70: 70% bucket 64: 100% Sorting block of length 4566243 for bucket 64 (Using difference cover) Getting block 88 of 203 Reserving size (5249070) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 83: 10% bucket 84: 10% bucket 82: 30% bucket 79: 70% Sorting block time: 00:00:04 Returning block of 4813046 for bucket 61 Sorting block time: 00:00:03 Returning block of 4952605 for bucket 56 bucket 87: 10% bucket 67: 90% bucket 80: 70% bucket 69: 80% Sorting block time: 00:00:03 Returning block of 4911201 for bucket 61 Getting block 89 of 203 Reserving size (5249070) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 71: 70% Getting block 86 of 202 Reserving size (5249070) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 78: 70% bucket 63: 100% Sorting block of length 4936603 for bucket 63 (Using difference cover) Getting block 87 of 202 Reserving size (5249070) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 85: 20% bucket 77: 70% bucket 74: 70% bucket 72: 80% bucket 66: 80% bucket 78: 70% bucket 72: 80% Sorting block time: 00:00:02 Returning block of 4374832 for bucket 64 bucket 81: 70% bucket 74: 80% bucket 76: 70% Getting block 90 of 203 Reserving size (5249070) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 86: 20% bucket 65: 90% bucket 73: 70% Sorting block time: 00:00:02 Returning block of 4354745 for bucket 63 bucket 75: 70% bucket 83: 20% Getting block 91 of 203 Reserving size (5249070) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 79: 70% bucket 69: 80% bucket 68: 80% bucket 70: 90% bucket 67: 80% bucket 81: 60% bucket 73: 90% bucket 71: 90% bucket 76: 80% bucket 77: 80% bucket 75: 70% Sorting block time: 00:00:03 Returning block of 4779945 for bucket 59 bucket 85: 10% bucket 84: 20% bucket 80: 70% bucket 84: 20% Getting block 88 of 202 Reserving size (5249070) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 82: 40% bucket 85: 30% bucket 87: 20% bucket 83: 20% bucket 65: 90% bucket 70: 80% Sorting block time: 00:00:03 Returning block of 4566244 for bucket 64 bucket 69: 90% bucket 79: 80% Sorting block time: 00:00:02 Returning block of 4936604 for bucket 63 Getting block 89 of 202 Reserving size (5249070) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 88: 10% bucket 82: 20% bucket 89: 10% bucket 66: 90% Getting block 90 of 202 Reserving size (5249070) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 68: 80% bucket 62: 100% Sorting block of length 4617415 for bucket 62 (Using difference cover) bucket 80: 80% bucket 86: 10% bucket 86: 30% bucket 72: 90% bucket 91: 10% bucket 78: 80% bucket 71: 80% bucket 70: 100% Sorting block of length 4667672 for bucket 70 (Using difference cover) bucket 74: 80% bucket 77: 80% bucket 83: 30% bucket 81: 80% bucket 76: 80% bucket 66: 90% bucket 75: 80% bucket 78: 80% bucket 67: 100% Sorting block of length 2588327 for bucket 67 (Using difference cover) bucket 69: 90% bucket 87: 10% bucket 85: 40% bucket 72: 90% bucket 74: 90% bucket 65: 100% Sorting block of length 3703300 for bucket 65 (Using difference cover) bucket 67: 90% bucket 79: 80% bucket 76: 90% bucket 73: 100% Sorting block of length 4870752 for bucket 73 (Using difference cover) bucket 82: 50% bucket 71: 100% Sorting block of length 4787552 for bucket 71 (Using difference cover) bucket 90: 10% bucket 77: 90% bucket 73: 80% bucket 75: 80% bucket 84: 30% bucket 81: 70% bucket 87: 30% bucket 68: 90% bucket 80: 90% bucket 85: 20% bucket 79: 90% Sorting block time: 00:00:02 Returning block of 2588328 for bucket 67 bucket 88: 20% bucket 88: 10% bucket 69: 100% Sorting block of length 2967403 for bucket 69 (Using difference cover) Getting block 92 of 203 Reserving size (5249070) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: bucket 70: 90% bucket 80: 80% bucket 83: 30% bucket 65: 100% Sorting block of length 4984383 for bucket 65 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4617416 for bucket 62 Sorting block time: 00:00:02 Returning block of 4667673 for bucket 70 bucket 84: 30% Getting block 91 of 202 Reserving size (5249070) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 89: 20% bucket 82: 30% bucket 82: 60% bucket 83: 40% bucket 68: 90% Getting block 93 of 203 Reserving size (5249070) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 89: 10% bucket 72: 100% Sorting block of length 5234728 for bucket 72 (Using difference cover) bucket 91: 20% bucket 86: 40% bucket 66: 100% Sorting block of length 4917371 for bucket 66 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3703301 for bucket 65 bucket 86: 20% bucket 78: 90% bucket 90: 10% bucket 75: 90% bucket 76: 90% Getting block 94 of 203 Reserving size (5249070) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: bucket 72: 100% Sorting block of length 3943395 for bucket 72 (Using difference cover) bucket 81: 90% bucket 87: 40% bucket 69: 100% Sorting block of length 1035231 for bucket 69 (Using difference cover) bucket 74: 100% Sorting block of length 5214948 for bucket 74 (Using difference cover) bucket 71: 90% bucket 77: 90% bucket 80: 100% bucket 76: 100% Sorting block of length 2541788 for bucket 80 (Using difference cover) Sorting block of length 1275550 for bucket 76 (Using difference cover) bucket 84: 40% bucket 75: 90% bucket 85: 50% bucket 90: 20% bucket 79: 90% bucket 87: 20% bucket 77: 100% Sorting block of length 2861820 for bucket 77 (Using difference cover) bucket 66: 100% Sorting block of length 4736122 for bucket 66 (Using difference cover) bucket 74: 90% bucket 67: 100% Sorting block of length 2199236 for bucket 67 (Using difference cover) bucket 78: 90% bucket 92: 10% Sorting block time: 00:00:02 Returning block of 2967404 for bucket 69 Sorting block time: 00:00:03 Returning block of 4787553 for bucket 71 Sorting block time: 00:00:03 Returning block of 4870753 for bucket 73 Sorting block time: 00:00:01 Returning block of 1035232 for bucket 69 Getting block 92 of 202 Reserving size (5249070) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: Getting block 95 of 203 Reserving size (5249070) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 68: 100% Sorting block of length 3973474 for bucket 68 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1275551 for bucket 76 Getting block 96 of 203 Reserving size (5249070) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 73: 90% bucket 79: 100% Sorting block of length 3880586 for bucket 79 (Using difference cover) bucket 81: 80% bucket 88: 30% bucket 88: 20% Getting block 97 of 203 Reserving size (5249070) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: Getting block 98 of 203 Reserving size (5249070) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 85: 30% bucket 83: 40% bucket 89: 30% Sorting block time: 00:00:02 Returning block of 3943396 for bucket 72 bucket 80: 90% bucket 82: 70% Sorting block time: 00:00:01 Returning block of 2541789 for bucket 80 bucket 91: 10% bucket 70: 100% Sorting block of length 7184319 for bucket 70 (Using difference cover) Getting block 93 of 202 Reserving size (5249070) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 83: 50% bucket 93: 10% Getting block 99 of 203 Reserving size (5249070) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: bucket 81: 100% Sorting block of length 5084725 for bucket 81 (Using difference cover) bucket 86: 50% bucket 91: 30% Sorting block time: 00:00:04 Returning block of 4984384 for bucket 65 Sorting block time: 00:00:02 Returning block of 2199237 for bucket 67 bucket 86: 30% Getting block 94 of 202 Reserving size (5249070) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: Sorting block time: 00:00:02 Returning block of 2861821 for bucket 77 bucket 78: 100% Sorting block of length 4825167 for bucket 78 (Using difference cover) bucket 87: 50% bucket 75: 100% Sorting block of length 5635022 for bucket 75 (Using difference cover) Getting block 95 of 202 Reserving size (5249070) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 82: 40% Getting block 100 of 203 Reserving size (5249070) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: bucket 68: 100% Sorting block of length 4326807 for bucket 68 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4917372 for bucket 66 bucket 84: 40% bucket 85: 60% bucket 89: 20% bucket 94: 10% Getting block 96 of 202 Reserving size (5249070) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 84: 50% bucket 76: 100% Sorting block of length 4530424 for bucket 76 (Using difference cover) bucket 92: 20% bucket 97: 10% bucket 77: 100% Sorting block of length 4681793 for bucket 77 (Using difference cover) bucket 92: 10% bucket 74: 100% Sorting block of length 5118675 for bucket 74 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5234729 for bucket 72 bucket 90: 20% bucket 90: 30% bucket 87: 30% Getting block 101 of 203 Reserving size (5249070) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 71: 100% Sorting block of length 2315031 for bucket 71 (Using difference cover) bucket 75: 100% Sorting block of length 4674846 for bucket 75 (Using difference cover) bucket 79: 100% Sorting block of length 5085749 for bucket 79 (Using difference cover) bucket 78: 100% Sorting block of length 1004987 for bucket 78 (Using difference cover) bucket 81: 90% bucket 88: 40% Sorting block time: 00:00:04 Returning block of 5214949 for bucket 74 bucket 88: 30% Sorting block time: 00:00:02 Returning block of 3880587 for bucket 79 bucket 73: 100% Sorting block of length 3594809 for bucket 73 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3973475 for bucket 68 Getting block 102 of 203 Reserving size (5249070) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 95: 10% bucket 96: 10% Getting block 103 of 203 Reserving size (5249070) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: Sorting block time: 00:00:04 Returning block of 4736123 for bucket 66 bucket 98: 10% Getting block 97 of 202 Reserving size (5249070) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: Getting block 104 of 203 Reserving size (5249070) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: bucket 82: 80% bucket 83: 60% Sorting block time: 00:00:01 Returning block of 1004988 for bucket 78 Getting block 98 of 202 Reserving size (5249070) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 80: 100% Sorting block of length 2268543 for bucket 80 (Using difference cover) bucket 93: 10% bucket 85: 70% bucket 93: 20% bucket 83: 50% bucket 86: 60% bucket 86: 40% bucket 91: 40% bucket 99: 10% Sorting block time: 00:00:03 Returning block of 4825168 for bucket 78 bucket 85: 40% bucket 89: 40% bucket 91: 20% Getting block 105 of 203 Reserving size (5249070) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: Sorting block time: 00:00:02 Returning block of 2315032 for bucket 71 Sorting block time: 00:00:03 Returning block of 5084726 for bucket 81 Getting block 99 of 202 Reserving size (5249070) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: bucket 94: 20% Getting block 106 of 203 Reserving size (5249070) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 89: 30% bucket 95: 10% bucket 87: 60% bucket 100: 10% bucket 92: 30% Sorting block time: 00:00:04 Returning block of 4326808 for bucket 68 bucket 84: 60% bucket 94: 10% bucket 88: 50% bucket 97: 20% Sorting block time: 00:00:02 Returning block of 2268544 for bucket 80 Getting block 107 of 203 Reserving size (5249070) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: Sorting block time: 00:00:03 Returning block of 4530425 for bucket 76 Getting block 100 of 202 Reserving size (5249070) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: bucket 84: 50% bucket 87: 40% bucket 82: 50% Getting block 101 of 202 Reserving size (5249070) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 86: 70% bucket 90: 30% bucket 90: 40% bucket 96: 10% Sorting block time: 00:00:02 Returning block of 3594810 for bucket 73 bucket 101: 10% Sorting block time: 00:00:03 Returning block of 4681794 for bucket 77 Sorting block time: 00:00:04 Returning block of 5635023 for bucket 75 Sorting block time: 00:00:05 Returning block of 7184320 for bucket 70 bucket 92: 20% bucket 83: 70% Getting block 102 of 202 Reserving size (5249070) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 93: 20% bucket 85: 80% Sorting block time: 00:00:03 Returning block of 4674847 for bucket 75 Getting block 103 of 202 Reserving size (5249070) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: Getting block 108 of 203 Reserving size (5249070) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: Sorting block time: 00:00:04 Returning block of 5118676 for bucket 74 Getting block 104 of 202 Reserving size (5249070) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: bucket 81: 100% Sorting block of length 5117221 for bucket 81 (Using difference cover) bucket 96: 20% Getting block 105 of 202 Reserving size (5249070) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 104: 10% bucket 98: 10% bucket 82: 90% bucket 103: 10% Getting block 106 of 202 Reserving size (5249070) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: Sorting block time: 00:00:04 Returning block of 5085750 for bucket 79 bucket 98: 20% bucket 95: 20% bucket 86: 50% Getting block 107 of 202 Reserving size (5249070) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 91: 50% bucket 85: 50% bucket 97: 10% bucket 93: 30% bucket 88: 40% bucket 102: 10% bucket 83: 60% bucket 89: 40% bucket 92: 40% bucket 105: 10% bucket 99: 20% bucket 89: 50% bucket 86: 80% bucket 94: 30% bucket 84: 70% bucket 97: 30% bucket 88: 60% bucket 93: 30% bucket 106: 10% bucket 91: 30% bucket 107: 10% bucket 100: 20% bucket 87: 70% bucket 94: 20% bucket 90: 40% bucket 90: 50% bucket 99: 10% bucket 103: 10% bucket 101: 20% bucket 85: 90% bucket 83: 80% bucket 95: 20% bucket 100: 10% bucket 82: 60% bucket 87: 50% bucket 95: 30% bucket 104: 10% bucket 92: 30% bucket 82: 100% Sorting block of length 4609886 for bucket 82 (Using difference cover) bucket 105: 10% bucket 84: 60% bucket 96: 30% bucket 108: 10% bucket 102: 10% Sorting block time: 00:00:03 Returning block of 5117222 for bucket 81 bucket 101: 10% bucket 96: 20% bucket 103: 20% bucket 107: 10% bucket 91: 60% Getting block 108 of 202 Reserving size (5249070) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 106: 10% bucket 93: 40% bucket 93: 40% bucket 98: 30% bucket 88: 50% bucket 94: 40% bucket 89: 50% bucket 89: 60% bucket 86: 90% bucket 84: 80% bucket 98: 20% bucket 85: 60% bucket 104: 20% bucket 97: 20% bucket 92: 50% bucket 86: 60% bucket 105: 20% bucket 102: 20% bucket 99: 30% bucket 83: 70% bucket 97: 40% bucket 87: 80% bucket 103: 20% bucket 94: 30% bucket 88: 70% bucket 100: 30% bucket 91: 40% bucket 90: 50% bucket 101: 30% bucket 90: 60% bucket 95: 40% bucket 82: 70% bucket 83: 90% bucket 104: 20% bucket 85: 100% Sorting block of length 5106497 for bucket 85 (Using difference cover) bucket 107: 20% bucket 96: 40% Sorting block time: 00:00:03 Returning block of 4609887 for bucket 82 bucket 106: 20% Getting block 109 of 203 Reserving size (5249070) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 93: 50% bucket 84: 70% bucket 87: 60% bucket 105: 20% bucket 99: 20% bucket 102: 20% bucket 92: 40% bucket 108: 20% bucket 95: 30% bucket 101: 20% bucket 100: 20% bucket 108: 10% bucket 107: 20% bucket 106: 20% bucket 86: 70% bucket 86: 100% Sorting block of length 4357758 for bucket 86 (Using difference cover) bucket 93: 50% bucket 92: 60% bucket 98: 40% bucket 91: 70% bucket 84: 90% bucket 94: 50% bucket 89: 70% bucket 96: 30% bucket 103: 30% bucket 88: 80% bucket 104: 30% bucket 97: 30% bucket 89: 60% bucket 88: 60% bucket 91: 50% bucket 83: 80% bucket 85: 70% bucket 105: 30% bucket 87: 90% bucket 103: 30% bucket 99: 40% bucket 90: 70% bucket 95: 50% bucket 97: 50% bucket 98: 30% bucket 100: 40% bucket 102: 30% bucket 83: 100% Sorting block of length 4932622 for bucket 83 (Using difference cover) bucket 86: 80% bucket 104: 30% bucket 94: 40% bucket 90: 60% bucket 82: 80% Sorting block time: 00:00:02 Returning block of 4357759 for bucket 86 bucket 101: 40% bucket 101: 30% bucket 108: 20% bucket 107: 30% Getting block 110 of 203 Reserving size (5249070) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 96: 50% bucket 84: 80% Sorting block time: 00:00:04 Returning block of 5106498 for bucket 85 bucket 87: 70% bucket 108: 30% bucket 93: 60% bucket 106: 30% bucket 106: 30% Getting block 111 of 203 Reserving size (5249070) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: bucket 91: 80% bucket 92: 70% bucket 105: 30% bucket 89: 80% bucket 94: 60% bucket 109: 10% bucket 98: 50% bucket 107: 30% bucket 102: 30% bucket 93: 60% bucket 92: 50% bucket 84: 100% Sorting block of length 5245113 for bucket 84 (Using difference cover) bucket 95: 40% bucket 85: 80% bucket 100: 30% bucket 99: 30% bucket 87: 100% Sorting block of length 1785621 for bucket 87 (Using difference cover) bucket 83: 90% bucket 86: 90% bucket 104: 40% bucket 88: 90% bucket 89: 70% bucket 95: 60% bucket 90: 80% bucket 91: 60% bucket 103: 40% bucket 103: 40% bucket 99: 50% bucket 105: 40% bucket 96: 40% bucket 97: 60% bucket 90: 70% bucket 97: 40% bucket 88: 70% Sorting block time: 00:00:01 Returning block of 1785622 for bucket 87 bucket 104: 40% Sorting block time: 00:00:03 Returning block of 4932623 for bucket 83 Getting block 112 of 203 Reserving size (5249070) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 82: 90% Getting block 113 of 203 Reserving size (5249070) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 105: 40% bucket 102: 40% bucket 93: 70% bucket 110: 10% bucket 87: 80% bucket 84: 90% bucket 100: 50% bucket 98: 40% bucket 91: 90% bucket 101: 50% bucket 92: 80% bucket 96: 60% bucket 94: 50% bucket 86: 100% Sorting block of length 1453498 for bucket 86 (Using difference cover) bucket 93: 70% bucket 107: 40% bucket 106: 40% bucket 108: 40% bucket 89: 90% bucket 101: 40% bucket 108: 30% bucket 107: 40% bucket 94: 70% Sorting block time: 00:00:04 Returning block of 5245114 for bucket 84 bucket 98: 60% bucket 111: 10% bucket 106: 40% bucket 91: 70% Getting block 114 of 203 Reserving size (5249070) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 90: 90% bucket 109: 20% bucket 102: 40% bucket 85: 90% bucket 103: 50% Sorting block time: 00:00:01 Returning block of 1453499 for bucket 86 bucket 99: 40% Getting block 109 of 202 Reserving size (5249070) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 100: 40% bucket 95: 70% bucket 92: 60% bucket 88: 100% Sorting block of length 4311787 for bucket 88 (Using difference cover) bucket 97: 70% bucket 104: 50% bucket 99: 60% bucket 105: 50% bucket 90: 80% bucket 113: 10% bucket 95: 50% bucket 104: 50% bucket 83: 100% Sorting block of length 4196994 for bucket 83 (Using difference cover) bucket 91: 100% Sorting block of length 4924675 for bucket 91 (Using difference cover) bucket 97: 50% bucket 92: 90% bucket 103: 50% bucket 105: 50% bucket 112: 10% bucket 110: 20% bucket 96: 50% bucket 82: 100% Sorting block of length 2440649 for bucket 82 (Using difference cover) bucket 96: 70% bucket 88: 80% bucket 100: 60% bucket 93: 80% bucket 87: 90% bucket 101: 60% bucket 108: 50% bucket 93: 80% bucket 89: 100% Sorting block of length 4085396 for bucket 89 (Using difference cover) bucket 109: 10% bucket 84: 100% Sorting block of length 3965866 for bucket 84 (Using difference cover) bucket 106: 50% bucket 111: 20% bucket 108: 40% bucket 107: 50% bucket 107: 50% bucket 98: 50% bucket 94: 80% bucket 102: 50% bucket 89: 80% bucket 114: 10% bucket 92: 100% Sorting block of length 1268844 for bucket 92 (Using difference cover) bucket 98: 70% bucket 94: 60% bucket 85: 100% Sorting block of length 3662552 for bucket 85 (Using difference cover) bucket 90: 100% Sorting block of length 4236251 for bucket 90 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4311788 for bucket 88 bucket 103: 60% bucket 101: 50% bucket 102: 50% Getting block 115 of 203 Reserving size (5249070) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: Sorting block time: 00:00:02 Returning block of 2440650 for bucket 82 bucket 91: 80% bucket 106: 50% Getting block 110 of 202 Reserving size (5249070) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 95: 80% Sorting block time: 00:00:02 Returning block of 4924676 for bucket 91 bucket 104: 60% bucket 99: 70% Sorting block time: 00:00:02 Returning block of 4196995 for bucket 83 Sorting block time: 00:00:00 Returning block of 1268845 for bucket 92 bucket 109: 30% bucket 109: 20% bucket 104: 60% Getting block 116 of 203 Reserving size (5249070) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: bucket 97: 80% Getting block 117 of 203 Reserving size (5249070) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: Getting block 111 of 202 Reserving size (5249070) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: bucket 105: 60% bucket 95: 60% bucket 90: 90% bucket 113: 20% bucket 100: 50% bucket 99: 50% bucket 97: 60% bucket 92: 70% bucket 112: 20% bucket 105: 60% bucket 103: 60% bucket 108: 50% bucket 93: 90% bucket 110: 30% bucket 96: 80% Sorting block time: 00:00:03 Returning block of 3965867 for bucket 84 Sorting block time: 00:00:03 Returning block of 4085397 for bucket 89 bucket 100: 70% Getting block 112 of 202 Reserving size (5249070) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 87: 100% Sorting block of length 3870911 for bucket 87 (Using difference cover) bucket 108: 60% bucket 111: 30% Getting block 118 of 203 Reserving size (5249070) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: bucket 96: 60% Sorting block time: 00:00:02 Returning block of 3662553 for bucket 85 bucket 106: 60% bucket 107: 60% bucket 93: 90% bucket 89: 90% bucket 88: 90% Getting block 113 of 202 Reserving size (5249070) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 101: 70% bucket 109: 30% bucket 98: 60% Sorting block time: 00:00:03 Returning block of 4236252 for bucket 90 bucket 94: 90% bucket 116: 10% bucket 107: 60% bucket 94: 70% Getting block 119 of 203 Reserving size (5249070) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: bucket 103: 70% bucket 98: 80% bucket 114: 20% bucket 102: 60% bucket 101: 60% bucket 99: 80% bucket 104: 70% bucket 110: 10% bucket 102: 60% bucket 104: 70% bucket 95: 90% bucket 106: 60% bucket 109: 40% bucket 105: 70% bucket 111: 10% bucket 91: 90% bucket 113: 30% bucket 97: 90% bucket 90: 100% Sorting block of length 2224146 for bucket 90 (Using difference cover) bucket 115: 10% bucket 117: 10% bucket 95: 70% bucket 108: 60% bucket 113: 10% bucket 105: 70% bucket 97: 70% bucket 93: 100% Sorting block of length 5093429 for bucket 93 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3870912 for bucket 87 bucket 112: 30% bucket 100: 60% Getting block 114 of 202 Reserving size (5249070) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 99: 60% bucket 103: 70% bucket 100: 80% bucket 118: 10% bucket 112: 10% bucket 96: 90% bucket 107: 70% bucket 93: 100% Sorting block of length 5055050 for bucket 93 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2224147 for bucket 90 bucket 88: 100% Sorting block of length 2803470 for bucket 88 (Using difference cover) bucket 108: 70% bucket 92: 80% bucket 96: 70% bucket 106: 70% bucket 110: 40% Getting block 115 of 202 Reserving size (5249070) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 109: 40% bucket 111: 40% bucket 116: 20% bucket 94: 100% Sorting block of length 4311072 for bucket 94 (Using difference cover) bucket 109: 50% bucket 98: 70% bucket 91: 100% Sorting block of length 3667615 for bucket 91 (Using difference cover) bucket 113: 40% bucket 99: 90% bucket 119: 10% bucket 114: 30% bucket 104: 80% bucket 89: 100% Sorting block of length 5201762 for bucket 89 (Using difference cover) bucket 101: 80% bucket 115: 20% bucket 94: 80% bucket 111: 20% bucket 103: 80% bucket 105: 80% bucket 102: 70% bucket 101: 70% bucket 95: 100% Sorting block of length 4218897 for bucket 95 (Using difference cover) bucket 98: 90% bucket 107: 70% bucket 97: 100% Sorting block of length 3214426 for bucket 97 (Using difference cover) bucket 104: 80% bucket 110: 20% bucket 113: 20% bucket 108: 70% bucket 105: 80% bucket 102: 70% Sorting block time: 00:00:02 Returning block of 2803471 for bucket 88 bucket 106: 70% Getting block 116 of 202 Reserving size (5249070) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: bucket 97: 80% bucket 114: 10% bucket 112: 40% bucket 117: 20% bucket 95: 80% bucket 116: 30% bucket 100: 70% bucket 96: 100% Sorting block of length 2708274 for bucket 96 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3667616 for bucket 91 bucket 109: 50% bucket 113: 30% bucket 112: 20% Sorting block time: 00:00:04 Returning block of 5093430 for bucket 93 bucket 100: 90% Getting block 117 of 202 Reserving size (5249070) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: bucket 118: 20% bucket 115: 10% bucket 103: 80% Getting block 120 of 203 Reserving size (5249070) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 99: 70% Sorting block time: 00:00:03 Returning block of 5055051 for bucket 93 bucket 92: 90% bucket 96: 80% bucket 107: 80% bucket 106: 80% bucket 110: 50% bucket 108: 80% bucket 111: 50% Getting block 118 of 202 Reserving size (5249070) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: Sorting block time: 00:00:03 Returning block of 4311073 for bucket 94 bucket 113: 50% bucket 111: 30% bucket 99: 100% Sorting block of length 3821647 for bucket 99 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3214427 for bucket 97 bucket 101: 90% Getting block 121 of 203 Reserving size (5249070) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: Getting block 122 of 203 Reserving size (5249070) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 119: 20% bucket 98: 80% bucket 104: 90% Sorting block time: 00:00:03 Returning block of 5201763 for bucket 89 Sorting block time: 00:00:03 Returning block of 4218898 for bucket 95 bucket 114: 40% bucket 98: 100% Sorting block of length 3729929 for bucket 98 (Using difference cover) bucket 107: 80% bucket 103: 90% Getting block 119 of 202 Reserving size (5249070) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: Getting block 123 of 203 Reserving size (5249070) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 94: 90% bucket 104: 90% bucket 108: 80% bucket 102: 80% bucket 109: 60% bucket 105: 90% bucket 115: 30% bucket 105: 90% bucket 101: 80% bucket 114: 20% bucket 110: 30% Sorting block time: 00:00:02 Returning block of 2708275 for bucket 96 Getting block 124 of 203 Reserving size (5249070) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 113: 40% bucket 106: 80% bucket 116: 10% bucket 116: 40% bucket 97: 90% bucket 112: 50% bucket 102: 80% bucket 117: 30% bucket 112: 30% bucket 120: 10% bucket 109: 60% bucket 100: 100% Sorting block of length 5086653 for bucket 100 (Using difference cover) bucket 110: 60% bucket 118: 10% bucket 107: 90% bucket 103: 90% bucket 100: 80% bucket 115: 20% bucket 106: 90% bucket 95: 90% bucket 108: 90% bucket 111: 40% bucket 111: 60% Sorting block time: 00:00:03 Returning block of 3821648 for bucket 99 bucket 92: 100% Sorting block of length 4804399 for bucket 92 (Using difference cover) Getting block 125 of 203 Reserving size (5249070) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: Sorting block time: 00:00:03 Returning block of 3729930 for bucket 98 bucket 118: 30% bucket 113: 60% bucket 122: 10% Getting block 126 of 203 Reserving size (5249070) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: bucket 114: 50% bucket 119: 30% bucket 104: 100% Sorting block of length 3322483 for bucket 104 (Using difference cover) bucket 114: 30% bucket 117: 10% bucket 113: 50% bucket 98: 90% bucket 121: 10% bucket 107: 90% bucket 103: 100% Sorting block of length 2245635 for bucket 103 (Using difference cover) bucket 105: 100% Sorting block of length 3547376 for bucket 105 (Using difference cover) bucket 101: 100% Sorting block of length 1590261 for bucket 101 (Using difference cover) bucket 104: 100% Sorting block of length 4131497 for bucket 104 (Using difference cover) bucket 99: 80% bucket 101: 90% bucket 109: 70% bucket 115: 40% bucket 105: 100% Sorting block of length 4168017 for bucket 105 (Using difference cover) bucket 123: 10% bucket 96: 90% bucket 108: 90% bucket 110: 40% bucket 124: 10% bucket 94: 100% Sorting block of length 4871664 for bucket 94 (Using difference cover) bucket 119: 10% bucket 102: 90% bucket 106: 90% bucket 109: 70% bucket 97: 100% Sorting block of length 4645037 for bucket 97 (Using difference cover) bucket 116: 50% bucket 116: 20% bucket 110: 70% bucket 120: 20% bucket 107: 100% Sorting block of length 3927893 for bucket 107 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1590262 for bucket 101 bucket 102: 90% Getting block 127 of 203 Reserving size (5249070) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 111: 50% bucket 118: 20% bucket 103: 100% Sorting block of length 1391343 for bucket 103 (Using difference cover) bucket 117: 20% bucket 112: 60% bucket 112: 40% bucket 111: 70% Sorting block time: 00:00:01 Returning block of 2245636 for bucket 103 bucket 106: 100% Sorting block of length 2629944 for bucket 106 (Using difference cover) Getting block 120 of 202 Reserving size (5249070) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 100: 90% bucket 108: 100% Sorting block of length 4796128 for bucket 108 (Using difference cover) bucket 117: 40% Sorting block time: 00:00:04 Returning block of 5086654 for bucket 100 Sorting block time: 00:00:03 Returning block of 3322484 for bucket 104 bucket 115: 30% Getting block 128 of 203 Reserving size (5249070) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: Getting block 121 of 202 Reserving size (5249070) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 114: 40% Sorting block time: 00:00:02 Returning block of 3547377 for bucket 105 Getting block 122 of 202 Reserving size (5249070) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 113: 70% Sorting block time: 00:00:01 Returning block of 1391344 for bucket 103 Getting block 129 of 203 Reserving size (5249070) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: bucket 122: 20% bucket 119: 40% Sorting block time: 00:00:03 Returning block of 4804400 for bucket 92 bucket 113: 60% bucket 125: 10% bucket 107: 100% Sorting block of length 3779134 for bucket 107 (Using difference cover) bucket 118: 40% Getting block 123 of 202 Reserving size (5249070) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 108: 100% Sorting block of length 3511598 for bucket 108 (Using difference cover) bucket 121: 20% bucket 126: 10% Sorting block time: 00:00:03 Returning block of 4131498 for bucket 104 bucket 95: 100% Sorting block of length 2424403 for bucket 95 (Using difference cover) bucket 114: 60% Getting block 130 of 203 Reserving size (5249070) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: bucket 110: 80% bucket 98: 100% Sorting block of length 2818883 for bucket 98 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4168018 for bucket 105 bucket 115: 50% bucket 101: 100% Sorting block of length 1790456 for bucket 101 (Using difference cover) bucket 110: 50% bucket 116: 30% bucket 102: 100% Sorting block of length 4020005 for bucket 102 (Using difference cover) Getting block 131 of 203 Reserving size (5249070) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 123: 20% bucket 99: 90% bucket 124: 20% bucket 109: 80% Sorting block time: 00:00:02 Returning block of 2629945 for bucket 106 bucket 96: 100% Sorting block of length 3906801 for bucket 96 (Using difference cover) bucket 114: 50% bucket 111: 60% Getting block 124 of 202 Reserving size (5249070) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 106: 100% Sorting block of length 3319018 for bucket 106 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3927894 for bucket 107 bucket 118: 30% bucket 119: 20% Sorting block time: 00:00:04 Returning block of 4871665 for bucket 94 bucket 116: 60% Getting block 125 of 202 Reserving size (5249070) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: bucket 109: 80% Getting block 126 of 202 Reserving size (5249070) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: Sorting block time: 00:00:03 Returning block of 4645038 for bucket 97 bucket 120: 30% Getting block 127 of 202 Reserving size (5249070) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 127: 10% Sorting block time: 00:00:01 Returning block of 1790457 for bucket 101 bucket 120: 10% bucket 117: 30% bucket 102: 100% Sorting block of length 4508234 for bucket 102 (Using difference cover) Getting block 128 of 202 Reserving size (5249070) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: bucket 115: 40% Sorting block time: 00:00:02 Returning block of 2424404 for bucket 95 bucket 112: 50% Getting block 129 of 202 Reserving size (5249070) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: bucket 111: 80% bucket 113: 70% Sorting block time: 00:00:02 Returning block of 2818884 for bucket 98 bucket 112: 70% bucket 122: 10% bucket 129: 10% bucket 128: 10% Getting block 130 of 202 Reserving size (5249070) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: bucket 122: 30% Sorting block time: 00:00:03 Returning block of 4796129 for bucket 108 bucket 100: 100% Sorting block of length 4665533 for bucket 100 (Using difference cover) bucket 113: 80% bucket 117: 50% Sorting block time: 00:00:02 Returning block of 3511599 for bucket 108 bucket 121: 10% Getting block 132 of 203 Reserving size (5249070) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 119: 50% Getting block 131 of 202 Reserving size (5249070) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 121: 30% bucket 123: 10% bucket 99: 100% Sorting block of length 3718043 for bucket 99 (Using difference cover) bucket 116: 40% Sorting block time: 00:00:03 Returning block of 3779135 for bucket 107 bucket 114: 60% bucket 109: 90% bucket 126: 20% Sorting block time: 00:00:03 Returning block of 3906802 for bucket 96 Getting block 133 of 203 Reserving size (5249070) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 124: 30% bucket 130: 10% Sorting block time: 00:00:02 Returning block of 3319019 for bucket 106 bucket 115: 60% Getting block 132 of 202 Reserving size (5249070) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: Getting block 134 of 203 Reserving size (5249070) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 110: 60% Sorting block time: 00:00:03 Returning block of 4020006 for bucket 102 bucket 125: 20% bucket 111: 70% bucket 120: 20% Getting block 133 of 202 Reserving size (5249070) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 124: 10% bucket 125: 10% bucket 110: 90% bucket 118: 50% bucket 114: 70% bucket 109: 90% bucket 131: 10% bucket 123: 30% bucket 116: 70% bucket 126: 10% bucket 127: 10% bucket 120: 40% bucket 112: 60% bucket 127: 20% bucket 119: 30% bucket 128: 10% bucket 118: 40% bucket 113: 80% bucket 117: 40% bucket 115: 50% bucket 122: 40% bucket 129: 10% bucket 111: 90% bucket 130: 10% bucket 121: 20% Sorting block time: 00:00:03 Returning block of 4508235 for bucket 102 bucket 122: 20% bucket 129: 20% bucket 120: 30% bucket 128: 20% Getting block 135 of 203 Reserving size (5249070) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 131: 10% Sorting block time: 00:00:03 Returning block of 4665534 for bucket 100 Sorting block time: 00:00:02 Returning block of 3718044 for bucket 99 bucket 113: 90% bucket 112: 80% bucket 132: 10% bucket 123: 20% Getting block 134 of 202 Reserving size (5249070) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: Getting block 135 of 202 Reserving size (5249070) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 114: 70% bucket 111: 80% bucket 116: 50% bucket 117: 60% bucket 119: 60% bucket 121: 40% bucket 124: 20% bucket 110: 70% bucket 133: 10% bucket 109: 100% Sorting block of length 2624417 for bucket 109 (Using difference cover) bucket 125: 20% bucket 130: 20% bucket 125: 30% bucket 126: 30% bucket 133: 10% bucket 115: 70% bucket 132: 10% bucket 118: 60% bucket 114: 80% bucket 127: 20% bucket 126: 20% bucket 128: 20% bucket 124: 40% bucket 120: 40% bucket 109: 100% Sorting block of length 4365698 for bucket 109 (Using difference cover) bucket 134: 10% bucket 110: 100% Sorting block of length 2751714 for bucket 110 (Using difference cover) bucket 112: 70% bucket 119: 40% bucket 123: 40% bucket 120: 50% bucket 116: 80% bucket 131: 20% bucket 118: 50% bucket 127: 30% bucket 122: 50% bucket 117: 50% bucket 111: 100% Sorting block of length 5003573 for bucket 111 (Using difference cover) bucket 113: 90% bucket 130: 20% bucket 122: 30% bucket 129: 20% Sorting block time: 00:00:02 Returning block of 2624418 for bucket 109 Getting block 136 of 203 Reserving size (5249070) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 111: 90% bucket 123: 30% bucket 131: 20% bucket 112: 90% bucket 115: 60% bucket 121: 30% bucket 135: 10% bucket 129: 30% bucket 128: 30% bucket 116: 60% bucket 135: 10% bucket 134: 10% bucket 114: 80% bucket 113: 100% Sorting block of length 4517715 for bucket 113 (Using difference cover) bucket 124: 30% bucket 120: 50% bucket 125: 30% Sorting block time: 00:00:02 Returning block of 2751715 for bucket 110 Getting block 137 of 203 Reserving size (5249070) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 133: 20% bucket 119: 70% bucket 121: 50% bucket 110: 80% bucket 127: 30% bucket 132: 20% bucket 117: 70% bucket 126: 40% bucket 124: 50% bucket 118: 70% bucket 128: 30% Sorting block time: 00:00:03 Returning block of 4365699 for bucket 109 bucket 126: 30% bucket 132: 20% Getting block 136 of 202 Reserving size (5249070) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 125: 40% bucket 115: 80% bucket 133: 20% bucket 120: 60% bucket 112: 80% bucket 114: 90% bucket 119: 50% bucket 130: 30% bucket 116: 90% bucket 123: 40% bucket 111: 100% Sorting block of length 1518961 for bucket 111 (Using difference cover) bucket 113: 100% Sorting block of length 3699331 for bucket 113 (Using difference cover) bucket 131: 30% bucket 131: 30% bucket 134: 20% bucket 130: 30% bucket 127: 40% bucket 129: 30% bucket 136: 10% bucket 117: 60% bucket 123: 50% bucket 118: 60% bucket 121: 40% bucket 122: 40% bucket 120: 60% bucket 122: 60% Sorting block time: 00:00:03 Returning block of 5003574 for bucket 111 bucket 114: 90% Getting block 138 of 203 Reserving size (5249070) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 115: 70% bucket 134: 20% bucket 135: 20% bucket 124: 40% Sorting block time: 00:00:00 Returning block of 1518962 for bucket 111 bucket 135: 20% Getting block 137 of 202 Reserving size (5249070) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 116: 70% bucket 132: 30% bucket 125: 40% bucket 119: 80% Sorting block time: 00:00:03 Returning block of 4517716 for bucket 113 bucket 128: 40% bucket 129: 40% bucket 112: 100% Sorting block of length 3448089 for bucket 112 (Using difference cover) Getting block 139 of 203 Reserving size (5249070) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 127: 40% bucket 128: 40% bucket 133: 30% bucket 121: 60% bucket 112: 90% bucket 126: 40% bucket 124: 60% bucket 117: 80% bucket 126: 50% bucket 123: 50% bucket 120: 70% bucket 132: 30% bucket 137: 10% bucket 110: 90% Sorting block time: 00:00:02 Returning block of 3699332 for bucket 113 bucket 125: 50% bucket 115: 90% bucket 136: 10% Getting block 138 of 202 Reserving size (5249070) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 118: 80% bucket 130: 40% bucket 119: 60% bucket 114: 100% Sorting block of length 1602723 for bucket 114 (Using difference cover) bucket 130: 40% bucket 120: 70% bucket 131: 40% bucket 131: 40% bucket 116: 100% Sorting block of length 4857958 for bucket 116 (Using difference cover) bucket 114: 100% Sorting block of length 1592107 for bucket 114 (Using difference cover) bucket 129: 40% bucket 121: 50% bucket 138: 10% bucket 123: 60% bucket 134: 30% bucket 116: 80% bucket 133: 30% bucket 127: 50% bucket 122: 50% Sorting block time: 00:00:02 Returning block of 3448090 for bucket 112 bucket 124: 50% Sorting block time: 00:00:01 Returning block of 1602724 for bucket 114 bucket 132: 40% bucket 117: 70% Getting block 140 of 203 Reserving size (5249070) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: Getting block 141 of 203 Reserving size (5249070) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 134: 30% bucket 129: 50% bucket 135: 30% bucket 115: 80% bucket 139: 10% bucket 120: 80% bucket 122: 70% Sorting block time: 00:00:01 Returning block of 1592108 for bucket 114 bucket 118: 70% bucket 135: 30% Getting block 139 of 202 Reserving size (5249070) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 112: 100% Sorting block of length 4119701 for bucket 112 (Using difference cover) bucket 136: 20% bucket 127: 50% bucket 128: 50% bucket 128: 50% bucket 137: 10% bucket 133: 40% bucket 121: 70% bucket 136: 20% bucket 124: 70% bucket 125: 50% bucket 119: 90% bucket 125: 60% bucket 126: 50% bucket 123: 60% bucket 117: 90% bucket 137: 20% bucket 118: 90% bucket 130: 50% bucket 138: 10% bucket 131: 50% bucket 130: 50% bucket 121: 60% bucket 120: 90% bucket 124: 60% bucket 119: 70% bucket 131: 50% Sorting block time: 00:00:03 Returning block of 4857959 for bucket 116 bucket 115: 100% Sorting block of length 3900232 for bucket 115 (Using difference cover) bucket 126: 60% bucket 110: 100% Sorting block of length 4283446 for bucket 110 (Using difference cover) bucket 132: 40% bucket 120: 80% Getting block 142 of 203 Reserving size (5249070) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 129: 50% bucket 116: 90% bucket 123: 70% bucket 135: 40% bucket 122: 80% bucket 133: 40% bucket 127: 60% bucket 122: 60% bucket 134: 40% bucket 134: 40% bucket 129: 60% Sorting block time: 00:00:03 Returning block of 4119702 for bucket 112 bucket 117: 80% bucket 139: 10% Getting block 140 of 202 Reserving size (5249070) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: bucket 127: 60% bucket 132: 50% bucket 140: 10% bucket 138: 20% bucket 136: 30% bucket 115: 90% bucket 118: 80% bucket 128: 60% bucket 119: 100% Sorting block of length 1169219 for bucket 119 (Using difference cover) bucket 123: 70% bucket 120: 100% Sorting block of length 2949970 for bucket 120 (Using difference cover) bucket 126: 60% bucket 141: 10% bucket 124: 70% bucket 128: 60% bucket 121: 80% bucket 139: 20% bucket 131: 60% bucket 133: 50% bucket 137: 20% bucket 125: 70% bucket 136: 30% bucket 130: 60% bucket 124: 80% Sorting block time: 00:00:01 Returning block of 1169220 for bucket 119 bucket 135: 40% Getting block 143 of 203 Reserving size (5249070) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 125: 60% Sorting block time: 00:00:02 Returning block of 3900233 for bucket 115 bucket 117: 100% Sorting block of length 4790436 for bucket 117 (Using difference cover) Getting block 144 of 203 Reserving size (5249070) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: Sorting block time: 00:00:03 Returning block of 4283447 for bucket 110 bucket 119: 80% bucket 129: 60% bucket 130: 60% bucket 118: 100% Sorting block of length 5048044 for bucket 118 (Using difference cover) Getting block 141 of 202 Reserving size (5249070) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 120: 90% bucket 138: 20% bucket 137: 30% bucket 116: 100% Sorting block of length 3297431 for bucket 116 (Using difference cover) bucket 132: 50% bucket 121: 70% bucket 123: 80% bucket 135: 50% Sorting block time: 00:00:02 Returning block of 2949971 for bucket 120 Getting block 142 of 202 Reserving size (5249070) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 126: 70% bucket 127: 70% bucket 131: 60% bucket 122: 70% bucket 129: 70% bucket 122: 90% bucket 123: 80% bucket 133: 50% bucket 134: 50% bucket 138: 30% bucket 127: 70% bucket 140: 20% bucket 115: 100% Sorting block of length 4512281 for bucket 115 (Using difference cover) bucket 142: 10% bucket 132: 60% bucket 118: 90% bucket 117: 90% bucket 128: 70% bucket 140: 10% bucket 134: 50% bucket 133: 60% bucket 126: 70% bucket 136: 40% bucket 139: 20% bucket 121: 90% bucket 124: 80% bucket 131: 70% bucket 136: 40% bucket 141: 20% Sorting block time: 00:00:02 Returning block of 3297432 for bucket 116 bucket 128: 70% bucket 124: 90% bucket 125: 80% bucket 139: 30% bucket 125: 70% Getting block 143 of 202 Reserving size (5249070) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 135: 50% bucket 142: 10% bucket 144: 10% bucket 143: 10% bucket 130: 70% bucket 129: 70% Sorting block time: 00:00:03 Returning block of 4790437 for bucket 117 Getting block 145 of 203 Reserving size (5249070) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 119: 90% bucket 137: 40% bucket 130: 70% bucket 120: 100% Sorting block of length 4511910 for bucket 120 (Using difference cover) bucket 135: 60% bucket 141: 10% bucket 121: 80% bucket 123: 90% bucket 127: 80% Sorting block time: 00:00:03 Returning block of 5048045 for bucket 118 bucket 123: 90% bucket 122: 80% bucket 138: 30% bucket 137: 30% bucket 132: 60% Getting block 146 of 203 Reserving size (5249070) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: bucket 129: 80% bucket 122: 100% Sorting block of length 3058555 for bucket 122 (Using difference cover) bucket 117: 100% Sorting block of length 4479562 for bucket 117 (Using difference cover) bucket 131: 70% bucket 126: 80% bucket 127: 80% Sorting block time: 00:00:03 Returning block of 4512282 for bucket 115 bucket 133: 70% bucket 142: 20% Getting block 144 of 202 Reserving size (5249070) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 128: 80% bucket 132: 70% bucket 126: 80% bucket 133: 60% bucket 140: 30% bucket 134: 60% bucket 118: 100% Sorting block of length 4933111 for bucket 118 (Using difference cover) bucket 142: 20% bucket 134: 60% bucket 144: 20% bucket 140: 20% bucket 138: 40% bucket 131: 80% bucket 139: 30% bucket 125: 80% bucket 121: 100% Sorting block of length 4502698 for bucket 121 (Using difference cover) bucket 136: 50% bucket 124: 90% bucket 136: 50% bucket 125: 90% bucket 128: 80% bucket 139: 40% bucket 129: 80% bucket 143: 10% bucket 141: 30% bucket 124: 100% Sorting block of length 4128495 for bucket 124 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3058556 for bucket 122 Getting block 147 of 203 Reserving size (5249070) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 135: 70% bucket 123: 100% Sorting block of length 3262887 for bucket 123 (Using difference cover) bucket 130: 80% bucket 121: 90% bucket 135: 60% bucket 137: 50% bucket 119: 100% Sorting block of length 4643201 for bucket 119 (Using difference cover) bucket 127: 90% Sorting block time: 00:00:03 Returning block of 4511911 for bucket 120 bucket 142: 30% bucket 143: 20% bucket 130: 80% bucket 122: 90% Getting block 148 of 203 Reserving size (5249070) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 145: 10% bucket 138: 40% Sorting block time: 00:00:03 Returning block of 4479563 for bucket 117 bucket 144: 30% bucket 137: 40% bucket 132: 70% bucket 123: 100% Sorting block of length 5224064 for bucket 123 (Using difference cover) Getting block 145 of 202 Reserving size (5249070) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 131: 80% bucket 146: 10% bucket 133: 80% bucket 141: 20% bucket 129: 90% bucket 126: 90% bucket 132: 80% bucket 126: 90% bucket 134: 70% bucket 140: 40% bucket 128: 90% Sorting block time: 00:00:03 Returning block of 4933112 for bucket 118 bucket 127: 90% bucket 124: 100% Sorting block of length 4079833 for bucket 124 (Using difference cover) bucket 131: 90% bucket 140: 30% bucket 136: 60% Getting block 146 of 202 Reserving size (5249070) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: bucket 133: 70% bucket 125: 90% bucket 138: 50% bucket 134: 70% Sorting block time: 00:00:03 Returning block of 4502699 for bucket 121 bucket 136: 60% bucket 142: 40% Sorting block time: 00:00:02 Returning block of 3262888 for bucket 123 Getting block 149 of 203 Reserving size (5249070) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: bucket 143: 20% bucket 142: 30% Getting block 147 of 202 Reserving size (5249070) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 144: 10% bucket 139: 40% Sorting block time: 00:00:03 Returning block of 4128496 for bucket 124 bucket 139: 50% bucket 125: 100% Sorting block of length 4727381 for bucket 125 (Using difference cover) bucket 141: 40% Getting block 150 of 203 Reserving size (5249070) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 128: 90% bucket 129: 90% bucket 127: 100% Sorting block of length 3279466 for bucket 127 (Using difference cover) bucket 121: 100% Sorting block of length 4698166 for bucket 121 (Using difference cover) bucket 130: 90% Sorting block time: 00:00:03 Returning block of 4643202 for bucket 119 bucket 147: 10% Getting block 148 of 202 Reserving size (5249070) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 135: 80% bucket 132: 90% bucket 148: 10% bucket 122: 100% Sorting block of length 4895193 for bucket 122 (Using difference cover) bucket 138: 50% bucket 133: 90% bucket 137: 50% bucket 132: 80% bucket 144: 40% bucket 143: 30% bucket 137: 60% bucket 130: 90% bucket 135: 70% bucket 126: 100% Sorting block of length 5219673 for bucket 126 (Using difference cover) bucket 142: 50% bucket 131: 90% bucket 129: 100% Sorting block of length 5154709 for bucket 129 (Using difference cover) bucket 145: 20% bucket 128: 100% Sorting block of length 3323849 for bucket 128 (Using difference cover) bucket 126: 100% Sorting block of length 2643784 for bucket 126 (Using difference cover) Sorting block time: 00:00:03 Returning block of 5224065 for bucket 123 bucket 131: 100% Sorting block of length 3926167 for bucket 131 (Using difference cover) bucket 136: 70% Sorting block time: 00:00:03 Returning block of 4079834 for bucket 124 bucket 146: 10% bucket 145: 10% bucket 125: 100% Sorting block of length 4849685 for bucket 125 (Using difference cover) bucket 140: 50% Getting block 149 of 202 Reserving size (5249070) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: Getting block 151 of 203 Reserving size (5249070) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 134: 80% bucket 141: 30% bucket 127: 100% Sorting block of length 4343177 for bucket 127 (Using difference cover) bucket 146: 20% bucket 133: 80% bucket 141: 50% bucket 147: 10% bucket 138: 60% Sorting block time: 00:00:02 Returning block of 3279467 for bucket 127 Getting block 150 of 202 Reserving size (5249070) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 139: 60% bucket 138: 60% bucket 150: 10% bucket 140: 40% bucket 130: 100% Sorting block of length 1953872 for bucket 130 (Using difference cover) bucket 149: 10% bucket 144: 20% bucket 142: 40% bucket 143: 30% bucket 136: 70% bucket 129: 100% Sorting block of length 4846174 for bucket 129 (Using difference cover) bucket 143: 40% Sorting block time: 00:00:03 Returning block of 4727382 for bucket 125 bucket 134: 80% bucket 133: 100% Sorting block of length 4272498 for bucket 133 (Using difference cover) Getting block 152 of 203 Reserving size (5249070) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: bucket 128: 100% Sorting block of length 4456704 for bucket 128 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4698167 for bucket 121 bucket 147: 20% Sorting block time: 00:00:02 Returning block of 2643785 for bucket 126 bucket 137: 70% Getting block 151 of 202 Reserving size (5249070) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: Getting block 153 of 203 Reserving size (5249070) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 135: 90% Sorting block time: 00:00:04 Returning block of 4895194 for bucket 122 bucket 142: 60% Sorting block time: 00:00:03 Returning block of 3323850 for bucket 128 Sorting block time: 00:00:01 Returning block of 1953873 for bucket 130 bucket 148: 10% bucket 132: 100% Sorting block of length 1922653 for bucket 132 (Using difference cover) Getting block 152 of 202 Reserving size (5249070) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: Getting block 153 of 202 Reserving size (5249070) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: Getting block 154 of 202 Reserving size (5249070) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 139: 50% bucket 144: 50% bucket 132: 90% bucket 148: 20% bucket 131: 100% Sorting block of length 4766064 for bucket 131 (Using difference cover) bucket 136: 80% Sorting block time: 00:00:03 Returning block of 3926168 for bucket 131 bucket 137: 60% bucket 141: 40% Getting block 155 of 202 Reserving size (5249070) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: bucket 140: 60% bucket 145: 30% Sorting block time: 00:00:04 Returning block of 5219674 for bucket 126 Sorting block time: 00:00:03 Returning block of 4343178 for bucket 127 Sorting block time: 00:00:03 Returning block of 4849686 for bucket 125 bucket 133: 90% bucket 134: 90% bucket 130: 100% Sorting block of length 3955374 for bucket 130 (Using difference cover) Getting block 156 of 202 Reserving size (5249070) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: Sorting block time: 00:00:01 Returning block of 1922654 for bucket 132 bucket 146: 20% Getting block 154 of 203 Reserving size (5249070) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 143: 50% Getting block 157 of 202 Reserving size (5249070) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 145: 20% bucket 144: 30% bucket 151: 10% Getting block 158 of 202 Reserving size (5249070) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: bucket 150: 10% bucket 138: 70% Sorting block time: 00:00:04 Returning block of 5154710 for bucket 129 bucket 142: 50% bucket 149: 10% bucket 135: 80% Getting block 155 of 203 Reserving size (5249070) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: bucket 146: 30% bucket 139: 70% bucket 147: 20% bucket 141: 60% bucket 138: 70% bucket 143: 40% bucket 144: 60% Sorting block time: 00:00:03 Returning block of 4272499 for bucket 133 bucket 148: 30% Getting block 159 of 202 Reserving size (5249070) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: Sorting block time: 00:00:03 Returning block of 4846175 for bucket 129 Getting block 160 of 202 Reserving size (5249070) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 136: 80% bucket 153: 10% bucket 150: 20% bucket 134: 90% bucket 140: 50% bucket 152: 10% bucket 149: 20% Sorting block time: 00:00:04 Returning block of 4456705 for bucket 128 bucket 147: 30% Getting block 156 of 203 Reserving size (5249070) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 142: 70% bucket 151: 10% bucket 143: 60% bucket 144: 40% bucket 139: 60% bucket 135: 100% Sorting block of length 2785175 for bucket 135 (Using difference cover) bucket 153: 10% bucket 152: 10% Sorting block time: 00:00:03 Returning block of 3955375 for bucket 130 bucket 154: 10% bucket 148: 20% bucket 156: 10% bucket 137: 80% Sorting block time: 00:00:04 Returning block of 4766065 for bucket 131 bucket 150: 20% Getting block 157 of 203 Reserving size (5249070) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 132: 100% Sorting block of length 4284401 for bucket 132 (Using difference cover) bucket 137: 70% bucket 140: 70% bucket 141: 50% bucket 146: 30% bucket 138: 80% bucket 155: 10% Getting block 158 of 203 Reserving size (5249070) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: bucket 136: 90% bucket 142: 60% bucket 134: 100% Sorting block of length 5016775 for bucket 134 (Using difference cover) bucket 138: 80% bucket 145: 30% bucket 157: 10% bucket 133: 100% Sorting block of length 2748080 for bucket 133 (Using difference cover) bucket 139: 80% bucket 158: 10% bucket 147: 30% bucket 151: 20% bucket 149: 20% bucket 145: 40% bucket 154: 10% bucket 153: 20% bucket 159: 10% bucket 143: 70% Sorting block time: 00:00:02 Returning block of 2785176 for bucket 135 bucket 136: 90% bucket 135: 90% bucket 155: 10% Getting block 161 of 202 Reserving size (5249070) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 143: 50% bucket 156: 10% bucket 141: 70% bucket 160: 10% bucket 144: 70% bucket 148: 40% bucket 140: 60% bucket 146: 40% bucket 144: 50% bucket 151: 20% bucket 147: 40% bucket 156: 20% bucket 134: 100% Sorting block of length 4428900 for bucket 134 (Using difference cover) bucket 150: 30% bucket 152: 20% bucket 149: 30% bucket 148: 30% bucket 139: 70% Sorting block time: 00:00:02 Returning block of 2748081 for bucket 133 bucket 137: 90% bucket 142: 70% bucket 138: 90% bucket 152: 20% Sorting block time: 00:00:03 Returning block of 4284402 for bucket 132 bucket 154: 20% Getting block 159 of 203 Reserving size (5249070) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 138: 90% bucket 157: 10% bucket 142: 80% Getting block 160 of 203 Reserving size (5249070) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 158: 10% bucket 143: 80% Sorting block time: 00:00:04 Returning block of 5016776 for bucket 134 bucket 157: 20% bucket 150: 30% bucket 155: 20% bucket 139: 90% bucket 146: 40% Getting block 162 of 202 Reserving size (5249070) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 140: 80% bucket 158: 20% bucket 136: 100% Sorting block of length 4270965 for bucket 136 (Using difference cover) bucket 144: 60% bucket 141: 80% bucket 137: 80% bucket 145: 40% bucket 153: 20% bucket 154: 20% bucket 141: 60% bucket 145: 50% bucket 161: 10% bucket 151: 30% bucket 149: 30% bucket 153: 30% bucket 136: 100% Sorting block of length 4411578 for bucket 136 (Using difference cover) bucket 160: 20% bucket 143: 60% bucket 146: 50% bucket 159: 20% bucket 142: 90% bucket 147: 40% bucket 156: 20% bucket 155: 20% bucket 135: 100% Sorting block of length 3178045 for bucket 135 (Using difference cover) bucket 148: 50% bucket 144: 80% bucket 151: 30% bucket 156: 30% bucket 138: 100% Sorting block of length 4420627 for bucket 138 (Using difference cover) bucket 143: 90% Sorting block time: 00:00:03 Returning block of 4428901 for bucket 134 bucket 140: 70% bucket 139: 80% Getting block 161 of 203 Reserving size (5249070) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 147: 50% bucket 148: 40% bucket 152: 30% bucket 150: 40% bucket 154: 30% bucket 159: 10% bucket 142: 80% bucket 157: 30% bucket 149: 40% bucket 138: 100% Sorting block of length 3894786 for bucket 138 (Using difference cover) bucket 137: 100% Sorting block of length 3655262 for bucket 137 (Using difference cover) bucket 152: 30% bucket 157: 20% bucket 158: 30% Sorting block time: 00:00:03 Returning block of 4270966 for bucket 136 bucket 150: 40% bucket 146: 50% Getting block 162 of 203 Reserving size (5249070) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 142: 100% Sorting block of length 2719105 for bucket 142 (Using difference cover) bucket 162: 10% bucket 141: 90% bucket 144: 70% bucket 155: 30% bucket 160: 10% bucket 139: 100% Sorting block of length 3572090 for bucket 139 (Using difference cover) bucket 158: 20% bucket 141: 70% Sorting block time: 00:00:02 Returning block of 4411579 for bucket 136 Sorting block time: 00:00:02 Returning block of 3178046 for bucket 135 bucket 145: 50% bucket 140: 90% bucket 161: 20% bucket 153: 40% bucket 160: 30% Getting block 163 of 202 Reserving size (5249070) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: Getting block 163 of 203 Reserving size (5249070) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: bucket 149: 40% bucket 143: 70% bucket 137: 90% bucket 147: 50% bucket 144: 90% bucket 159: 30% bucket 139: 90% bucket 145: 60% bucket 151: 40% bucket 155: 30% bucket 156: 40% bucket 143: 100% Sorting block of length 3503722 for bucket 143 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4420628 for bucket 138 Getting block 164 of 203 Reserving size (5249070) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 153: 30% bucket 148: 60% bucket 154: 30% bucket 152: 40% Sorting block time: 00:00:02 Returning block of 2719106 for bucket 142 Sorting block time: 00:00:03 Returning block of 3894787 for bucket 138 Getting block 164 of 202 Reserving size (5249070) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 148: 50% bucket 140: 80% Getting block 165 of 202 Reserving size (5249070) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: Sorting block time: 00:00:03 Returning block of 3655263 for bucket 137 bucket 146: 60% bucket 161: 10% bucket 151: 40% Getting block 165 of 203 Reserving size (5249070) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 142: 90% bucket 147: 60% bucket 157: 40% bucket 154: 40% bucket 156: 30% bucket 146: 60% bucket 150: 50% bucket 162: 20% Sorting block time: 00:00:03 Returning block of 3572091 for bucket 139 bucket 159: 20% bucket 158: 40% bucket 141: 100% Sorting block of length 2123205 for bucket 141 (Using difference cover) bucket 150: 50% bucket 149: 50% Getting block 166 of 203 Reserving size (5249070) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 152: 40% bucket 160: 20% Sorting block time: 00:00:02 Returning block of 3503723 for bucket 143 bucket 153: 50% bucket 163: 10% bucket 144: 80% bucket 141: 80% bucket 162: 10% bucket 160: 40% bucket 161: 30% Getting block 167 of 203 Reserving size (5249070) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: bucket 155: 40% bucket 157: 30% bucket 158: 30% bucket 149: 50% bucket 139: 100% Sorting block of length 1961332 for bucket 139 (Using difference cover) bucket 145: 60% bucket 145: 70% bucket 163: 10% bucket 147: 60% bucket 140: 100% Sorting block of length 3605269 for bucket 140 (Using difference cover) bucket 159: 40% bucket 143: 80% Sorting block time: 00:00:01 Returning block of 2123206 for bucket 141 bucket 156: 50% bucket 137: 100% Sorting block of length 4501409 for bucket 137 (Using difference cover) Getting block 168 of 203 Reserving size (5249070) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 165: 10% bucket 155: 40% bucket 151: 50% bucket 164: 10% bucket 144: 100% Sorting block of length 1816099 for bucket 144 (Using difference cover) bucket 161: 20% bucket 164: 10% bucket 148: 70% bucket 146: 70% bucket 142: 100% Sorting block of length 3601544 for bucket 142 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1961333 for bucket 139 Getting block 166 of 202 Reserving size (5249070) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 157: 50% bucket 154: 50% bucket 151: 50% bucket 154: 40% bucket 152: 50% bucket 156: 40% bucket 148: 60% bucket 147: 70% bucket 162: 30% bucket 153: 40% bucket 162: 20% bucket 165: 10% bucket 150: 60% bucket 146: 70% bucket 158: 50% bucket 149: 60% bucket 140: 90% bucket 166: 10% bucket 167: 10% Sorting block time: 00:00:01 Returning block of 1816100 for bucket 144 bucket 155: 50% bucket 163: 20% Getting block 169 of 203 Reserving size (5249070) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 160: 50% bucket 144: 90% bucket 141: 90% bucket 150: 60% bucket 152: 50% bucket 161: 40% Sorting block time: 00:00:02 Returning block of 3605270 for bucket 140 bucket 153: 60% Getting block 170 of 203 Reserving size (5249070) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 159: 30% bucket 158: 40% bucket 160: 30% bucket 157: 40% Sorting block time: 00:00:03 Returning block of 4501410 for bucket 137 bucket 145: 70% bucket 145: 80% bucket 149: 60% Getting block 167 of 202 Reserving size (5249070) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: bucket 165: 20% Sorting block time: 00:00:02 Returning block of 3601545 for bucket 142 bucket 159: 50% bucket 147: 70% bucket 156: 60% bucket 143: 90% Getting block 171 of 203 Reserving size (5249070) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 163: 20% bucket 164: 20% bucket 168: 10% bucket 157: 60% bucket 154: 60% bucket 148: 80% bucket 164: 20% bucket 166: 10% bucket 144: 100% Sorting block of length 4242238 for bucket 144 (Using difference cover) bucket 161: 30% bucket 151: 60% bucket 146: 80% bucket 151: 60% bucket 155: 50% bucket 156: 50% bucket 162: 40% bucket 148: 70% bucket 154: 50% bucket 147: 80% bucket 146: 80% bucket 162: 30% bucket 152: 60% bucket 166: 20% bucket 158: 60% bucket 150: 70% bucket 140: 100% Sorting block of length 4681892 for bucket 140 (Using difference cover) bucket 167: 20% bucket 149: 70% bucket 163: 30% bucket 150: 70% bucket 155: 60% bucket 160: 60% bucket 152: 60% bucket 157: 50% bucket 161: 50% bucket 143: 100% Sorting block of length 2712080 for bucket 143 (Using difference cover) bucket 145: 80% bucket 165: 20% bucket 159: 40% bucket 141: 100% Sorting block of length 4035672 for bucket 141 (Using difference cover) bucket 153: 50% bucket 158: 50% bucket 153: 70% bucket 156: 70% bucket 164: 30% bucket 160: 40% bucket 159: 60% bucket 167: 10% bucket 164: 30% bucket 165: 30% bucket 149: 70% bucket 169: 10% bucket 147: 80% bucket 170: 10% bucket 145: 90% bucket 171: 10% Sorting block time: 00:00:03 Returning block of 4242239 for bucket 144 bucket 163: 30% bucket 166: 20% Getting block 168 of 202 Reserving size (5249070) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 146: 90% bucket 154: 70% bucket 156: 60% bucket 157: 70% bucket 161: 40% bucket 162: 50% bucket 146: 90% Sorting block time: 00:00:01 Returning block of 2712081 for bucket 143 Getting block 169 of 202 Reserving size (5249070) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 148: 90% bucket 151: 70% bucket 147: 90% bucket 168: 20% bucket 148: 80% bucket 155: 60% Sorting block time: 00:00:02 Returning block of 4035673 for bucket 141 bucket 162: 40% bucket 151: 70% bucket 154: 60% Getting block 170 of 202 Reserving size (5249070) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 158: 70% bucket 150: 80% bucket 152: 70% Sorting block time: 00:00:03 Returning block of 4681893 for bucket 140 bucket 166: 30% bucket 163: 40% bucket 152: 70% bucket 167: 30% bucket 150: 80% Getting block 171 of 202 Reserving size (5249070) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 161: 60% bucket 155: 70% bucket 168: 10% bucket 157: 60% bucket 149: 80% bucket 160: 70% bucket 145: 90% bucket 153: 80% bucket 164: 40% bucket 165: 40% bucket 156: 80% bucket 160: 50% bucket 146: 100% Sorting block of length 4069160 for bucket 146 (Using difference cover) bucket 153: 60% bucket 159: 50% bucket 165: 30% bucket 169: 10% bucket 164: 40% bucket 159: 70% bucket 158: 60% bucket 169: 20% bucket 146: 100% Sorting block of length 4954810 for bucket 146 (Using difference cover) bucket 162: 60% bucket 147: 90% bucket 170: 20% bucket 167: 20% bucket 149: 80% bucket 145: 100% Sorting block of length 4913452 for bucket 145 (Using difference cover) bucket 162: 50% bucket 161: 50% bucket 163: 40% bucket 154: 80% bucket 171: 20% bucket 148: 100% Sorting block of length 4278805 for bucket 148 (Using difference cover) bucket 168: 30% bucket 152: 80% bucket 166: 30% bucket 170: 10% bucket 147: 100% Sorting block of length 5098094 for bucket 147 (Using difference cover) bucket 168: 20% bucket 154: 70% bucket 155: 70% bucket 166: 40% bucket 156: 70% bucket 157: 80% bucket 151: 80% bucket 152: 80% bucket 161: 70% bucket 167: 40% bucket 151: 80% bucket 150: 90% bucket 148: 90% bucket 171: 10% bucket 150: 90% bucket 158: 80% bucket 155: 80% Sorting block time: 00:00:03 Returning block of 4069161 for bucket 146 bucket 149: 90% Getting block 172 of 203 Reserving size (5249070) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: bucket 145: 100% Sorting block of length 1377030 for bucket 145 (Using difference cover) bucket 163: 50% bucket 160: 80% bucket 160: 60% bucket 165: 40% bucket 159: 60% bucket 157: 70% bucket 169: 20% bucket 169: 30% bucket 156: 90% bucket 165: 50% bucket 162: 70% bucket 167: 30% bucket 153: 90% bucket 158: 70% bucket 153: 70% bucket 164: 50% Sorting block time: 00:00:03 Returning block of 4954811 for bucket 146 bucket 163: 50% Sorting block time: 00:00:01 Returning block of 1377031 for bucket 145 Getting block 172 of 202 Reserving size (5249070) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: bucket 171: 30% Getting block 173 of 202 Reserving size (5249070) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: bucket 149: 90% bucket 159: 80% Sorting block time: 00:00:03 Returning block of 4913453 for bucket 145 bucket 162: 60% Sorting block time: 00:00:02 Returning block of 4278806 for bucket 148 bucket 170: 30% bucket 147: 100% Sorting block of length 3516411 for bucket 147 (Using difference cover) Getting block 173 of 203 Reserving size (5249070) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: bucket 164: 50% Getting block 174 of 203 Reserving size (5249070) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 166: 40% bucket 157: 90% bucket 152: 90% bucket 154: 90% bucket 166: 50% bucket 161: 80% bucket 151: 90% bucket 161: 60% bucket 168: 30% bucket 168: 40% Sorting block time: 00:00:03 Returning block of 5098095 for bucket 147 bucket 167: 50% bucket 150: 100% Sorting block of length 4284928 for bucket 150 (Using difference cover) bucket 148: 100% Sorting block of length 4149296 for bucket 148 (Using difference cover) Getting block 175 of 203 Reserving size (5249070) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 171: 20% bucket 152: 90% bucket 156: 80% bucket 150: 100% Sorting block of length 1993427 for bucket 150 (Using difference cover) bucket 170: 20% bucket 154: 80% bucket 155: 90% bucket 163: 60% bucket 155: 80% bucket 173: 10% bucket 160: 70% bucket 171: 40% bucket 149: 100% Sorting block of length 2625830 for bucket 149 (Using difference cover) bucket 158: 90% bucket 165: 60% bucket 160: 90% bucket 151: 90% bucket 167: 40% bucket 172: 10% bucket 157: 80% bucket 153: 100% Sorting block of length 3673139 for bucket 153 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3516412 for bucket 147 bucket 156: 100% Sorting block of length 4229904 for bucket 156 (Using difference cover) bucket 159: 90% Getting block 174 of 202 Reserving size (5249070) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: Sorting block time: 00:00:01 Returning block of 1993428 for bucket 150 bucket 165: 50% Getting block 175 of 202 Reserving size (5249070) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 169: 40% bucket 169: 30% bucket 158: 80% bucket 164: 60% bucket 170: 40% bucket 159: 70% bucket 162: 80% bucket 149: 100% Sorting block of length 4783645 for bucket 149 (Using difference cover) bucket 153: 80% bucket 163: 60% bucket 168: 50% bucket 162: 70% bucket 164: 60% bucket 173: 10% bucket 152: 100% Sorting block of length 4646880 for bucket 152 (Using difference cover) bucket 172: 10% bucket 157: 100% Sorting block of length 3814893 for bucket 157 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2625831 for bucket 149 bucket 174: 10% bucket 161: 90% bucket 161: 70% bucket 173: 20% Sorting block time: 00:00:03 Returning block of 4149297 for bucket 148 Getting block 176 of 203 Reserving size (5249070) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: bucket 166: 60% bucket 170: 30% bucket 171: 50% bucket 166: 50% bucket 151: 100% Sorting block of length 3463602 for bucket 151 (Using difference cover) Getting block 176 of 202 Reserving size (5249070) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: bucket 154: 100% Sorting block of length 5210359 for bucket 154 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4284929 for bucket 150 Getting block 177 of 203 Reserving size (5249070) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 168: 40% bucket 171: 30% bucket 160: 80% bucket 152: 100% Sorting block of length 1618411 for bucket 152 (Using difference cover) bucket 155: 100% Sorting block of length 3568674 for bucket 155 (Using difference cover) bucket 158: 100% Sorting block of length 5135362 for bucket 158 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3673140 for bucket 153 bucket 156: 90% bucket 175: 10% Getting block 177 of 202 Reserving size (5249070) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 163: 70% bucket 167: 50% bucket 160: 100% Sorting block of length 2602067 for bucket 160 (Using difference cover) bucket 155: 90% bucket 172: 20% Sorting block time: 00:00:03 Returning block of 4229905 for bucket 156 bucket 169: 40% bucket 165: 70% bucket 158: 90% Sorting block time: 00:00:02 Returning block of 3814894 for bucket 157 bucket 154: 90% Getting block 178 of 202 Reserving size (5249070) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: Getting block 179 of 202 Reserving size (5249070) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 167: 60% bucket 168: 60% bucket 159: 100% Sorting block of length 3771026 for bucket 159 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1618412 for bucket 152 bucket 174: 10% bucket 164: 70% Getting block 178 of 203 Reserving size (5249070) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: bucket 162: 90% bucket 157: 90% Sorting block time: 00:00:03 Returning block of 4646881 for bucket 152 bucket 165: 60% bucket 151: 100% Sorting block of length 5109323 for bucket 151 (Using difference cover) Getting block 180 of 202 Reserving size (5249070) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: Sorting block time: 00:00:03 Returning block of 4783646 for bucket 149 bucket 173: 20% bucket 173: 30% bucket 163: 70% bucket 169: 50% Sorting block time: 00:00:02 Returning block of 3463603 for bucket 151 bucket 153: 90% bucket 170: 50% Getting block 181 of 202 Reserving size (5249070) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: bucket 172: 20% bucket 160: 90% bucket 175: 10% Getting block 182 of 202 Reserving size (5249070) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 161: 100% Sorting block of length 4613170 for bucket 161 (Using difference cover) bucket 162: 80% bucket 170: 40% bucket 166: 60% bucket 164: 70% bucket 174: 20% Sorting block time: 00:00:03 Returning block of 3568675 for bucket 155 Sorting block time: 00:00:02 Returning block of 2602068 for bucket 160 bucket 168: 50% bucket 159: 80% Getting block 183 of 202 Reserving size (5249070) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: Getting block 184 of 202 Reserving size (5249070) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 176: 10% bucket 166: 70% bucket 176: 10% bucket 161: 80% bucket 179: 10% bucket 177: 10% Sorting block time: 00:00:04 Returning block of 5210360 for bucket 154 bucket 178: 10% bucket 172: 30% bucket 177: 10% Getting block 185 of 202 Reserving size (5249070) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 171: 60% bucket 165: 80% Sorting block time: 00:00:04 Returning block of 5135363 for bucket 158 bucket 167: 60% bucket 163: 80% bucket 171: 40% Getting block 186 of 202 Reserving size (5249070) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: Sorting block time: 00:00:02 Returning block of 3771027 for bucket 159 bucket 173: 30% Getting block 187 of 202 Reserving size (5249070) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: bucket 156: 100% Sorting block of length 3251023 for bucket 156 (Using difference cover) bucket 174: 20% bucket 175: 20% bucket 167: 70% bucket 158: 100% Sorting block of length 4390500 for bucket 158 (Using difference cover) bucket 168: 70% bucket 157: 100% Sorting block of length 3335604 for bucket 157 (Using difference cover) bucket 155: 100% Sorting block of length 4545327 for bucket 155 (Using difference cover) bucket 164: 80% bucket 160: 100% Sorting block of length 2743902 for bucket 160 (Using difference cover) bucket 163: 80% bucket 169: 50% bucket 180: 10% bucket 173: 40% bucket 178: 10% bucket 154: 100% Sorting block of length 1553748 for bucket 154 (Using difference cover) bucket 184: 10% bucket 179: 20% bucket 170: 60% Sorting block time: 00:00:03 Returning block of 5109324 for bucket 151 bucket 166: 70% bucket 175: 20% Getting block 179 of 203 Reserving size (5249070) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 181: 10% bucket 162: 100% Sorting block of length 4932938 for bucket 162 (Using difference cover) bucket 165: 70% Sorting block time: 00:00:04 Returning block of 4613171 for bucket 161 bucket 176: 20% bucket 183: 10% bucket 172: 30% Getting block 188 of 202 Reserving size (5249070) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 169: 60% bucket 182: 10% bucket 162: 90% bucket 176: 20% bucket 153: 100% Sorting block of length 4586573 for bucket 153 (Using difference cover) bucket 164: 80% bucket 174: 30% bucket 166: 80% bucket 173: 40% bucket 159: 90% Sorting block time: 00:00:01 Returning block of 1553749 for bucket 154 bucket 185: 10% bucket 178: 20% Getting block 180 of 203 Reserving size (5249070) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 170: 50% bucket 161: 90% bucket 168: 60% Sorting block time: 00:00:03 Returning block of 3251024 for bucket 156 bucket 177: 20% bucket 165: 90% Getting block 181 of 203 Reserving size (5249070) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: Sorting block time: 00:00:02 Returning block of 2743903 for bucket 160 bucket 179: 30% bucket 167: 70% bucket 187: 10% Getting block 182 of 203 Reserving size (5249070) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 172: 40% Sorting block time: 00:00:02 Returning block of 3335605 for bucket 157 bucket 177: 20% bucket 171: 50% Getting block 183 of 203 Reserving size (5249070) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: bucket 186: 10% bucket 184: 20% bucket 167: 80% bucket 171: 70% bucket 174: 30% bucket 163: 90% bucket 168: 80% bucket 175: 30% Sorting block time: 00:00:03 Returning block of 4390501 for bucket 158 bucket 163: 90% bucket 169: 60% bucket 170: 70% Sorting block time: 00:00:03 Returning block of 4545328 for bucket 155 Getting block 184 of 203 Reserving size (5249070) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 164: 90% Getting block 185 of 203 Reserving size (5249070) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 178: 20% bucket 183: 20% bucket 172: 40% bucket 173: 50% bucket 181: 20% bucket 166: 80% bucket 175: 30% bucket 165: 80% bucket 179: 10% bucket 182: 20% Sorting block time: 00:00:03 Returning block of 4932939 for bucket 162 bucket 162: 100% Sorting block of length 4491044 for bucket 162 (Using difference cover) bucket 179: 40% bucket 176: 30% bucket 188: 10% bucket 174: 40% bucket 176: 30% bucket 180: 20% bucket 169: 70% bucket 166: 90% Sorting block time: 00:00:03 Returning block of 4586574 for bucket 153 bucket 159: 100% Sorting block of length 5126724 for bucket 159 (Using difference cover) bucket 173: 50% bucket 170: 60% bucket 168: 70% bucket 164: 90% bucket 165: 100% Sorting block of length 2931781 for bucket 165 (Using difference cover) bucket 185: 20% Getting block 189 of 202 Reserving size (5249070) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: Getting block 186 of 203 Reserving size (5249070) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: bucket 161: 100% Sorting block of length 4424689 for bucket 161 (Using difference cover) bucket 180: 10% bucket 178: 30% bucket 186: 20% bucket 187: 20% bucket 167: 80% bucket 177: 30% bucket 172: 50% bucket 181: 10% bucket 177: 30% bucket 171: 80% bucket 182: 10% bucket 167: 90% bucket 171: 60% bucket 179: 50% bucket 172: 50% bucket 174: 40% bucket 184: 30% bucket 183: 10% bucket 175: 40% bucket 170: 80% bucket 163: 100% Sorting block of length 4247085 for bucket 163 (Using difference cover) bucket 163: 100% Sorting block of length 3291505 for bucket 163 (Using difference cover) bucket 168: 90% bucket 169: 70% bucket 173: 60% bucket 164: 100% Sorting block of length 2552328 for bucket 164 (Using difference cover) bucket 183: 30% bucket 184: 10% Sorting block time: 00:00:02 Returning block of 2931782 for bucket 165 bucket 185: 10% Getting block 190 of 202 Reserving size (5249070) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 182: 30% bucket 175: 40% bucket 179: 20% bucket 165: 90% bucket 166: 90% bucket 181: 30% bucket 176: 40% bucket 188: 20% bucket 174: 50% bucket 185: 30% bucket 178: 30% bucket 166: 100% Sorting block of length 3655360 for bucket 166 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4491045 for bucket 162 bucket 189: 10% bucket 173: 60% Getting block 187 of 203 Reserving size (5249070) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: bucket 180: 30% bucket 176: 40% bucket 187: 30% bucket 164: 100% Sorting block of length 4857454 for bucket 164 (Using difference cover) bucket 179: 60% Sorting block time: 00:00:03 Returning block of 4424690 for bucket 161 bucket 169: 80% bucket 180: 20% bucket 178: 40% bucket 186: 10% Sorting block time: 00:00:04 Returning block of 5126725 for bucket 159 bucket 170: 70% Sorting block time: 00:00:02 Returning block of 2552329 for bucket 164 Getting block 188 of 203 Reserving size (5249070) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 167: 90% Getting block 191 of 202 Reserving size (5249070) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: Getting block 189 of 203 Reserving size (5249070) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 186: 30% bucket 177: 40% Sorting block time: 00:00:02 Returning block of 3291506 for bucket 163 Getting block 190 of 203 Reserving size (5249070) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: Sorting block time: 00:00:02 Returning block of 4247086 for bucket 163 bucket 182: 20% bucket 172: 60% bucket 177: 40% bucket 168: 80% bucket 181: 20% bucket 171: 70% bucket 171: 90% Getting block 192 of 202 Reserving size (5249070) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 167: 100% Sorting block of length 3444878 for bucket 167 (Using difference cover) bucket 175: 50% bucket 184: 40% bucket 170: 90% bucket 184: 20% bucket 174: 50% bucket 168: 100% Sorting block of length 4781905 for bucket 168 (Using difference cover) bucket 183: 40% bucket 176: 50% bucket 175: 50% bucket 166: 100% Sorting block of length 4275735 for bucket 166 (Using difference cover) bucket 188: 30% Sorting block time: 00:00:03 Returning block of 3655361 for bucket 166 bucket 172: 60% bucket 183: 20% Getting block 191 of 203 Reserving size (5249070) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: bucket 179: 30% bucket 181: 40% bucket 180: 40% bucket 169: 80% bucket 185: 40% bucket 182: 40% bucket 189: 20% bucket 185: 20% bucket 173: 70% bucket 176: 50% bucket 165: 100% Sorting block of length 4479271 for bucket 165 (Using difference cover) bucket 190: 10% bucket 187: 40% bucket 173: 70% bucket 168: 90% bucket 174: 60% bucket 178: 40% bucket 191: 10% Sorting block time: 00:00:04 Returning block of 4857455 for bucket 164 bucket 187: 10% bucket 179: 70% bucket 186: 40% bucket 178: 50% bucket 167: 100% Sorting block of length 4258908 for bucket 167 (Using difference cover) Getting block 192 of 203 Reserving size (5249070) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 180: 30% bucket 169: 90% Sorting block time: 00:00:02 Returning block of 3444879 for bucket 167 bucket 190: 10% bucket 170: 80% Getting block 193 of 203 Reserving size (5249070) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: bucket 171: 80% bucket 177: 50% bucket 188: 10% bucket 186: 20% bucket 174: 60% bucket 171: 100% Sorting block of length 5182065 for bucket 171 (Using difference cover) bucket 183: 50% bucket 177: 50% bucket 192: 10% bucket 184: 50% bucket 172: 70% bucket 189: 10% bucket 184: 30% bucket 175: 60% bucket 182: 50% bucket 176: 60% bucket 182: 30% bucket 181: 30% bucket 168: 100% Sorting block of length 5027967 for bucket 168 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4275736 for bucket 166 Sorting block time: 00:00:03 Returning block of 4781906 for bucket 168 Getting block 193 of 202 Reserving size (5249070) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: Getting block 194 of 203 Reserving size (5249070) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 175: 60% bucket 188: 40% bucket 169: 90% bucket 183: 30% bucket 172: 70% bucket 179: 40% bucket 181: 50% bucket 170: 100% Sorting block of length 2075113 for bucket 170 (Using difference cover) bucket 185: 50% bucket 189: 30% bucket 180: 50% Sorting block time: 00:00:03 Returning block of 4479272 for bucket 165 bucket 173: 80% bucket 191: 10% bucket 174: 70% bucket 190: 20% bucket 187: 20% bucket 173: 80% bucket 176: 60% bucket 179: 80% bucket 186: 50% Sorting block time: 00:00:03 Returning block of 4258909 for bucket 167 bucket 187: 50% bucket 193: 10% Sorting block time: 00:00:01 Returning block of 2075114 for bucket 170 bucket 178: 50% Getting block 195 of 203 Reserving size (5249070) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: Getting block 194 of 202 Reserving size (5249070) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: Getting block 196 of 203 Reserving size (5249070) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 185: 30% bucket 191: 20% bucket 178: 60% bucket 180: 40% bucket 177: 60% bucket 170: 90% bucket 190: 20% Sorting block time: 00:00:03 Returning block of 5182066 for bucket 171 bucket 177: 60% bucket 171: 90% bucket 184: 60% bucket 182: 40% Sorting block time: 00:00:03 Returning block of 5027968 for bucket 168 bucket 188: 20% Getting block 197 of 203 Reserving size (5249070) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: bucket 183: 60% bucket 172: 80% bucket 192: 10% bucket 174: 70% Getting block 195 of 202 Reserving size (5249070) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 189: 20% bucket 176: 70% bucket 192: 20% bucket 186: 30% bucket 182: 60% bucket 184: 40% bucket 169: 100% Sorting block of length 4781115 for bucket 169 (Using difference cover) bucket 193: 10% bucket 194: 10% bucket 185: 60% bucket 175: 70% bucket 175: 70% bucket 180: 60% bucket 173: 90% bucket 181: 40% bucket 181: 60% bucket 188: 50% bucket 179: 90% bucket 189: 40% bucket 179: 50% bucket 190: 30% bucket 187: 30% bucket 169: 100% Sorting block of length 4303310 for bucket 169 (Using difference cover) bucket 183: 40% bucket 172: 80% bucket 191: 20% bucket 191: 30% bucket 194: 10% bucket 174: 80% bucket 195: 10% bucket 187: 60% bucket 186: 60% bucket 178: 70% bucket 176: 70% bucket 177: 70% bucket 180: 50% bucket 173: 90% bucket 182: 70% bucket 185: 40% bucket 193: 20% bucket 192: 30% bucket 174: 80% bucket 178: 60% bucket 184: 70% bucket 170: 100% Sorting block of length 4618941 for bucket 170 (Using difference cover) bucket 190: 40% bucket 196: 10% bucket 172: 90% bucket 171: 100% Sorting block of length 4527567 for bucket 171 (Using difference cover) bucket 197: 10% bucket 195: 10% bucket 194: 20% bucket 173: 100% Sorting block of length 4434577 for bucket 173 (Using difference cover) bucket 176: 80% bucket 183: 70% bucket 179: 100% Sorting block of length 4121665 for bucket 179 (Using difference cover) bucket 185: 70% bucket 177: 70% bucket 193: 20% bucket 180: 70% bucket 189: 50% bucket 189: 30% bucket 190: 30% bucket 182: 50% bucket 186: 40% bucket 195: 20% bucket 188: 30% bucket 181: 50% bucket 175: 80% bucket 184: 50% Sorting block time: 00:00:03 Returning block of 4303311 for bucket 169 Sorting block time: 00:00:03 Returning block of 4781116 for bucket 169 bucket 188: 60% bucket 181: 70% bucket 194: 20% bucket 192: 20% Getting block 198 of 203 Reserving size (5249070) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 191: 40% Getting block 196 of 202 Reserving size (5249070) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 186: 70% bucket 175: 80% bucket 177: 80% bucket 190: 50% bucket 187: 70% bucket 178: 80% bucket 172: 90% bucket 183: 50% bucket 191: 30% bucket 173: 100% Sorting block of length 5136448 for bucket 173 (Using difference cover) bucket 187: 40% bucket 182: 80% bucket 174: 90% bucket 179: 60% bucket 174: 90% bucket 193: 30% bucket 176: 80% bucket 194: 30% bucket 185: 50% bucket 192: 40% Sorting block time: 00:00:03 Returning block of 4618942 for bucket 170 Sorting block time: 00:00:02 Returning block of 4121666 for bucket 179 bucket 172: 100% Sorting block of length 5246970 for bucket 172 (Using difference cover) bucket 195: 20% bucket 180: 80% bucket 196: 20% Getting block 197 of 202 Reserving size (5249070) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: bucket 184: 80% bucket 185: 80% Getting block 198 of 202 Reserving size (5249070) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 197: 20% bucket 180: 60% bucket 178: 70% Sorting block time: 00:00:03 Returning block of 4527568 for bucket 171 bucket 193: 30% Sorting block time: 00:00:02 Returning block of 4434578 for bucket 173 bucket 196: 10% Getting block 199 of 202 Reserving size (5249070) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: bucket 183: 80% bucket 195: 30% Getting block 200 of 202 Reserving size (5249070) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 176: 90% bucket 194: 30% bucket 189: 60% bucket 181: 60% bucket 189: 40% bucket 188: 40% bucket 182: 60% bucket 175: 90% bucket 186: 80% bucket 186: 50% bucket 190: 40% bucket 188: 70% bucket 190: 60% bucket 181: 80% bucket 177: 80% bucket 177: 90% bucket 182: 90% bucket 191: 50% bucket 187: 80% bucket 178: 90% bucket 191: 40% bucket 184: 60% bucket 192: 30% bucket 172: 100% Sorting block of length 5018692 for bucket 172 (Using difference cover) bucket 175: 90% bucket 198: 10% bucket 174: 100% Sorting block of length 4839046 for bucket 174 (Using difference cover) bucket 174: 100% Sorting block of length 3816602 for bucket 174 (Using difference cover) bucket 192: 50% Sorting block time: 00:00:03 Returning block of 5136449 for bucket 173 bucket 196: 20% bucket 198: 10% bucket 179: 70% Getting block 199 of 203 Reserving size (5249070) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: bucket 194: 40% bucket 183: 60% bucket 195: 30% bucket 176: 90% bucket 187: 50% bucket 180: 90% bucket 185: 60% bucket 185: 90% bucket 200: 10% bucket 196: 30% bucket 176: 100% Sorting block of length 4213295 for bucket 176 (Using difference cover) bucket 193: 40% bucket 197: 10% bucket 199: 10% bucket 180: 70% bucket 189: 70% bucket 195: 40% bucket 197: 30% bucket 178: 80% Sorting block time: 00:00:04 Returning block of 5246971 for bucket 172 bucket 183: 90% bucket 194: 40% bucket 193: 40% Getting block 200 of 203 Reserving size (5249070) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 188: 80% bucket 189: 50% bucket 184: 90% bucket 196: 30% bucket 192: 40% bucket 186: 90% bucket 182: 70% bucket 190: 70% bucket 175: 100% Sorting block of length 4232944 for bucket 175 (Using difference cover) bucket 181: 70% bucket 177: 90% bucket 188: 50% bucket 182: 100% Sorting block of length 3172736 for bucket 182 (Using difference cover) bucket 181: 90% bucket 186: 60% bucket 187: 90% bucket 191: 60% Sorting block time: 00:00:03 Returning block of 3816603 for bucket 174 bucket 191: 50% bucket 177: 100% Sorting block of length 4102365 for bucket 177 (Using difference cover) bucket 178: 100% Sorting block of length 1656721 for bucket 178 (Using difference cover) bucket 179: 80% Getting block 201 of 203 Reserving size (5249070) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: bucket 198: 20% bucket 192: 60% bucket 198: 20% Sorting block time: 00:00:03 Returning block of 4839047 for bucket 174 bucket 175: 100% Sorting block of length 5142741 for bucket 175 (Using difference cover) Sorting block time: 00:00:03 Returning block of 5018693 for bucket 172 Getting block 201 of 202 Reserving size (5249070) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: bucket 199: 10% bucket 185: 100% Sorting block of length 5049643 for bucket 185 (Using difference cover) Getting block 202 of 202 Reserving size (5249070) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 195: 40% bucket 190: 50% bucket 196: 40% bucket 200: 20% bucket 184: 70% Sorting block time: 00:00:03 Returning block of 4213296 for bucket 176 bucket 180: 100% Sorting block of length 3002556 for bucket 180 (Using difference cover) bucket 197: 20% bucket 189: 80% Sorting block time: 00:00:01 Returning block of 1656722 for bucket 178 bucket 187: 60% bucket 199: 20% bucket 183: 70% bucket 196: 40% bucket 176: 100% Sorting block of length 2637941 for bucket 176 (Using difference cover) bucket 193: 50% bucket 185: 70% bucket 194: 50% bucket 189: 60% bucket 193: 50% Sorting block time: 00:00:02 Returning block of 4102366 for bucket 177 bucket 190: 80% bucket 181: 100% Sorting block of length 4040082 for bucket 181 (Using difference cover) bucket 184: 100% Sorting block of length 4704118 for bucket 184 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3172737 for bucket 182 bucket 197: 40% bucket 202: 10% bucket 188: 90% bucket 180: 80% bucket 183: 100% Sorting block of length 3119188 for bucket 183 (Using difference cover) bucket 194: 50% bucket 192: 50% bucket 186: 100% Sorting block of length 5094730 for bucket 186 (Using difference cover) bucket 195: 50% Sorting block time: 00:00:03 Returning block of 4232945 for bucket 175 bucket 178: 90% bucket 196: 50% bucket 200: 10% bucket 187: 100% Sorting block of length 4437791 for bucket 187 (Using difference cover) bucket 191: 60% bucket 182: 80% bucket 181: 80% bucket 177: 100% Sorting block of length 4227885 for bucket 177 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3002557 for bucket 180 bucket 188: 60% bucket 192: 70% bucket 179: 90% bucket 201: 10% bucket 202: 20% bucket 195: 50% bucket 198: 30% bucket 191: 70% bucket 198: 30% bucket 200: 30% bucket 186: 70% Sorting block time: 00:00:02 Returning block of 2637942 for bucket 176 bucket 201: 10% Sorting block time: 00:00:02 Returning block of 3119189 for bucket 183 Getting block 202 of 203 Reserving size (5249070) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 189: 90% bucket 197: 30% bucket 199: 30% bucket 184: 80% Sorting block time: 00:00:04 Returning block of 5142742 for bucket 175 Sorting block time: 00:00:03 Returning block of 5049644 for bucket 185 Getting block 203 of 203 Reserving size (5249070) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: bucket 196: 50% bucket 190: 60% Sorting block time: 00:00:02 Returning block of 4040083 for bucket 181 bucket 199: 20% bucket 187: 70% bucket 190: 90% bucket 183: 80% bucket 196: 60% bucket 202: 30% bucket 194: 60% bucket 193: 60% bucket 178: 100% Sorting block of length 3998715 for bucket 178 (Using difference cover) bucket 180: 90% bucket 188: 100% Sorting block of length 4267456 for bucket 188 (Using difference cover) bucket 189: 70% bucket 197: 50% bucket 193: 60% bucket 194: 60% Sorting block time: 00:00:03 Returning block of 4704119 for bucket 184 bucket 185: 80% Sorting block time: 00:00:02 Returning block of 4437792 for bucket 187 bucket 195: 60% bucket 201: 20% bucket 200: 40% bucket 191: 80% bucket 182: 90% bucket 192: 80% bucket 198: 40% bucket 191: 70% bucket 200: 20% Sorting block time: 00:00:04 Returning block of 5094731 for bucket 186 bucket 192: 60% bucket 195: 60% bucket 189: 100% Sorting block of length 4444356 for bucket 189 (Using difference cover) bucket 202: 40% bucket 199: 40% Sorting block time: 00:00:03 Returning block of 4227886 for bucket 177 bucket 181: 90% bucket 179: 100% Sorting block of length 5205390 for bucket 179 (Using difference cover) bucket 196: 70% bucket 197: 40% bucket 201: 20% bucket 190: 100% Sorting block of length 3777576 for bucket 190 (Using difference cover) bucket 203: 10% bucket 199: 30% bucket 198: 40% Sorting block time: 00:00:02 Returning block of 4267457 for bucket 188 bucket 194: 70% bucket 188: 70% bucket 186: 80% Sorting block time: 00:00:02 Returning block of 3998716 for bucket 178 bucket 202: 10% bucket 193: 70% bucket 191: 90% bucket 193: 70% bucket 196: 60% bucket 184: 90% bucket 187: 80% bucket 195: 70% bucket 189: 80% bucket 190: 70% bucket 200: 50% bucket 201: 30% bucket 183: 90% bucket 180: 100% Sorting block of length 3673150 for bucket 180 (Using difference cover) bucket 197: 60% bucket 202: 50% bucket 197: 50% bucket 192: 90% bucket 198: 50% bucket 199: 50% bucket 185: 90% bucket 200: 30% bucket 196: 80% Sorting block time: 00:00:02 Returning block of 3777577 for bucket 190 Sorting block time: 00:00:02 Returning block of 5205391 for bucket 179 bucket 203: 20% Sorting block time: 00:00:02 Returning block of 4444357 for bucket 189 bucket 194: 70% bucket 181: 100% Sorting block of length 4548361 for bucket 181 (Using difference cover) bucket 182: 100% Sorting block of length 2884529 for bucket 182 (Using difference cover) bucket 201: 30% bucket 195: 70% bucket 192: 70% bucket 194: 80% bucket 191: 80% bucket 199: 40% bucket 198: 50% bucket 202: 20% bucket 193: 80% Sorting block time: 00:00:01 Returning block of 3673151 for bucket 180 bucket 186: 90% bucket 191: 100% Sorting block of length 4787484 for bucket 191 (Using difference cover) bucket 201: 40% bucket 195: 80% bucket 184: 100% Sorting block of length 5178218 for bucket 184 (Using difference cover) bucket 188: 80% bucket 202: 60% bucket 197: 60% Sorting block time: 00:00:01 Returning block of 2884530 for bucket 182 bucket 190: 80% bucket 199: 60% bucket 196: 90% bucket 193: 80% bucket 203: 30% bucket 183: 100% Sorting block of length 4773647 for bucket 183 (Using difference cover) bucket 189: 90% bucket 187: 90% bucket 200: 60% bucket 185: 100% Sorting block of length 4827644 for bucket 185 (Using difference cover) bucket 198: 60% bucket 200: 40% Sorting block time: 00:00:02 Returning block of 4548362 for bucket 181 bucket 194: 90% bucket 195: 80% bucket 197: 70% bucket 201: 40% bucket 196: 70% bucket 192: 100% Sorting block of length 4722824 for bucket 192 (Using difference cover) bucket 192: 80% bucket 202: 30% bucket 199: 50% bucket 194: 80% Sorting block time: 00:00:01 Returning block of 4787485 for bucket 191 bucket 201: 50% bucket 203: 40% bucket 202: 70% bucket 191: 90% bucket 186: 100% Sorting block of length 4343508 for bucket 186 (Using difference cover) bucket 193: 90% Sorting block time: 00:00:02 Returning block of 5178219 for bucket 184 bucket 195: 90% bucket 193: 90% Sorting block time: 00:00:02 Returning block of 4773648 for bucket 183 bucket 196: 100% Sorting block of length 4415883 for bucket 196 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4827645 for bucket 185 bucket 188: 90% bucket 190: 90% bucket 189: 100% Sorting block of length 4328971 for bucket 189 (Using difference cover) bucket 198: 60% bucket 197: 70% bucket 187: 100% Sorting block of length 2632579 for bucket 187 (Using difference cover) bucket 199: 70% bucket 198: 70% bucket 195: 90% bucket 203: 50% Sorting block time: 00:00:02 Returning block of 4722825 for bucket 192 bucket 197: 80% bucket 202: 40% bucket 201: 50% bucket 199: 60% bucket 200: 70% bucket 201: 60% bucket 192: 90% Sorting block time: 00:00:01 Returning block of 4343509 for bucket 186 bucket 202: 80% bucket 196: 80% bucket 194: 100% Sorting block of length 4725015 for bucket 194 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4415884 for bucket 196 bucket 200: 50% Sorting block time: 00:00:02 Returning block of 2632580 for bucket 187 Sorting block time: 00:00:02 Returning block of 4328972 for bucket 189 bucket 194: 90% bucket 193: 100% Sorting block of length 3568311 for bucket 193 (Using difference cover) bucket 191: 100% Sorting block of length 3469710 for bucket 191 (Using difference cover) bucket 188: 100% Sorting block of length 5150913 for bucket 188 (Using difference cover) bucket 190: 100% Sorting block of length 2685153 for bucket 190 (Using difference cover) bucket 203: 60% bucket 198: 70% bucket 195: 100% Sorting block of length 4454446 for bucket 195 (Using difference cover) bucket 193: 100% Sorting block of length 3768466 for bucket 193 (Using difference cover) bucket 198: 80% bucket 197: 80% bucket 197: 90% bucket 195: 100% Sorting block of length 4181966 for bucket 195 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4725016 for bucket 194 bucket 202: 50% bucket 201: 60% bucket 202: 90% bucket 199: 70% Sorting block time: 00:00:01 Returning block of 2685154 for bucket 190 bucket 201: 70% bucket 192: 100% Sorting block of length 4451874 for bucket 192 (Using difference cover) bucket 199: 80% Sorting block time: 00:00:01 Returning block of 3469711 for bucket 191 Sorting block time: 00:00:01 Returning block of 3568312 for bucket 193 bucket 196: 90% Sorting block time: 00:00:01 Returning block of 3768467 for bucket 193 bucket 200: 60% bucket 203: 70% Sorting block time: 00:00:02 Returning block of 5150914 for bucket 188 bucket 200: 80% Sorting block time: 00:00:02 Returning block of 4454447 for bucket 195 bucket 194: 100% Sorting block of length 2158286 for bucket 194 (Using difference cover) bucket 202: 100% Sorting block of length 3568840 for bucket 202 (Using difference cover) bucket 198: 90% Sorting block time: 00:00:02 Returning block of 4181967 for bucket 195 bucket 201: 80% bucket 197: 90% bucket 199: 90% bucket 198: 80% Sorting block time: 00:00:01 Returning block of 2158287 for bucket 194 bucket 200: 90% Sorting block time: 00:00:02 Returning block of 4451875 for bucket 192 bucket 202: 60% Sorting block time: 00:00:02 Returning block of 3568841 for bucket 202 bucket 197: 100% Sorting block of length 4417938 for bucket 197 (Using difference cover) bucket 201: 70% bucket 199: 80% bucket 203: 80% bucket 198: 100% Sorting block of length 2862547 for bucket 198 (Using difference cover) bucket 196: 100% Sorting block of length 3998163 for bucket 196 (Using difference cover) bucket 201: 90% bucket 197: 100% Sorting block of length 3838774 for bucket 197 (Using difference cover) bucket 199: 100% Sorting block of length 3292285 for bucket 199 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2862548 for bucket 198 bucket 200: 70% bucket 198: 90% Sorting block time: 00:00:01 Returning block of 4417939 for bucket 197 bucket 200: 100% Sorting block of length 4291379 for bucket 200 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3998164 for bucket 196 bucket 203: 90% bucket 202: 70% bucket 201: 80% Sorting block time: 00:00:01 Returning block of 3292286 for bucket 199 bucket 201: 100% Sorting block of length 4667018 for bucket 201 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3838775 for bucket 197 bucket 199: 90% Sorting block time: 00:00:02 Returning block of 4291380 for bucket 200 bucket 200: 80% bucket 203: 100% Sorting block of length 1000948 for bucket 203 (Using difference cover) bucket 198: 100% Sorting block of length 5068310 for bucket 198 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4667019 for bucket 201 Sorting block time: 00:00:01 Returning block of 1000949 for bucket 203 bucket 202: 80% bucket 199: 100% Sorting block of length 1375718 for bucket 199 (Using difference cover) bucket 201: 90% Sorting block time: 00:00:01 Returning block of 5068311 for bucket 198 Sorting block time: 00:00:00 Returning block of 1375719 for bucket 199 bucket 200: 90% bucket 202: 90% bucket 201: 100% Sorting block of length 1705328 for bucket 201 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1705329 for bucket 201 bucket 200: 100% Sorting block of length 4415005 for bucket 200 (Using difference cover) bucket 202: 100% Sorting block of length 5030221 for bucket 202 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4415006 for bucket 200 Sorting block time: 00:00:01 Returning block of 5030222 for bucket 202 Exited Ebwt loop fchr[A]: 0 fchr[C]: 391954798 fchr[G]: 524347498 fchr[T]: 524347498 fchr[$]: 783861161 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 266840223 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 195965296 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 783861161 bwtLen: 783861162 sz: 195965291 bwtSz: 195965291 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 48991323 offsSz: 195965292 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 4082611 numLines: 4082611 ebwtTotLen: 261287104 ebwtTotSz: 261287104 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:05:30 Reading reference sizes Exited Ebwt loop fchr[A]: 0 fchr[C]: 259567700 fchr[G]: 259567700 fchr[T]: 391954798 fchr[$]: 783861161 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 266840223 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 195965296 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 783861161 bwtLen: 783861162 sz: 195965291 bwtSz: 195965291 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 48991323 offsSz: 195965292 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 4082611 numLines: 4082611 ebwtTotLen: 261287104 ebwtTotSz: 261287104 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:05:36 Reading reference sizes Time reading reference sizes: 00:00:06 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:03 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 6998760 Using parameters --bmax 5249070 --dcv 1024 Doing ahead-of-time memory usage test Time reading reference sizes: 00:00:06 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Passed! Constructing with these parameters: --bmax 5249070 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Time to join reference sequences: 00:00:04 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 6998760 Using parameters --bmax 5249070 --dcv 1024 Doing ahead-of-time memory usage test V-Sorting samples time: 00:00:05 Allocating rank array Ranking v-sort output Passed! Constructing with these parameters: --bmax 5249070 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Ranking v-sort output time: 00:00:04 Invoking Larsson-Sadakane on ranks V-Sorting samples time: 00:00:06 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:03 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:06 Sanity-checking and returning Building samples Reserving space for 300 sample suffixes Generating random suffixes QSorting 300 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 300 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 44, merged 136; iterating... Invoking Larsson-Sadakane on ranks time: 00:00:07 Sanity-checking and returning Building samples Reserving space for 300 sample suffixes Generating random suffixes QSorting 300 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 300 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 23, merged 18; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 38, merged 135; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 11, merged 13; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 23, merged 19; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 9; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 10, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 2; iterating... Avg bucket size: 3.82371e+06 (target: 5249069) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 205 Reserving size (5249070) for bucket 1 Getting block 2 of 205 Getting block 3 of 205 Getting block 4 of 205 Getting block 5 of 205 Getting block 6 of 205 Getting block 7 of 205 Getting block 8 of 205 Getting block 9 of 205 Getting block 10 of 205 Getting block 11 of 205 Getting block 12 of 205 Getting block 13 of 205 Getting block 14 of 205 Calculating Z arrays for bucket 1 Reserving size (5249070) for bucket 2 Reserving size (5249070) for bucket 3 Reserving size (5249070) for bucket 4 Reserving size (5249070) for bucket 5 Reserving size (5249070) for bucket 6 Reserving size (5249070) for bucket 7 Getting block 15 of 205 Getting block 16 of 205 Reserving size (5249070) for bucket 8 Getting block 17 of 205 Reserving size (5249070) for bucket 9 Getting block 18 of 205 Reserving size (5249070) for bucket 10 Reserving size (5249070) for bucket 11 Reserving size (5249070) for bucket 12 Reserving size (5249070) for bucket 13 Reserving size (5249070) for bucket 14 Getting block 19 of 205 Getting block 20 of 205 Getting block 21 of 205 Getting block 22 of 205 Getting block 23 of 205 Getting block 24 of 205 Getting block 25 of 205 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 1: Getting block 26 of 205 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 7 Reserving size (5249070) for bucket 15 Reserving size (5249070) for bucket 16 Calculating Z arrays for bucket 8 Reserving size (5249070) for bucket 17 Calculating Z arrays for bucket 9 Reserving size (5249070) for bucket 18 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 11 Calculating Z arrays for bucket 12 Calculating Z arrays for bucket 13 Calculating Z arrays for bucket 14 Reserving size (5249070) for bucket 19 Reserving size (5249070) for bucket 20 Reserving size (5249070) for bucket 21 Reserving size (5249070) for bucket 22 Reserving size (5249070) for bucket 23 Reserving size (5249070) for bucket 24 Reserving size (5249070) for bucket 25 Entering block accumulator loop for bucket 2: Reserving size (5249070) for bucket 26 Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 6: Calculating Z arrays for bucket 15 Entering block accumulator loop for bucket 7: Calculating Z arrays for bucket 16 Calculating Z arrays for bucket 17 Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 10: Calculating Z arrays for bucket 18 Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 12: Calculating Z arrays for bucket 19 Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 14: Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 26 Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 25: Getting block 27 of 205 Reserving size (5249070) for bucket 27 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 27: bucket 27: 10% bucket 13: 10% bucket 2: 10% bucket 1: 10% bucket 4: 10% bucket 3: 10% bucket 5: 10% bucket 8: 10% bucket 17: 10% bucket 11: 10% bucket 16: 10% bucket 14: 10% bucket 19: 10% bucket 6: 10% bucket 10: 10% bucket 23: 10% bucket 22: 10% bucket 24: 10% bucket 7: 10% bucket 12: 10% bucket 21: 10% bucket 18: 10% bucket 25: 10% bucket 27: 20% bucket 9: 10% bucket 26: 10% bucket 20: 10% bucket 15: 10% bucket 1: 20% bucket 13: 20% bucket 8: 20% bucket 5: 20% bucket 2: 20% bucket 22: 20% bucket 3: 20% bucket 4: 20% bucket 7: 20% bucket 10: 20% bucket 11: 20% bucket 14: 20% bucket 19: 20% bucket 16: 20% bucket 18: 20% bucket 17: 20% bucket 25: 20% bucket 6: 20% bucket 23: 20% bucket 26: 20% bucket 1: 30% bucket 9: 20% bucket 24: 20% bucket 27: 30% bucket 12: 20% bucket 13: 30% bucket 21: 20% bucket 8: 30% bucket 2: 30% bucket 15: 20% bucket 20: 20% bucket 3: 30% bucket 4: 30% bucket 5: 30% Splitting and merging Splitting and merging time: 00:00:00 Split 6, merged 6; iterating... bucket 22: 30% bucket 7: 30% bucket 19: 30% bucket 11: 30% bucket 16: 30% bucket 18: 30% bucket 8: 40% bucket 17: 30% bucket 14: 30% bucket 2: 40% bucket 10: 30% bucket 25: 30% bucket 9: 30% bucket 5: 40% bucket 15: 30% bucket 6: 30% bucket 4: 40% bucket 1: 40% bucket 24: 30% bucket 12: 30% bucket 23: 30% bucket 22: 40% bucket 26: 30% bucket 21: 30% bucket 19: 40% bucket 27: 40% bucket 13: 40% bucket 3: 40% bucket 20: 30% bucket 18: 40% bucket 7: 40% bucket 11: 40% bucket 16: 40% bucket 8: 50% bucket 4: 50% bucket 2: 50% bucket 12: 40% bucket 15: 40% bucket 17: 40% bucket 14: 40% bucket 1: 50% bucket 5: 50% bucket 10: 40% bucket 9: 40% bucket 6: 40% bucket 25: 40% bucket 3: 50% bucket 24: 40% bucket 23: 40% bucket 26: 40% bucket 22: 50% bucket 13: 50% bucket 21: 40% bucket 19: 50% bucket 27: 50% bucket 7: 50% bucket 20: 40% bucket 18: 50% bucket 3: 60% bucket 11: 50% bucket 16: 50% bucket 8: 60% bucket 12: 50% bucket 4: 60% bucket 2: 60% bucket 1: 60% bucket 15: 50% bucket 5: 60% bucket 10: 50% bucket 14: 50% bucket 17: 50% bucket 6: 50% bucket 9: 50% bucket 25: 50% bucket 23: 50% bucket 24: 50% bucket 13: 60% bucket 26: 50% bucket 22: 60% bucket 19: 60% bucket 21: 50% bucket 7: 60% bucket 3: 70% bucket 16: 60% bucket 20: 50% bucket 27: 60% bucket 18: 60% bucket 11: 60% bucket 12: 60% bucket 8: 70% bucket 4: 70% bucket 5: 70% bucket 2: 70% bucket 1: 70% bucket 14: 60% bucket 15: 60% bucket 17: 60% bucket 10: 60% bucket 9: 60% bucket 6: 60% Splitting and merging Splitting and merging time: 00:00:00 Split 4, merged 3; iterating... Avg bucket size: 3.69746e+06 (target: 5249069) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 212 Reserving size (5249070) for bucket 1 Getting block 2 of 212 Getting block 3 of 212 Getting block 4 of 212 Getting block 5 of 212 Getting block 6 of 212 Getting block 7 of 212 Getting block 8 of 212 Getting block 9 of 212 Getting block 10 of 212 Getting block 11 of 212 Getting block 12 of 212 Getting block 13 of 212 Getting block 14 of 212 Getting block 15 of 212 Getting block 16 of 212 Getting block 17 of 212 Getting block 18 of 212 Getting block 19 of 212 Getting block 20 of 212 Getting block 21 of 212 Getting block 22 of 212 Getting block 23 of 212 Calculating Z arrays for bucket 1 Reserving size (5249070) for bucket 2 Reserving size (5249070) for bucket 3 Reserving size (5249070) for bucket 4 Reserving size (5249070) for bucket 5 Reserving size (5249070) for bucket 6 Reserving size (5249070) for bucket 7 Reserving size (5249070) for bucket 8 Reserving size (5249070) for bucket 9 Getting block 24 of 212 Getting block 25 of 212 Reserving size (5249070) for bucket 10 Reserving size (5249070) for bucket 11 Reserving size (5249070) for bucket 12 Reserving size (5249070) for bucket 13 Reserving size (5249070) for bucket 14 Reserving size (5249070) for bucket 15 Reserving size (5249070) for bucket 16 Reserving size (5249070) for bucket 17 Reserving size (5249070) for bucket 18 Reserving size (5249070) for bucket 19 Reserving size (5249070) for bucket 20 Reserving size (5249070) for bucket 21 Reserving size (5249070) for bucket 22 Reserving size (5249070) for bucket 23 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 2 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 9 Calculating Z arrays for bucket 8 Reserving size (5249070) for bucket 24 Reserving size (5249070) for bucket 25 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 12 Calculating Z arrays for bucket 11 Calculating Z arrays for bucket 13 Calculating Z arrays for bucket 14 Calculating Z arrays for bucket 15 Calculating Z arrays for bucket 16 Calculating Z arrays for bucket 17 Calculating Z arrays for bucket 18 Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 22 Entering block accumulator loop for bucket 2: Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 7: Calculating Z arrays for bucket 24 Entering block accumulator loop for bucket 9: Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 10: Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 25: Getting block 26 of 212 Getting block 27 of 212 Reserving size (5249070) for bucket 26 Reserving size (5249070) for bucket 27 Calculating Z arrays for bucket 26 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 27: bucket 25: 60% bucket 13: 70% bucket 11: 70% bucket 24: 60% bucket 19: 70% bucket 26: 60% bucket 16: 70% bucket 7: 70% bucket 23: 60% bucket 3: 80% bucket 22: 70% bucket 1: 80% bucket 20: 60% bucket 18: 70% bucket 5: 80% bucket 27: 70% bucket 21: 60% bucket 8: 80% bucket 2: 80% bucket 4: 80% bucket 11: 80% bucket 9: 70% bucket 26: 70% bucket 14: 70% bucket 10: 70% bucket 12: 70% bucket 13: 10% bucket 1: 10% bucket 2: 10% bucket 3: 10% bucket 4: 10% bucket 7: 10% bucket 8: 10% bucket 6: 10% bucket 9: 10% bucket 15: 10% bucket 12: 10% bucket 5: 10% bucket 6: 70% bucket 11: 10% bucket 19: 10% bucket 1: 90% bucket 17: 10% bucket 24: 70% bucket 15: 70% bucket 10: 10% bucket 14: 10% bucket 16: 10% bucket 26: 10% bucket 24: 10% bucket 21: 10% bucket 20: 10% bucket 17: 70% bucket 27: 10% bucket 18: 10% bucket 19: 80% bucket 23: 10% bucket 22: 10% bucket 13: 80% bucket 25: 10% bucket 7: 80% bucket 25: 70% bucket 3: 90% bucket 16: 80% bucket 23: 70% bucket 5: 90% bucket 20: 70% bucket 13: 20% bucket 22: 80% bucket 18: 80% bucket 4: 90% bucket 2: 90% bucket 8: 90% bucket 27: 80% bucket 21: 70% bucket 8: 20% bucket 1: 20% bucket 12: 80% bucket 2: 20% bucket 27: 20% bucket 4: 20% bucket 3: 20% bucket 11: 90% bucket 23: 20% bucket 9: 80% bucket 7: 20% bucket 6: 20% bucket 10: 80% bucket 5: 20% bucket 14: 80% bucket 24: 20% bucket 9: 20% bucket 12: 20% bucket 15: 20% bucket 26: 80% bucket 10: 20% bucket 11: 20% bucket 16: 20% bucket 14: 20% bucket 1: 100% Sorting block of length 3200949 for bucket 1 (Using difference cover) bucket 19: 20% bucket 17: 20% bucket 26: 20% bucket 6: 80% bucket 20: 20% bucket 18: 20% bucket 21: 20% bucket 15: 80% bucket 22: 20% bucket 25: 20% bucket 7: 90% bucket 23: 80% bucket 24: 80% bucket 17: 80% bucket 3: 100% Sorting block of length 3863873 for bucket 3 (Using difference cover) bucket 19: 90% bucket 13: 90% bucket 16: 90% bucket 25: 80% bucket 24: 30% bucket 13: 30% bucket 2: 100% Sorting block of length 2546184 for bucket 2 (Using difference cover) bucket 5: 100% Sorting block of length 2393678 for bucket 5 (Using difference cover) bucket 3: 30% bucket 1: 30% bucket 4: 100% Sorting block of length 3629365 for bucket 4 (Using difference cover) bucket 8: 30% bucket 20: 80% bucket 2: 30% bucket 8: 100% Sorting block of length 3561048 for bucket 8 (Using difference cover) bucket 18: 90% bucket 22: 90% bucket 4: 30% bucket 12: 90% bucket 27: 90% bucket 5: 30% bucket 7: 30% bucket 6: 30% bucket 21: 80% bucket 27: 30% bucket 9: 30% bucket 12: 30% bucket 23: 30% bucket 11: 100% Sorting block of length 4231464 for bucket 11 (Using difference cover) bucket 15: 30% bucket 9: 90% bucket 10: 30% bucket 11: 30% bucket 10: 90% bucket 19: 100% Sorting block of length 2300290 for bucket 19 (Using difference cover) bucket 14: 90% bucket 14: 30% bucket 21: 30% bucket 16: 30% bucket 3: 40% bucket 19: 30% bucket 17: 30% bucket 26: 30% bucket 26: 90% bucket 18: 30% bucket 6: 90% bucket 20: 30% bucket 22: 30% bucket 7: 100% Sorting block of length 2827571 for bucket 7 (Using difference cover) bucket 15: 90% bucket 5: 40% bucket 25: 30% bucket 23: 90% Sorting block time: 00:00:02 Returning block of 3200950 for bucket 1 bucket 1: 40% bucket 17: 90% bucket 13: 100% Sorting block of length 4962602 for bucket 13 (Using difference cover) bucket 24: 90% bucket 16: 100% Sorting block of length 1334352 for bucket 16 (Using difference cover) bucket 13: 40% Getting block 28 of 205 Reserving size (5249070) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 24: 40% bucket 2: 40% bucket 8: 40% bucket 25: 90% bucket 4: 40% Sorting block time: 00:00:02 Returning block of 2393679 for bucket 5 Sorting block time: 00:00:02 Returning block of 2546185 for bucket 2 Getting block 29 of 205 Reserving size (5249070) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: Getting block 30 of 205 Reserving size (5249070) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 6: 40% bucket 12: 40% bucket 7: 40% bucket 1: 50% bucket 21: 40% bucket 20: 90% bucket 9: 40% bucket 10: 40% bucket 18: 100% Sorting block of length 4254999 for bucket 18 (Using difference cover) bucket 27: 40% bucket 15: 40% bucket 12: 100% Sorting block of length 2951085 for bucket 12 (Using difference cover) bucket 27: 100% Sorting block of length 4912305 for bucket 27 (Using difference cover) bucket 11: 40% Sorting block time: 00:00:02 Returning block of 3863874 for bucket 3 bucket 23: 40% bucket 14: 40% bucket 16: 40% bucket 3: 50% Sorting block time: 00:00:01 Returning block of 2300291 for bucket 19 Sorting block time: 00:00:01 Returning block of 1334353 for bucket 16 bucket 22: 100% Sorting block of length 3990622 for bucket 22 (Using difference cover) bucket 5: 50% Sorting block time: 00:00:01 Returning block of 2827572 for bucket 7 Getting block 31 of 205 Reserving size (5249070) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: Getting block 32 of 205 Reserving size (5249070) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: bucket 19: 40% bucket 18: 40% Getting block 33 of 205 Reserving size (5249070) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: bucket 17: 40% Getting block 34 of 205 Reserving size (5249070) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: bucket 26: 40% bucket 21: 90% bucket 9: 100% Sorting block of length 4377465 for bucket 9 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3629366 for bucket 4 bucket 10: 100% Sorting block of length 4652777 for bucket 10 (Using difference cover) bucket 22: 40% Getting block 35 of 205 Reserving size (5249070) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: bucket 20: 40% bucket 25: 40% bucket 2: 50% Sorting block time: 00:00:03 Returning block of 3561049 for bucket 8 bucket 13: 50% bucket 6: 100% Sorting block of length 4430338 for bucket 6 (Using difference cover) bucket 4: 50% bucket 1: 60% Getting block 36 of 205 Reserving size (5249070) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: bucket 24: 50% bucket 14: 100% Sorting block of length 4840364 for bucket 14 (Using difference cover) bucket 8: 50% bucket 26: 100% Sorting block of length 744359 for bucket 26 (Using difference cover) bucket 6: 50% bucket 7: 50% bucket 12: 50% bucket 21: 50% Sorting block time: 00:00:02 Returning block of 4231465 for bucket 11 bucket 10: 50% bucket 11: 50% bucket 9: 50% Getting block 37 of 205 Reserving size (5249070) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: bucket 3: 60% bucket 15: 50% bucket 17: 100% Sorting block of length 5049479 for bucket 17 (Using difference cover) bucket 5: 60% Sorting block time: 00:00:01 Returning block of 744360 for bucket 26 bucket 27: 50% Getting block 38 of 205 Reserving size (5249070) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: bucket 24: 100% Sorting block of length 4558106 for bucket 24 (Using difference cover) bucket 14: 50% bucket 16: 50% bucket 13: 60% bucket 23: 100% Sorting block of length 3967567 for bucket 23 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2951086 for bucket 12 bucket 23: 50% bucket 15: 100% Sorting block of length 3920295 for bucket 15 (Using difference cover) bucket 18: 50% Getting block 39 of 205 Reserving size (5249070) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: bucket 19: 50% bucket 17: 50% bucket 26: 50% bucket 29: 10% bucket 30: 10% bucket 2: 60% bucket 1: 70% bucket 22: 50% bucket 25: 100% Sorting block of length 5148269 for bucket 25 (Using difference cover) bucket 4: 60% bucket 20: 50% bucket 25: 50% bucket 5: 70% bucket 8: 60% bucket 24: 60% bucket 13: 70% Sorting block time: 00:00:04 Returning block of 4962603 for bucket 13 bucket 6: 60% bucket 7: 60% bucket 12: 60% Sorting block time: 00:00:03 Returning block of 4255000 for bucket 18 bucket 20: 100% Sorting block of length 4685110 for bucket 20 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3990623 for bucket 22 bucket 34: 10% bucket 35: 10% Getting block 40 of 205 Reserving size (5249070) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: bucket 28: 10% bucket 10: 60% Getting block 41 of 205 Reserving size (5249070) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: bucket 32: 10% bucket 3: 70% Getting block 42 of 205 Reserving size (5249070) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: bucket 21: 60% bucket 11: 60% bucket 9: 60% bucket 15: 60% bucket 27: 60% bucket 21: 100% Sorting block of length 4618197 for bucket 21 (Using difference cover) bucket 14: 60% bucket 36: 10% bucket 16: 60% Sorting block time: 00:00:02 Returning block of 4377466 for bucket 9 bucket 33: 10% bucket 23: 60% bucket 2: 70% Getting block 43 of 205 Reserving size (5249070) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: bucket 18: 60% bucket 1: 80% bucket 31: 10% bucket 19: 60% bucket 17: 60% bucket 26: 60% bucket 4: 70% bucket 13: 80% Sorting block time: 00:00:03 Returning block of 4652778 for bucket 10 bucket 5: 80% Sorting block time: 00:00:04 Returning block of 4912306 for bucket 27 bucket 38: 10% Sorting block time: 00:00:03 Returning block of 4430339 for bucket 6 Getting block 44 of 205 Reserving size (5249070) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: bucket 20: 60% bucket 8: 70% Getting block 45 of 205 Reserving size (5249070) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: bucket 25: 60% bucket 22: 60% bucket 3: 80% Getting block 46 of 205 Reserving size (5249070) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: bucket 12: 70% bucket 6: 70% bucket 7: 70% bucket 10: 70% bucket 24: 70% bucket 30: 20% bucket 9: 70% bucket 11: 70% bucket 28: 20% bucket 5: 90% Sorting block time: 00:00:04 Returning block of 4840365 for bucket 14 bucket 29: 20% Sorting block time: 00:00:03 Returning block of 3967568 for bucket 23 bucket 21: 70% bucket 15: 70% bucket 37: 10% bucket 39: 10% bucket 14: 70% bucket 27: 70% bucket 1: 90% Getting block 47 of 205 Reserving size (5249070) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 16: 70% Sorting block time: 00:00:03 Returning block of 3920296 for bucket 15 bucket 2: 80% bucket 35: 20% Sorting block time: 00:00:03 Returning block of 4558107 for bucket 24 Getting block 48 of 205 Reserving size (5249070) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Getting block 49 of 205 Reserving size (5249070) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: bucket 4: 80% bucket 18: 70% bucket 12: 80% bucket 19: 70% Getting block 50 of 205 Reserving size (5249070) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: Sorting block time: 00:00:03 Returning block of 5049480 for bucket 17 bucket 34: 20% bucket 13: 90% bucket 17: 70% bucket 23: 70% Getting block 51 of 205 Reserving size (5249070) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 8: 80% bucket 26: 70% bucket 3: 90% bucket 1: 100% Sorting block of length 4845308 for bucket 1 (Using difference cover) bucket 41: 10% bucket 32: 20% bucket 20: 70% bucket 6: 80% bucket 7: 80% bucket 2: 90% bucket 22: 70% bucket 5: 100% Sorting block of length 3369875 for bucket 5 (Using difference cover) bucket 10: 80% bucket 25: 70% Sorting block time: 00:00:04 Returning block of 5148270 for bucket 25 bucket 24: 80% bucket 11: 80% bucket 9: 80% bucket 42: 10% Getting block 52 of 205 Reserving size (5249070) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: Sorting block time: 00:00:03 Returning block of 4685111 for bucket 20 bucket 40: 10% bucket 36: 20% bucket 15: 80% bucket 28: 30% bucket 14: 80% bucket 27: 80% Sorting block time: 00:00:03 Returning block of 4618198 for bucket 21 Getting block 53 of 205 Reserving size (5249070) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 45: 10% bucket 16: 80% bucket 21: 80% bucket 43: 10% bucket 33: 20% bucket 4: 90% Getting block 54 of 205 Reserving size (5249070) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 12: 90% bucket 18: 80% bucket 13: 100% Sorting block of length 4435347 for bucket 13 (Using difference cover) bucket 19: 80% bucket 25: 80% bucket 2: 100% Sorting block of length 5208862 for bucket 2 (Using difference cover) bucket 17: 80% bucket 8: 90% bucket 3: 100% Sorting block of length 4862215 for bucket 3 (Using difference cover) bucket 31: 20% bucket 38: 20% bucket 23: 80% bucket 6: 90% bucket 26: 80% bucket 7: 90% bucket 44: 10% bucket 20: 80% bucket 46: 10% bucket 29: 30% bucket 10: 90% bucket 22: 80% bucket 18: 90% bucket 30: 30% bucket 11: 90% bucket 34: 30% bucket 9: 90% bucket 24: 90% bucket 47: 10% bucket 48: 10% bucket 39: 20% bucket 15: 90% bucket 4: 100% Sorting block of length 2628655 for bucket 4 (Using difference cover) bucket 14: 90% bucket 37: 20% bucket 28: 40% bucket 27: 90% Sorting block time: 00:00:02 Returning block of 3369876 for bucket 5 bucket 21: 90% bucket 16: 90% bucket 35: 30% bucket 12: 100% Sorting block of length 1751674 for bucket 12 (Using difference cover) Getting block 28 of 212 Reserving size (5249070) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 51: 10% bucket 32: 30% bucket 8: 100% Sorting block of length 1804905 for bucket 8 (Using difference cover) bucket 19: 90% bucket 6: 100% Sorting block of length 4547582 for bucket 6 (Using difference cover) bucket 25: 90% bucket 17: 90% bucket 41: 20% bucket 23: 90% Sorting block time: 00:00:03 Returning block of 4845309 for bucket 1 bucket 49: 10% bucket 18: 100% Sorting block of length 4801808 for bucket 18 (Using difference cover) bucket 10: 100% Sorting block of length 3883503 for bucket 10 (Using difference cover) bucket 7: 100% Sorting block of length 4499628 for bucket 7 (Using difference cover) bucket 26: 90% bucket 42: 20% bucket 20: 90% Getting block 29 of 212 Reserving size (5249070) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 45: 20% bucket 50: 10% bucket 36: 30% bucket 52: 10% bucket 54: 10% bucket 22: 90% bucket 11: 100% Sorting block of length 3976956 for bucket 11 (Using difference cover) bucket 40: 20% bucket 9: 100% Sorting block of length 4399637 for bucket 9 (Using difference cover) bucket 27: 100% Sorting block of length 4821547 for bucket 27 (Using difference cover) bucket 24: 100% Sorting block of length 4236581 for bucket 24 (Using difference cover) bucket 15: 100% Sorting block of length 3379267 for bucket 15 (Using difference cover) bucket 43: 20% Sorting block time: 00:00:01 Returning block of 1751675 for bucket 12 Getting block 30 of 212 Reserving size (5249070) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 38: 30% bucket 14: 100% Sorting block of length 4887236 for bucket 14 (Using difference cover) bucket 28: 50% bucket 29: 40% Sorting block time: 00:00:02 Returning block of 2628656 for bucket 4 Sorting block time: 00:00:02 Returning block of 1804906 for bucket 8 Getting block 31 of 212 Reserving size (5249070) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: Getting block 32 of 212 Reserving size (5249070) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: bucket 16: 100% Sorting block of length 3879954 for bucket 16 (Using difference cover) bucket 21: 100% Sorting block of length 5224866 for bucket 21 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4435348 for bucket 13 bucket 47: 20% bucket 31: 30% bucket 48: 20% bucket 53: 10% bucket 33: 30% Getting block 33 of 212 Reserving size (5249070) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: Sorting block time: 00:00:03 Returning block of 4862216 for bucket 3 Sorting block time: 00:00:03 Returning block of 5208863 for bucket 2 bucket 44: 20% bucket 39: 30% bucket 28: 10% bucket 34: 40% bucket 46: 20% Getting block 34 of 212 Reserving size (5249070) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: Getting block 35 of 212 Reserving size (5249070) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: bucket 17: 100% Sorting block of length 5046966 for bucket 17 (Using difference cover) bucket 37: 30% bucket 19: 100% Sorting block of length 3149834 for bucket 19 (Using difference cover) bucket 23: 100% Sorting block of length 4527241 for bucket 23 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3883504 for bucket 10 bucket 26: 100% Sorting block of length 900221 for bucket 26 (Using difference cover) bucket 32: 40% bucket 20: 100% bucket 25: 100% Sorting block of length 3333335 for bucket 20 (Using difference cover) Sorting block of length 4488468 for bucket 25 (Using difference cover) Getting block 36 of 212 Reserving size (5249070) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: bucket 35: 40% bucket 30: 40% bucket 22: 100% Sorting block of length 3469042 for bucket 22 (Using difference cover) bucket 28: 60% bucket 49: 20% bucket 51: 20% bucket 41: 30% bucket 29: 10% bucket 42: 30% Sorting block time: 00:00:01 Returning block of 900222 for bucket 26 Getting block 37 of 212 Reserving size (5249070) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: Sorting block time: 00:00:04 Returning block of 4547583 for bucket 6 bucket 45: 30% Sorting block time: 00:00:03 Returning block of 3379268 for bucket 15 Sorting block time: 00:00:03 Returning block of 3976957 for bucket 11 Sorting block time: 00:00:03 Returning block of 4801809 for bucket 18 bucket 52: 20% bucket 36: 40% Getting block 38 of 212 Reserving size (5249070) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: Getting block 39 of 212 Reserving size (5249070) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: bucket 30: 10% Getting block 40 of 212 Reserving size (5249070) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: Sorting block time: 00:00:03 Returning block of 4499629 for bucket 7 bucket 31: 10% bucket 32: 10% Getting block 41 of 212 Reserving size (5249070) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: bucket 38: 40% Sorting block time: 00:00:03 Returning block of 4236582 for bucket 24 Sorting block time: 00:00:03 Returning block of 4821548 for bucket 27 Getting block 42 of 212 Reserving size (5249070) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: bucket 54: 20% bucket 43: 30% bucket 33: 40% Getting block 43 of 212 Reserving size (5249070) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: bucket 47: 30% bucket 50: 20% Getting block 44 of 212 Reserving size (5249070) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: Sorting block time: 00:00:04 Returning block of 4399638 for bucket 9 bucket 48: 30% Sorting block time: 00:00:03 Returning block of 3879955 for bucket 16 bucket 40: 30% bucket 35: 10% Getting block 45 of 212 Reserving size (5249070) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Sorting block time: 00:00:03 Returning block of 4887237 for bucket 14 bucket 33: 10% bucket 28: 20% Getting block 46 of 212 Reserving size (5249070) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: Sorting block time: 00:00:02 Returning block of 3149835 for bucket 19 Getting block 47 of 212 Reserving size (5249070) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: Getting block 48 of 212 Reserving size (5249070) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: bucket 28: 70% bucket 34: 50% bucket 34: 10% bucket 37: 40% bucket 29: 50% bucket 36: 10% bucket 44: 30% bucket 39: 40% bucket 53: 20% bucket 46: 30% Sorting block time: 00:00:03 Returning block of 3333336 for bucket 20 bucket 31: 40% Getting block 49 of 212 Reserving size (5249070) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: Sorting block time: 00:00:04 Returning block of 5224867 for bucket 21 Sorting block time: 00:00:03 Returning block of 3469043 for bucket 22 Getting block 50 of 212 Reserving size (5249070) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: Getting block 51 of 212 Reserving size (5249070) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: Sorting block time: 00:00:03 Returning block of 4488469 for bucket 25 bucket 30: 50% bucket 32: 50% Sorting block time: 00:00:03 Returning block of 5046967 for bucket 17 bucket 30: 20% bucket 29: 20% bucket 37: 10% bucket 49: 30% bucket 41: 40% Getting block 52 of 212 Reserving size (5249070) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: Sorting block time: 00:00:03 Returning block of 4527242 for bucket 23 Getting block 53 of 212 Reserving size (5249070) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 42: 40% bucket 39: 10% Getting block 54 of 212 Reserving size (5249070) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 32: 20% bucket 45: 40% bucket 51: 30% bucket 35: 50% bucket 31: 20% bucket 28: 80% bucket 41: 10% bucket 38: 50% bucket 48: 40% bucket 36: 50% bucket 42: 10% bucket 43: 10% bucket 36: 20% bucket 40: 10% bucket 38: 10% bucket 52: 30% bucket 47: 40% bucket 40: 40% bucket 43: 40% bucket 34: 20% bucket 54: 30% bucket 34: 60% bucket 50: 30% bucket 33: 50% bucket 44: 10% bucket 37: 50% bucket 45: 10% bucket 28: 30% bucket 39: 50% bucket 33: 20% bucket 35: 20% bucket 46: 10% bucket 31: 50% bucket 48: 10% bucket 47: 10% bucket 44: 40% bucket 46: 40% bucket 30: 30% bucket 36: 60% bucket 37: 20% bucket 36: 30% bucket 51: 10% bucket 49: 10% bucket 49: 40% bucket 29: 60% bucket 30: 60% bucket 50: 10% bucket 29: 30% bucket 39: 20% bucket 32: 30% bucket 41: 20% bucket 53: 10% bucket 31: 30% bucket 53: 30% bucket 52: 10% bucket 54: 10% bucket 43: 20% bucket 42: 20% bucket 51: 40% bucket 38: 20% bucket 42: 50% bucket 34: 30% bucket 45: 50% bucket 38: 60% bucket 52: 40% bucket 32: 60% bucket 41: 50% bucket 47: 50% bucket 48: 50% bucket 28: 90% bucket 43: 50% bucket 36: 40% bucket 40: 20% bucket 35: 60% bucket 36: 70% bucket 33: 60% bucket 54: 40% bucket 37: 60% bucket 39: 60% bucket 40: 50% bucket 28: 40% bucket 44: 20% bucket 30: 40% bucket 45: 20% bucket 33: 30% bucket 50: 40% bucket 37: 30% bucket 35: 30% bucket 34: 70% bucket 44: 50% bucket 46: 20% bucket 46: 50% bucket 30: 70% bucket 48: 20% bucket 31: 60% bucket 29: 70% bucket 49: 20% bucket 51: 20% bucket 47: 20% bucket 50: 20% bucket 53: 20% bucket 39: 30% bucket 36: 50% bucket 32: 40% bucket 41: 30% bucket 31: 40% bucket 29: 40% bucket 36: 80% bucket 43: 30% bucket 49: 50% bucket 53: 40% bucket 42: 60% bucket 38: 70% bucket 32: 70% bucket 38: 30% bucket 42: 30% bucket 54: 20% bucket 47: 60% bucket 52: 50% bucket 51: 50% bucket 41: 60% bucket 48: 60% bucket 45: 60% bucket 52: 20% bucket 34: 40% bucket 43: 60% bucket 28: 100% Sorting block of length 2901193 for bucket 28 (Using difference cover) bucket 54: 50% bucket 35: 70% bucket 33: 70% bucket 40: 30% bucket 30: 50% bucket 40: 60% bucket 28: 50% bucket 37: 70% bucket 34: 80% bucket 36: 60% bucket 50: 50% bucket 44: 30% bucket 31: 50% bucket 39: 70% bucket 46: 60% bucket 29: 80% bucket 31: 70% bucket 33: 40% bucket 44: 60% bucket 37: 40% bucket 35: 40% bucket 45: 30% bucket 46: 30% bucket 49: 30% bucket 30: 80% bucket 51: 30% bucket 38: 80% bucket 50: 30% bucket 39: 40% bucket 32: 50% bucket 47: 30% bucket 48: 30% bucket 36: 90% bucket 43: 40% bucket 38: 40% bucket 32: 80% bucket 41: 40% Sorting block time: 00:00:02 Returning block of 2901194 for bucket 28 bucket 29: 50% bucket 53: 30% bucket 42: 40% Getting block 55 of 205 Reserving size (5249070) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 48: 70% bucket 41: 70% bucket 36: 70% bucket 54: 30% bucket 42: 70% bucket 49: 60% bucket 47: 70% bucket 51: 60% bucket 34: 50% bucket 52: 60% bucket 30: 60% bucket 35: 80% bucket 40: 70% bucket 40: 40% bucket 29: 90% bucket 43: 70% bucket 54: 60% bucket 53: 50% bucket 28: 60% bucket 52: 30% bucket 45: 70% bucket 31: 60% bucket 37: 50% bucket 34: 90% bucket 44: 70% bucket 33: 80% bucket 33: 50% bucket 39: 80% bucket 36: 80% bucket 35: 50% bucket 44: 40% bucket 38: 90% bucket 46: 70% bucket 49: 40% bucket 50: 60% bucket 32: 60% bucket 39: 50% bucket 37: 80% bucket 45: 40% bucket 51: 40% bucket 38: 50% bucket 43: 50% bucket 31: 80% bucket 50: 40% bucket 46: 40% bucket 48: 80% bucket 30: 90% bucket 42: 50% bucket 41: 50% bucket 47: 40% bucket 36: 100% Sorting block of length 859971 for bucket 36 (Using difference cover) bucket 29: 60% bucket 53: 40% bucket 48: 40% Sorting block time: 00:00:01 Returning block of 859972 for bucket 36 Getting block 56 of 205 Reserving size (5249070) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 30: 70% bucket 54: 40% bucket 49: 70% bucket 32: 90% bucket 42: 80% bucket 34: 60% bucket 47: 80% bucket 31: 70% bucket 40: 80% bucket 29: 100% Sorting block of length 4157488 for bucket 29 (Using difference cover) bucket 37: 60% bucket 51: 70% bucket 55: 10% bucket 43: 80% bucket 40: 50% bucket 35: 90% bucket 28: 70% bucket 41: 80% bucket 52: 40% bucket 33: 60% bucket 44: 80% bucket 33: 90% bucket 45: 80% bucket 53: 60% bucket 52: 70% bucket 38: 60% bucket 50: 50% bucket 34: 100% Sorting block of length 4647686 for bucket 34 (Using difference cover) bucket 54: 70% bucket 32: 70% bucket 36: 90% bucket 39: 60% bucket 39: 90% bucket 44: 50% bucket 45: 50% bucket 50: 70% bucket 49: 50% bucket 41: 60% bucket 38: 100% Sorting block of length 4662745 for bucket 38 (Using difference cover) bucket 37: 90% bucket 29: 70% bucket 31: 90% bucket 42: 60% bucket 46: 80% bucket 48: 90% bucket 53: 50% bucket 35: 60% bucket 46: 50% bucket 51: 50% bucket 30: 100% Sorting block of length 1867845 for bucket 30 (Using difference cover) bucket 43: 60% bucket 49: 80% bucket 54: 50% bucket 47: 50% bucket 30: 80% bucket 42: 90% bucket 47: 90% Sorting block time: 00:00:03 Returning block of 4157489 for bucket 29 bucket 34: 70% bucket 40: 90% bucket 37: 70% bucket 31: 80% Getting block 57 of 205 Reserving size (5249070) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 35: 100% Sorting block of length 5153746 for bucket 35 (Using difference cover) bucket 55: 20% bucket 28: 80% bucket 38: 70% Sorting block time: 00:00:01 Returning block of 1867846 for bucket 30 bucket 50: 60% bucket 39: 70% bucket 56: 10% bucket 51: 80% Getting block 58 of 205 Reserving size (5249070) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: bucket 32: 80% bucket 32: 100% Sorting block of length 2648080 for bucket 32 (Using difference cover) bucket 40: 60% bucket 41: 70% bucket 48: 50% bucket 43: 90% bucket 36: 100% Sorting block of length 4400219 for bucket 36 (Using difference cover) bucket 52: 80% bucket 33: 70% bucket 39: 100% Sorting block of length 3544596 for bucket 39 (Using difference cover) bucket 49: 60% bucket 33: 100% Sorting block of length 3076234 for bucket 33 (Using difference cover) bucket 45: 90% bucket 29: 80% bucket 41: 90% bucket 53: 60% bucket 44: 90% bucket 54: 80% bucket 44: 60% bucket 53: 70% Sorting block time: 00:00:03 Returning block of 4647687 for bucket 34 bucket 46: 90% bucket 37: 100% Sorting block of length 5113176 for bucket 37 (Using difference cover) Getting block 59 of 205 Reserving size (5249070) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 52: 50% bucket 35: 70% bucket 42: 70% bucket 48: 100% Sorting block of length 2021347 for bucket 48 (Using difference cover) bucket 46: 60% bucket 50: 80% bucket 45: 60% bucket 54: 60% bucket 43: 70% Sorting block time: 00:00:03 Returning block of 4662746 for bucket 38 bucket 31: 90% bucket 31: 100% Sorting block of length 3585683 for bucket 31 (Using difference cover) Getting block 60 of 205 Reserving size (5249070) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 30: 90% Sorting block time: 00:00:01 Returning block of 2648081 for bucket 32 bucket 51: 60% bucket 47: 100% Sorting block of length 3776972 for bucket 47 (Using difference cover) Getting block 61 of 205 Reserving size (5249070) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: bucket 32: 90% bucket 42: 100% Sorting block of length 4969900 for bucket 42 (Using difference cover) bucket 49: 90% bucket 37: 80% Sorting block time: 00:00:02 Returning block of 3076235 for bucket 33 Sorting block time: 00:00:01 Returning block of 2021348 for bucket 48 bucket 50: 70% bucket 55: 30% Getting block 62 of 205 Reserving size (5249070) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 29: 90% Getting block 63 of 205 Reserving size (5249070) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 47: 60% bucket 39: 80% bucket 57: 10% bucket 41: 80% bucket 28: 90% bucket 38: 80% bucket 40: 70% bucket 40: 100% Sorting block of length 3905706 for bucket 40 (Using difference cover) bucket 49: 70% bucket 52: 90% Sorting block time: 00:00:02 Returning block of 3544597 for bucket 39 bucket 33: 80% Getting block 64 of 205 Reserving size (5249070) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: Sorting block time: 00:00:03 Returning block of 5153747 for bucket 35 bucket 51: 90% Sorting block time: 00:00:02 Returning block of 4400220 for bucket 36 bucket 48: 60% bucket 41: 100% Sorting block of length 3368907 for bucket 41 (Using difference cover) bucket 34: 80% Getting block 65 of 205 Reserving size (5249070) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: Getting block 55 of 212 Reserving size (5249070) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 43: 100% Sorting block of length 2456964 for bucket 43 (Using difference cover) bucket 54: 90% bucket 35: 80% bucket 56: 20% bucket 53: 70% bucket 44: 70% bucket 45: 100% Sorting block of length 2807517 for bucket 45 (Using difference cover) bucket 58: 10% bucket 54: 70% bucket 42: 80% bucket 44: 100% Sorting block of length 2960448 for bucket 44 (Using difference cover) bucket 46: 100% Sorting block of length 4654685 for bucket 46 (Using difference cover) bucket 31: 100% Sorting block of length 3906557 for bucket 31 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3585684 for bucket 31 bucket 52: 60% bucket 53: 80% bucket 43: 80% bucket 32: 100% Sorting block of length 3166570 for bucket 32 (Using difference cover) Getting block 66 of 205 Reserving size (5249070) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: bucket 46: 70% Sorting block time: 00:00:04 Returning block of 5113177 for bucket 37 Sorting block time: 00:00:03 Returning block of 3776973 for bucket 47 bucket 60: 10% bucket 30: 100% Sorting block of length 3370746 for bucket 30 (Using difference cover) Getting block 67 of 205 Reserving size (5249070) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: Getting block 68 of 205 Reserving size (5249070) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 51: 70% bucket 61: 10% bucket 45: 70% bucket 59: 10% bucket 38: 90% bucket 50: 90% Sorting block time: 00:00:02 Returning block of 2456965 for bucket 43 bucket 41: 90% bucket 50: 80% Getting block 69 of 205 Reserving size (5249070) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: bucket 39: 90% bucket 63: 10% bucket 28: 100% Sorting block of length 3932586 for bucket 28 (Using difference cover) bucket 33: 90% bucket 37: 90% bucket 49: 80% bucket 34: 90% Sorting block time: 00:00:04 Returning block of 4969901 for bucket 42 bucket 49: 100% Sorting block of length 4821071 for bucket 49 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3905707 for bucket 40 bucket 29: 100% Sorting block of length 2816923 for bucket 29 (Using difference cover) bucket 40: 80% Sorting block time: 00:00:02 Returning block of 3368908 for bucket 41 bucket 52: 100% Sorting block of length 1448242 for bucket 52 (Using difference cover) Getting block 70 of 205 Reserving size (5249070) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: bucket 62: 10% bucket 57: 20% bucket 64: 10% Getting block 71 of 205 Reserving size (5249070) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: Getting block 72 of 205 Reserving size (5249070) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 47: 70% Sorting block time: 00:00:02 Returning block of 2807518 for bucket 45 bucket 44: 80% bucket 55: 40% Getting block 73 of 205 Reserving size (5249070) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: bucket 48: 70% bucket 56: 30% Sorting block time: 00:00:02 Returning block of 2960449 for bucket 44 bucket 54: 100% Sorting block of length 4614709 for bucket 54 (Using difference cover) bucket 46: 80% Getting block 74 of 205 Reserving size (5249070) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: bucket 35: 90% bucket 42: 90% bucket 55: 10% bucket 54: 80% Sorting block time: 00:00:02 Returning block of 3906558 for bucket 31 bucket 51: 100% Sorting block of length 5246512 for bucket 51 (Using difference cover) bucket 53: 80% Getting block 56 of 212 Reserving size (5249070) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: Sorting block time: 00:00:01 Returning block of 1448243 for bucket 52 bucket 43: 90% Getting block 75 of 205 Reserving size (5249070) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: Sorting block time: 00:00:02 Returning block of 3166571 for bucket 32 Getting block 57 of 212 Reserving size (5249070) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 65: 10% bucket 58: 20% Sorting block time: 00:00:02 Returning block of 3370747 for bucket 30 bucket 52: 70% bucket 51: 80% Getting block 58 of 212 Reserving size (5249070) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: Sorting block time: 00:00:02 Returning block of 2816924 for bucket 29 Sorting block time: 00:00:04 Returning block of 4654686 for bucket 46 bucket 66: 10% bucket 53: 90% Getting block 59 of 212 Reserving size (5249070) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 38: 100% Sorting block of length 2475472 for bucket 38 (Using difference cover) bucket 39: 100% Sorting block of length 4949827 for bucket 39 (Using difference cover) bucket 45: 80% Getting block 76 of 205 Reserving size (5249070) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 41: 100% Sorting block of length 4306816 for bucket 41 (Using difference cover) bucket 60: 20% bucket 61: 20% bucket 49: 90% bucket 33: 100% Sorting block of length 2826894 for bucket 33 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3932587 for bucket 28 bucket 67: 10% bucket 50: 100% Sorting block of length 4427266 for bucket 50 (Using difference cover) bucket 63: 20% bucket 37: 100% Sorting block of length 3625390 for bucket 37 (Using difference cover) Getting block 60 of 212 Reserving size (5249070) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 34: 100% Sorting block of length 3812651 for bucket 34 (Using difference cover) bucket 50: 90% bucket 68: 10% bucket 59: 20% bucket 73: 10% bucket 57: 30% bucket 70: 10% bucket 40: 90% bucket 69: 10% Sorting block time: 00:00:03 Returning block of 4821072 for bucket 49 bucket 42: 100% Sorting block of length 4397802 for bucket 42 (Using difference cover) bucket 56: 40% bucket 56: 10% bucket 44: 90% bucket 74: 10% bucket 54: 90% bucket 57: 10% bucket 64: 20% Getting block 77 of 205 Reserving size (5249070) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 43: 100% Sorting block of length 4646092 for bucket 43 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2475473 for bucket 38 Getting block 61 of 212 Reserving size (5249070) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: Sorting block time: 00:00:03 Returning block of 4614710 for bucket 54 bucket 51: 90% bucket 58: 10% bucket 35: 100% Sorting block of length 2834120 for bucket 35 (Using difference cover) bucket 72: 10% bucket 48: 80% Getting block 78 of 205 Reserving size (5249070) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: Sorting block time: 00:00:02 Returning block of 2826895 for bucket 33 bucket 71: 10% bucket 59: 10% bucket 55: 20% Getting block 62 of 212 Reserving size (5249070) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 62: 20% bucket 58: 30% bucket 55: 50% bucket 46: 90% bucket 53: 90% bucket 47: 80% bucket 49: 100% Sorting block of length 4962665 for bucket 49 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5246513 for bucket 51 bucket 63: 30% Getting block 79 of 205 Reserving size (5249070) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: Sorting block time: 00:00:03 Returning block of 3625391 for bucket 37 bucket 66: 20% bucket 53: 100% Sorting block of length 4120564 for bucket 53 (Using difference cover) bucket 75: 10% bucket 50: 100% Sorting block of length 3664577 for bucket 50 (Using difference cover) bucket 52: 80% Getting block 63 of 212 Reserving size (5249070) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 67: 20% Sorting block time: 00:00:03 Returning block of 4306817 for bucket 41 bucket 65: 20% Sorting block time: 00:00:03 Returning block of 3812652 for bucket 34 bucket 45: 90% Getting block 64 of 212 Reserving size (5249070) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 60: 10% bucket 56: 20% Getting block 65 of 212 Reserving size (5249070) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: bucket 57: 20% bucket 73: 20% bucket 59: 30% bucket 40: 100% Sorting block of length 1363320 for bucket 40 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4427267 for bucket 50 Sorting block time: 00:00:03 Returning block of 4949828 for bucket 39 bucket 44: 100% Sorting block of length 3108624 for bucket 44 (Using difference cover) bucket 68: 20% Getting block 80 of 205 Reserving size (5249070) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 60: 30% bucket 76: 10% Getting block 66 of 212 Reserving size (5249070) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: bucket 57: 40% Sorting block time: 00:00:02 Returning block of 2834121 for bucket 35 bucket 54: 100% Sorting block of length 4314419 for bucket 54 (Using difference cover) bucket 61: 30% Getting block 67 of 212 Reserving size (5249070) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: bucket 61: 10% bucket 74: 20% bucket 51: 100% Sorting block of length 2517703 for bucket 51 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4397803 for bucket 42 Sorting block time: 00:00:01 Returning block of 1363321 for bucket 40 bucket 58: 20% bucket 77: 10% bucket 64: 30% bucket 56: 50% Getting block 68 of 212 Reserving size (5249070) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: Getting block 69 of 212 Reserving size (5249070) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: bucket 70: 20% bucket 69: 20% bucket 59: 20% bucket 48: 90% Sorting block time: 00:00:03 Returning block of 4646093 for bucket 43 bucket 67: 30% bucket 47: 90% bucket 55: 30% bucket 55: 60% bucket 72: 20% bucket 53: 100% Sorting block of length 955251 for bucket 53 (Using difference cover) Getting block 70 of 212 Reserving size (5249070) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: bucket 62: 30% bucket 71: 20% bucket 58: 40% bucket 65: 30% bucket 78: 10% bucket 63: 10% Sorting block time: 00:00:03 Returning block of 3664578 for bucket 50 Getting block 71 of 212 Reserving size (5249070) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: Sorting block time: 00:00:01 Returning block of 955252 for bucket 53 Getting block 72 of 212 Reserving size (5249070) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 63: 40% Sorting block time: 00:00:03 Returning block of 4120565 for bucket 53 Sorting block time: 00:00:02 Returning block of 2517704 for bucket 51 Sorting block time: 00:00:02 Returning block of 3108625 for bucket 44 bucket 79: 10% bucket 60: 20% bucket 62: 10% Sorting block time: 00:00:03 Returning block of 4962666 for bucket 49 Getting block 73 of 212 Reserving size (5249070) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: Getting block 74 of 212 Reserving size (5249070) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: Getting block 81 of 205 Reserving size (5249070) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 45: 100% Sorting block of length 4896101 for bucket 45 (Using difference cover) bucket 46: 100% Sorting block of length 2388357 for bucket 46 (Using difference cover) bucket 64: 10% Getting block 75 of 212 Reserving size (5249070) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 57: 50% bucket 52: 90% bucket 56: 30% bucket 57: 30% bucket 75: 20% bucket 73: 30% bucket 66: 10% bucket 66: 30% bucket 68: 30% bucket 80: 10% bucket 65: 10% bucket 60: 40% Sorting block time: 00:00:03 Returning block of 4314420 for bucket 54 Getting block 76 of 212 Reserving size (5249070) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 61: 20% bucket 59: 40% bucket 61: 40% bucket 74: 30% bucket 69: 10% bucket 70: 30% bucket 76: 20% bucket 64: 40% bucket 77: 20% bucket 58: 30% bucket 67: 10% bucket 67: 40% bucket 70: 10% Sorting block time: 00:00:02 Returning block of 2388358 for bucket 46 bucket 69: 30% bucket 56: 60% Getting block 77 of 212 Reserving size (5249070) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 63: 20% bucket 68: 10% bucket 71: 10% bucket 72: 30% bucket 55: 40% bucket 78: 20% bucket 48: 100% Sorting block of length 2151181 for bucket 48 (Using difference cover) bucket 59: 30% bucket 55: 70% bucket 71: 30% bucket 63: 50% bucket 65: 40% bucket 72: 10% bucket 47: 100% Sorting block of length 3196200 for bucket 47 (Using difference cover) bucket 56: 40% bucket 58: 50% bucket 75: 10% bucket 73: 10% bucket 62: 20% bucket 57: 60% bucket 57: 40% bucket 66: 40% bucket 76: 10% bucket 60: 50% bucket 60: 30% Sorting block time: 00:00:03 Returning block of 4896102 for bucket 45 bucket 68: 40% bucket 79: 20% bucket 52: 100% Sorting block of length 4537268 for bucket 52 (Using difference cover) bucket 62: 40% bucket 74: 10% Getting block 78 of 212 Reserving size (5249070) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 59: 50% bucket 65: 20% bucket 81: 10% bucket 61: 30% Sorting block time: 00:00:02 Returning block of 2151182 for bucket 48 bucket 66: 20% bucket 64: 20% Getting block 79 of 212 Reserving size (5249070) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 69: 20% bucket 70: 40% bucket 58: 40% bucket 67: 50% bucket 71: 20% bucket 80: 20% bucket 73: 40% bucket 75: 30% bucket 74: 40% Sorting block time: 00:00:02 Returning block of 3196201 for bucket 47 bucket 77: 30% Getting block 80 of 212 Reserving size (5249070) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 67: 20% bucket 55: 80% bucket 63: 60% bucket 76: 30% bucket 56: 50% bucket 63: 30% bucket 72: 40% bucket 73: 20% bucket 56: 70% bucket 70: 20% bucket 64: 50% bucket 75: 20% bucket 68: 20% bucket 69: 40% bucket 66: 50% bucket 72: 20% bucket 78: 30% bucket 55: 50% bucket 60: 60% bucket 57: 70% bucket 62: 30% bucket 57: 50% bucket 65: 50% bucket 58: 60% bucket 77: 10% bucket 61: 40% bucket 74: 20% Sorting block time: 00:00:03 Returning block of 4537269 for bucket 52 bucket 66: 30% bucket 59: 40% bucket 76: 20% bucket 79: 30% bucket 71: 30% Getting block 81 of 212 Reserving size (5249070) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 60: 40% bucket 61: 50% bucket 81: 20% bucket 62: 50% bucket 79: 10% bucket 64: 30% bucket 71: 40% bucket 59: 60% bucket 70: 50% bucket 67: 60% bucket 74: 50% bucket 73: 30% bucket 63: 40% bucket 72: 50% bucket 69: 30% bucket 72: 30% bucket 77: 40% bucket 78: 10% bucket 80: 30% bucket 75: 30% bucket 76: 40% bucket 56: 80% bucket 55: 90% bucket 75: 40% bucket 80: 10% bucket 65: 30% bucket 56: 60% bucket 58: 50% bucket 68: 50% bucket 63: 70% bucket 60: 70% bucket 64: 60% bucket 57: 60% bucket 73: 50% bucket 66: 60% bucket 67: 30% bucket 74: 30% bucket 57: 80% bucket 71: 40% bucket 58: 70% bucket 70: 30% bucket 69: 50% bucket 68: 30% bucket 76: 30% bucket 61: 50% bucket 55: 60% bucket 77: 20% bucket 62: 40% bucket 65: 60% bucket 81: 10% bucket 81: 30% bucket 59: 50% bucket 78: 40% bucket 60: 50% bucket 71: 50% bucket 59: 70% bucket 61: 60% bucket 70: 60% bucket 72: 40% bucket 79: 40% bucket 66: 40% bucket 64: 40% bucket 73: 40% bucket 62: 60% bucket 79: 20% bucket 69: 40% bucket 55: 100% Sorting block of length 5211818 for bucket 55 (Using difference cover) bucket 68: 60% bucket 74: 40% bucket 75: 40% bucket 67: 70% bucket 78: 20% bucket 56: 70% bucket 63: 50% bucket 58: 60% bucket 66: 70% bucket 56: 90% bucket 72: 60% bucket 74: 60% bucket 64: 70% bucket 65: 40% bucket 77: 50% bucket 60: 80% bucket 80: 20% bucket 63: 80% bucket 69: 60% bucket 58: 80% bucket 61: 60% bucket 71: 50% bucket 80: 40% bucket 73: 60% bucket 77: 30% bucket 67: 40% bucket 76: 50% bucket 78: 50% bucket 57: 70% bucket 76: 40% bucket 57: 90% bucket 70: 40% bucket 59: 60% bucket 81: 20% bucket 75: 50% bucket 55: 70% bucket 59: 80% bucket 62: 50% bucket 65: 70% bucket 81: 40% bucket 75: 50% bucket 73: 50% bucket 66: 50% bucket 64: 50% bucket 74: 50% bucket 69: 50% bucket 72: 50% bucket 63: 60% bucket 68: 40% bucket 79: 30% bucket 66: 80% bucket 71: 60% bucket 78: 30% bucket 60: 60% bucket 56: 100% Sorting block of length 4848769 for bucket 56 (Using difference cover) bucket 79: 50% bucket 62: 70% bucket 58: 70% bucket 70: 70% bucket 60: 90% bucket 68: 70% bucket 63: 90% bucket 71: 60% bucket 56: 80% Sorting block time: 00:00:03 Returning block of 5211819 for bucket 55 bucket 80: 30% Getting block 82 of 205 Reserving size (5249070) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 67: 80% bucket 74: 70% bucket 57: 80% bucket 64: 80% bucket 65: 50% bucket 59: 90% bucket 61: 70% bucket 61: 70% bucket 80: 50% bucket 72: 70% bucket 77: 60% bucket 69: 70% bucket 77: 40% bucket 70: 50% bucket 58: 90% bucket 78: 60% bucket 76: 50% bucket 76: 60% bucket 73: 60% bucket 71: 70% bucket 81: 30% bucket 73: 70% bucket 75: 60% bucket 78: 40% bucket 75: 60% bucket 55: 80% bucket 72: 60% bucket 59: 70% bucket 63: 70% bucket 62: 80% bucket 64: 60% bucket 68: 50% bucket 81: 50% bucket 57: 100% Sorting block of length 4292259 for bucket 57 (Using difference cover) bucket 80: 40% bucket 60: 100% Sorting block of length 3973270 for bucket 60 (Using difference cover) bucket 58: 80% Sorting block time: 00:00:02 Returning block of 4848770 for bucket 56 bucket 59: 100% Sorting block of length 4636806 for bucket 59 (Using difference cover) bucket 74: 60% bucket 62: 60% bucket 67: 90% Getting block 83 of 205 Reserving size (5249070) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 66: 90% bucket 79: 60% bucket 69: 60% bucket 66: 60% bucket 71: 70% bucket 57: 90% bucket 79: 40% bucket 80: 60% bucket 65: 80% bucket 64: 90% bucket 67: 50% bucket 56: 90% bucket 63: 100% Sorting block of length 2069442 for bucket 63 (Using difference cover) bucket 68: 80% bucket 78: 70% bucket 77: 50% bucket 70: 60% bucket 71: 80% bucket 73: 70% bucket 61: 80% bucket 74: 80% bucket 60: 70% bucket 82: 10% bucket 72: 80% bucket 78: 50% bucket 70: 80% bucket 61: 80% bucket 58: 100% Sorting block of length 3440882 for bucket 58 (Using difference cover) bucket 76: 60% bucket 80: 50% bucket 81: 40% bucket 73: 80% Sorting block time: 00:00:02 Returning block of 2069443 for bucket 63 bucket 64: 70% Getting block 84 of 205 Reserving size (5249070) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 75: 70% bucket 69: 80% bucket 72: 70% Sorting block time: 00:00:03 Returning block of 4292260 for bucket 57 bucket 76: 70% Sorting block time: 00:00:02 Returning block of 4636807 for bucket 59 bucket 75: 70% bucket 65: 60% bucket 77: 70% Getting block 85 of 205 Reserving size (5249070) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: Sorting block time: 00:00:03 Returning block of 3973271 for bucket 60 Getting block 86 of 205 Reserving size (5249070) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 66: 100% Sorting block of length 2886810 for bucket 66 (Using difference cover) Getting block 87 of 205 Reserving size (5249070) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 55: 90% bucket 58: 90% bucket 80: 70% bucket 56: 100% Sorting block of length 3829903 for bucket 56 (Using difference cover) bucket 68: 60% bucket 62: 90% bucket 65: 90% bucket 57: 100% Sorting block of length 5105815 for bucket 57 (Using difference cover) bucket 79: 50% Sorting block time: 00:00:02 Returning block of 3440883 for bucket 58 bucket 63: 80% Getting block 88 of 205 Reserving size (5249070) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 77: 60% bucket 62: 70% bucket 67: 100% Sorting block of length 3704937 for bucket 67 (Using difference cover) bucket 59: 80% bucket 73: 80% bucket 79: 70% bucket 71: 90% bucket 64: 100% Sorting block of length 4548963 for bucket 64 (Using difference cover) bucket 71: 80% bucket 60: 80% bucket 74: 90% bucket 76: 70% bucket 61: 90% bucket 81: 60% bucket 69: 70% bucket 66: 70% bucket 74: 70% bucket 68: 90% bucket 78: 80% bucket 70: 70% bucket 67: 60% Sorting block time: 00:00:02 Returning block of 2886811 for bucket 66 bucket 82: 20% bucket 75: 80% bucket 81: 50% bucket 64: 80% bucket 78: 60% bucket 83: 10% Getting block 89 of 205 Reserving size (5249070) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 86: 10% bucket 69: 90% bucket 61: 90% bucket 84: 10% bucket 72: 90% bucket 70: 90% bucket 72: 80% bucket 77: 80% Sorting block time: 00:00:02 Returning block of 3829904 for bucket 56 bucket 76: 80% bucket 80: 60% bucket 58: 100% Sorting block of length 5147499 for bucket 58 (Using difference cover) bucket 73: 90% Getting block 82 of 212 Reserving size (5249070) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 75: 80% bucket 79: 60% bucket 63: 90% bucket 85: 10% Sorting block time: 00:00:03 Returning block of 3704938 for bucket 67 bucket 76: 80% bucket 80: 80% bucket 62: 100% Sorting block of length 4769012 for bucket 62 (Using difference cover) Getting block 90 of 205 Reserving size (5249070) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 55: 100% Sorting block of length 3226188 for bucket 55 (Using difference cover) bucket 77: 70% bucket 65: 100% Sorting block of length 3024431 for bucket 65 (Using difference cover) bucket 60: 90% bucket 87: 10% bucket 88: 10% bucket 71: 100% Sorting block of length 5024341 for bucket 71 (Using difference cover) bucket 59: 90% bucket 61: 100% Sorting block of length 4436110 for bucket 61 (Using difference cover) bucket 79: 80% bucket 71: 90% bucket 73: 90% bucket 65: 70% Sorting block time: 00:00:03 Returning block of 4548964 for bucket 64 Sorting block time: 00:00:03 Returning block of 5105816 for bucket 57 bucket 78: 90% bucket 74: 100% Sorting block of length 4870304 for bucket 74 (Using difference cover) Getting block 91 of 205 Reserving size (5249070) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 68: 100% Sorting block of length 2953131 for bucket 68 (Using difference cover) bucket 75: 90% bucket 62: 80% bucket 70: 80% bucket 74: 80% bucket 81: 70% bucket 61: 100% Sorting block of length 2918450 for bucket 61 (Using difference cover) Getting block 83 of 212 Reserving size (5249070) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 66: 80% bucket 68: 70% bucket 81: 60% bucket 69: 80% bucket 67: 70% Sorting block time: 00:00:01 Returning block of 3024432 for bucket 65 bucket 72: 90% Getting block 92 of 205 Reserving size (5249070) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: bucket 82: 10% bucket 76: 90% bucket 78: 70% bucket 64: 90% bucket 82: 30% bucket 69: 100% Sorting block of length 3784130 for bucket 69 (Using difference cover) bucket 70: 100% Sorting block of length 4701350 for bucket 70 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3226189 for bucket 55 bucket 73: 100% Sorting block of length 3244840 for bucket 73 (Using difference cover) bucket 80: 70% bucket 89: 10% Getting block 84 of 212 Reserving size (5249070) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 77: 90% bucket 72: 100% Sorting block of length 4221656 for bucket 72 (Using difference cover) bucket 83: 20% Sorting block time: 00:00:03 Returning block of 5147500 for bucket 58 bucket 59: 100% Sorting block of length 5051962 for bucket 59 (Using difference cover) bucket 84: 20% Getting block 85 of 212 Reserving size (5249070) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 76: 90% bucket 86: 20% bucket 63: 100% Sorting block of length 4532499 for bucket 63 (Using difference cover) bucket 79: 70% Sorting block time: 00:00:02 Returning block of 2953132 for bucket 68 Sorting block time: 00:00:03 Returning block of 4769013 for bucket 62 Getting block 93 of 205 Reserving size (5249070) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 75: 90% bucket 87: 20% Getting block 94 of 205 Reserving size (5249070) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: bucket 73: 100% Sorting block of length 3844408 for bucket 73 (Using difference cover) bucket 79: 90% bucket 70: 90% bucket 71: 100% Sorting block of length 5218577 for bucket 71 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4436111 for bucket 61 bucket 77: 80% Getting block 95 of 205 Reserving size (5249070) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 75: 100% Sorting block of length 5040398 for bucket 75 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2918451 for bucket 61 bucket 80: 90% bucket 85: 20% Getting block 86 of 212 Reserving size (5249070) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 60: 100% Sorting block of length 4850770 for bucket 60 (Using difference cover) bucket 88: 20% bucket 83: 10% bucket 65: 80% bucket 90: 10% bucket 72: 100% Sorting block of length 1615399 for bucket 72 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5024342 for bucket 71 bucket 74: 90% bucket 81: 80% bucket 78: 100% Sorting block of length 4782455 for bucket 78 (Using difference cover) Getting block 87 of 212 Reserving size (5249070) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 81: 70% bucket 66: 90% bucket 82: 20% bucket 62: 90% bucket 69: 90% Sorting block time: 00:00:03 Returning block of 4870305 for bucket 74 Sorting block time: 00:00:02 Returning block of 3244841 for bucket 73 Getting block 96 of 205 Reserving size (5249070) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: Sorting block time: 00:00:02 Returning block of 3784131 for bucket 69 Getting block 97 of 205 Reserving size (5249070) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: bucket 64: 100% Sorting block of length 1278048 for bucket 64 (Using difference cover) Getting block 98 of 205 Reserving size (5249070) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 76: 100% Sorting block of length 3939846 for bucket 76 (Using difference cover) bucket 76: 100% Sorting block of length 1554697 for bucket 76 (Using difference cover) bucket 78: 80% bucket 68: 80% bucket 91: 10% Sorting block time: 00:00:03 Returning block of 4701351 for bucket 70 bucket 85: 10% Sorting block time: 00:00:03 Returning block of 4221657 for bucket 72 bucket 84: 10% bucket 82: 40% Sorting block time: 00:00:01 Returning block of 1615400 for bucket 72 bucket 67: 80% Getting block 88 of 212 Reserving size (5249070) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: Getting block 99 of 205 Reserving size (5249070) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: bucket 89: 20% Getting block 100 of 205 Reserving size (5249070) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: bucket 80: 80% bucket 92: 10% bucket 86: 30% bucket 79: 80% bucket 84: 30% Sorting block time: 00:00:01 Returning block of 1278049 for bucket 64 bucket 70: 100% Sorting block of length 4985066 for bucket 70 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5051963 for bucket 59 Getting block 89 of 212 Reserving size (5249070) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: Sorting block time: 00:00:03 Returning block of 3844409 for bucket 73 bucket 75: 100% Sorting block of length 1100198 for bucket 75 (Using difference cover) Getting block 90 of 212 Reserving size (5249070) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: Sorting block time: 00:00:04 Returning block of 4532500 for bucket 63 bucket 77: 100% Sorting block of length 3999949 for bucket 77 (Using difference cover) Getting block 91 of 212 Reserving size (5249070) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 83: 30% Sorting block time: 00:00:01 Returning block of 1554698 for bucket 76 Getting block 92 of 212 Reserving size (5249070) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: Getting block 101 of 205 Reserving size (5249070) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 77: 90% bucket 83: 20% bucket 85: 30% bucket 82: 30% bucket 86: 10% bucket 87: 30% Sorting block time: 00:00:01 Returning block of 1100199 for bucket 75 bucket 81: 80% Sorting block time: 00:00:03 Returning block of 4850771 for bucket 60 Sorting block time: 00:00:04 Returning block of 5218578 for bucket 71 Getting block 102 of 205 Reserving size (5249070) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 74: 100% Sorting block of length 3549842 for bucket 74 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3939847 for bucket 76 bucket 94: 10% Sorting block time: 00:00:04 Returning block of 5040399 for bucket 75 bucket 87: 10% Getting block 93 of 212 Reserving size (5249070) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 78: 90% bucket 80: 100% Sorting block of length 3611155 for bucket 80 (Using difference cover) bucket 79: 100% Sorting block of length 5219659 for bucket 79 (Using difference cover) bucket 69: 100% Sorting block of length 1353860 for bucket 69 (Using difference cover) Getting block 94 of 212 Reserving size (5249070) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: Getting block 103 of 205 Reserving size (5249070) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: Getting block 95 of 212 Reserving size (5249070) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 62: 100% Sorting block of length 4334977 for bucket 62 (Using difference cover) bucket 66: 100% Sorting block of length 4649176 for bucket 66 (Using difference cover) bucket 65: 90% bucket 93: 10% bucket 95: 10% Sorting block time: 00:00:03 Returning block of 4782456 for bucket 78 bucket 81: 90% bucket 85: 20% bucket 68: 90% bucket 88: 30% Getting block 104 of 205 Reserving size (5249070) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: bucket 89: 30% bucket 84: 20% bucket 90: 20% bucket 100: 10% bucket 89: 10% Sorting block time: 00:00:01 Returning block of 1353861 for bucket 69 bucket 82: 50% Getting block 96 of 212 Reserving size (5249070) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 88: 10% bucket 79: 90% bucket 97: 10% bucket 98: 10% bucket 92: 10% bucket 80: 90% bucket 82: 40% bucket 96: 10% bucket 92: 20% bucket 91: 20% bucket 83: 30% bucket 84: 40% bucket 86: 20% bucket 91: 10% bucket 67: 90% bucket 87: 40% bucket 86: 40% Sorting block time: 00:00:03 Returning block of 3999950 for bucket 77 bucket 77: 100% Sorting block of length 3957669 for bucket 77 (Using difference cover) bucket 90: 10% Sorting block time: 00:00:02 Returning block of 3549843 for bucket 74 bucket 85: 40% Getting block 105 of 205 Reserving size (5249070) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 83: 40% Getting block 97 of 212 Reserving size (5249070) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: bucket 99: 10% bucket 87: 20% Sorting block time: 00:00:03 Returning block of 4985067 for bucket 70 bucket 94: 10% bucket 95: 10% Sorting block time: 00:00:03 Returning block of 3611156 for bucket 80 Getting block 98 of 212 Reserving size (5249070) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 101: 10% Getting block 106 of 205 Reserving size (5249070) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 85: 30% Sorting block time: 00:00:03 Returning block of 4334978 for bucket 62 bucket 81: 90% bucket 82: 50% bucket 102: 10% bucket 65: 100% Sorting block of length 675992 for bucket 65 (Using difference cover) Getting block 99 of 212 Reserving size (5249070) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: bucket 78: 100% Sorting block of length 4458921 for bucket 78 (Using difference cover) bucket 104: 10% bucket 94: 20% bucket 90: 30% bucket 82: 60% bucket 93: 10% bucket 89: 20% Sorting block time: 00:00:03 Returning block of 4649177 for bucket 66 bucket 84: 30% Sorting block time: 00:00:01 Returning block of 675993 for bucket 65 Getting block 100 of 212 Reserving size (5249070) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: Getting block 101 of 212 Reserving size (5249070) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 81: 100% Sorting block of length 5196289 for bucket 81 (Using difference cover) bucket 96: 10% bucket 103: 10% bucket 88: 40% bucket 88: 20% bucket 95: 20% bucket 79: 100% Sorting block of length 3704015 for bucket 79 (Using difference cover) bucket 93: 20% Sorting block time: 00:00:04 Returning block of 5219660 for bucket 79 bucket 100: 20% bucket 92: 20% bucket 83: 40% Getting block 107 of 205 Reserving size (5249070) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 68: 100% Sorting block of length 4856501 for bucket 68 (Using difference cover) bucket 80: 100% Sorting block of length 3880932 for bucket 80 (Using difference cover) bucket 89: 40% bucket 91: 20% bucket 98: 20% bucket 96: 20% bucket 91: 30% bucket 97: 20% bucket 87: 50% bucket 94: 20% bucket 87: 30% Sorting block time: 00:00:03 Returning block of 3957670 for bucket 77 bucket 92: 30% bucket 67: 100% Sorting block of length 3841879 for bucket 67 (Using difference cover) Getting block 102 of 212 Reserving size (5249070) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 84: 50% bucket 85: 40% bucket 83: 50% bucket 85: 50% bucket 98: 10% bucket 90: 20% bucket 105: 10% bucket 86: 30% bucket 97: 10% bucket 95: 20% bucket 82: 60% bucket 86: 50% bucket 101: 20% bucket 99: 20% bucket 81: 100% Sorting block of length 5223911 for bucket 81 (Using difference cover) bucket 104: 20% Sorting block time: 00:00:03 Returning block of 4458922 for bucket 78 bucket 89: 30% bucket 106: 10% bucket 88: 30% bucket 84: 40% bucket 101: 10% Getting block 103 of 212 Reserving size (5249070) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: bucket 96: 20% bucket 99: 10% bucket 93: 20% bucket 92: 30% bucket 102: 20% bucket 83: 50% bucket 82: 70% Sorting block time: 00:00:03 Returning block of 3704016 for bucket 79 Sorting block time: 00:00:03 Returning block of 5196290 for bucket 81 bucket 93: 30% bucket 100: 10% bucket 91: 30% bucket 94: 30% Getting block 104 of 212 Reserving size (5249070) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: bucket 103: 20% Getting block 108 of 205 Reserving size (5249070) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: Sorting block time: 00:00:03 Returning block of 3880933 for bucket 80 bucket 90: 40% bucket 95: 30% Getting block 105 of 212 Reserving size (5249070) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 86: 40% bucket 85: 50% bucket 88: 50% bucket 82: 70% bucket 87: 40% bucket 94: 30% bucket 98: 20% bucket 84: 60% bucket 91: 40% bucket 89: 50% bucket 107: 10% bucket 87: 60% bucket 100: 30% bucket 92: 40% bucket 83: 60% bucket 95: 30% bucket 105: 20% Sorting block time: 00:00:03 Returning block of 3841880 for bucket 67 bucket 98: 30% bucket 102: 10% bucket 97: 20% bucket 97: 30% Getting block 106 of 212 Reserving size (5249070) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 96: 30% Sorting block time: 00:00:04 Returning block of 4856502 for bucket 68 bucket 90: 30% bucket 85: 60% bucket 106: 20% Getting block 107 of 212 Reserving size (5249070) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 86: 60% bucket 89: 40% bucket 96: 30% bucket 104: 30% bucket 84: 50% bucket 101: 20% bucket 101: 30% bucket 83: 60% bucket 99: 30% bucket 92: 40% Sorting block time: 00:00:03 Returning block of 5223912 for bucket 81 bucket 88: 40% bucket 103: 10% bucket 99: 20% bucket 94: 40% Getting block 108 of 212 Reserving size (5249070) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 85: 60% bucket 100: 40% bucket 103: 30% bucket 95: 40% bucket 102: 30% bucket 100: 20% bucket 108: 10% bucket 82: 80% bucket 93: 40% bucket 105: 10% bucket 93: 30% bucket 91: 40% bucket 82: 80% bucket 98: 30% bucket 87: 50% bucket 88: 60% bucket 92: 50% bucket 104: 10% bucket 86: 50% bucket 94: 40% bucket 107: 20% bucket 87: 70% bucket 90: 50% bucket 91: 50% bucket 105: 30% bucket 97: 40% bucket 106: 10% bucket 86: 70% bucket 96: 40% bucket 84: 70% bucket 106: 30% bucket 95: 40% bucket 90: 40% bucket 83: 70% bucket 97: 30% bucket 89: 50% bucket 96: 40% bucket 101: 30% bucket 84: 60% bucket 83: 70% bucket 104: 40% bucket 89: 60% bucket 98: 40% bucket 102: 20% bucket 100: 50% bucket 82: 90% bucket 100: 30% bucket 88: 50% bucket 92: 50% bucket 85: 70% bucket 85: 70% bucket 87: 60% bucket 94: 50% bucket 108: 20% bucket 99: 30% bucket 95: 50% bucket 105: 20% bucket 98: 40% bucket 91: 50% bucket 103: 40% bucket 99: 40% bucket 107: 10% bucket 108: 10% bucket 93: 40% bucket 101: 40% bucket 103: 20% bucket 102: 40% bucket 107: 30% bucket 86: 60% bucket 82: 90% bucket 104: 20% bucket 93: 50% bucket 87: 80% bucket 95: 50% bucket 89: 60% bucket 96: 50% bucket 105: 40% bucket 97: 50% bucket 94: 50% bucket 90: 50% bucket 84: 70% bucket 83: 80% bucket 88: 70% bucket 106: 20% bucket 84: 80% bucket 89: 70% bucket 82: 100% Sorting block of length 4562531 for bucket 82 (Using difference cover) bucket 101: 40% bucket 97: 40% bucket 90: 60% bucket 88: 60% bucket 85: 80% bucket 104: 50% bucket 100: 60% bucket 98: 50% bucket 92: 60% bucket 106: 40% bucket 86: 80% bucket 87: 70% bucket 83: 80% bucket 92: 60% bucket 91: 60% bucket 91: 60% bucket 94: 60% bucket 100: 40% bucket 96: 50% bucket 102: 30% bucket 108: 30% bucket 95: 60% bucket 98: 50% bucket 103: 50% bucket 105: 30% bucket 99: 40% bucket 101: 50% bucket 84: 80% bucket 85: 80% bucket 89: 70% bucket 105: 50% bucket 99: 50% bucket 86: 70% bucket 102: 50% Sorting block time: 00:00:03 Returning block of 4562532 for bucket 82 bucket 101: 50% bucket 107: 40% Getting block 109 of 212 Reserving size (5249070) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 96: 60% bucket 83: 90% bucket 93: 50% bucket 104: 60% bucket 88: 70% bucket 95: 60% bucket 94: 60% bucket 93: 60% bucket 82: 100% Sorting block of length 260046 for bucket 82 (Using difference cover) bucket 108: 20% bucket 107: 20% bucket 85: 90% bucket 88: 80% bucket 97: 60% Sorting block time: 00:00:00 Returning block of 260047 for bucket 82 bucket 90: 70% Getting block 109 of 205 Reserving size (5249070) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 106: 50% bucket 84: 90% bucket 103: 30% bucket 98: 60% bucket 92: 70% bucket 92: 70% bucket 104: 30% bucket 90: 60% bucket 91: 70% bucket 89: 80% bucket 97: 50% bucket 87: 90% bucket 83: 90% bucket 94: 70% bucket 87: 80% bucket 100: 70% bucket 106: 30% bucket 108: 40% bucket 86: 90% bucket 96: 60% bucket 98: 60% bucket 101: 60% bucket 89: 80% bucket 95: 70% bucket 91: 70% bucket 99: 60% bucket 84: 90% bucket 96: 70% bucket 105: 60% bucket 100: 50% bucket 85: 90% bucket 99: 50% bucket 83: 100% Sorting block of length 4912916 for bucket 83 (Using difference cover) bucket 102: 40% bucket 85: 100% Sorting block of length 4707358 for bucket 85 (Using difference cover) bucket 93: 60% bucket 103: 60% bucket 109: 10% bucket 88: 80% bucket 94: 80% bucket 86: 80% bucket 95: 70% bucket 105: 40% bucket 84: 100% Sorting block of length 3971295 for bucket 84 (Using difference cover) bucket 107: 50% bucket 106: 60% bucket 101: 60% bucket 91: 80% bucket 104: 70% bucket 98: 70% bucket 109: 10% bucket 88: 90% bucket 108: 30% bucket 107: 30% bucket 94: 70% bucket 87: 90% bucket 92: 80% bucket 93: 70% bucket 90: 70% bucket 101: 70% bucket 103: 40% bucket 92: 80% bucket 97: 70% bucket 83: 100% Sorting block of length 5147653 for bucket 83 (Using difference cover) bucket 102: 60% bucket 108: 50% bucket 104: 40% bucket 86: 100% Sorting block of length 4165408 for bucket 86 (Using difference cover) bucket 90: 80% bucket 87: 100% Sorting block of length 4732945 for bucket 87 (Using difference cover) bucket 89: 90% bucket 84: 100% Sorting block of length 1718077 for bucket 84 (Using difference cover) bucket 100: 80% bucket 106: 40% bucket 88: 90% bucket 109: 20% bucket 97: 60% bucket 89: 90% bucket 96: 80% bucket 96: 70% bucket 94: 90% bucket 95: 80% bucket 105: 70% bucket 91: 80% bucket 93: 70% bucket 106: 70% bucket 103: 70% bucket 99: 60% bucket 95: 80% Sorting block time: 00:00:04 Returning block of 4912917 for bucket 83 bucket 98: 70% Sorting block time: 00:00:03 Returning block of 3971296 for bucket 84 bucket 100: 60% bucket 99: 70% Sorting block time: 00:00:03 Returning block of 4707359 for bucket 85 bucket 91: 90% Sorting block time: 00:00:01 Returning block of 1718078 for bucket 84 Getting block 110 of 212 Reserving size (5249070) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: Getting block 110 of 205 Reserving size (5249070) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: Getting block 111 of 212 Reserving size (5249070) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: bucket 86: 90% Getting block 112 of 212 Reserving size (5249070) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 92: 90% bucket 102: 50% bucket 101: 80% bucket 98: 80% bucket 87: 100% Sorting block of length 2555999 for bucket 87 (Using difference cover) bucket 105: 50% bucket 109: 20% bucket 88: 100% Sorting block of length 3689548 for bucket 88 (Using difference cover) bucket 107: 60% bucket 85: 100% Sorting block of length 2700830 for bucket 85 (Using difference cover) bucket 104: 80% bucket 90: 80% bucket 103: 50% bucket 108: 40% bucket 94: 80% Sorting block time: 00:00:03 Returning block of 4165409 for bucket 86 bucket 92: 90% bucket 108: 60% Sorting block time: 00:00:03 Returning block of 5147654 for bucket 83 bucket 89: 100% Sorting block of length 3024790 for bucket 89 (Using difference cover) Getting block 111 of 205 Reserving size (5249070) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: bucket 101: 70% Getting block 112 of 205 Reserving size (5249070) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 107: 40% Sorting block time: 00:00:03 Returning block of 4732946 for bucket 87 bucket 93: 80% bucket 97: 80% bucket 88: 100% Sorting block of length 4727016 for bucket 88 (Using difference cover) Getting block 113 of 205 Reserving size (5249070) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 89: 100% Sorting block of length 1284743 for bucket 89 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2556000 for bucket 87 bucket 104: 50% bucket 94: 100% Sorting block of length 4240718 for bucket 94 (Using difference cover) Getting block 113 of 212 Reserving size (5249070) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 95: 90% bucket 109: 30% bucket 112: 10% bucket 96: 90% bucket 102: 70% bucket 106: 80% bucket 100: 90% bucket 97: 70% Sorting block time: 00:00:01 Returning block of 2700831 for bucket 85 bucket 91: 90% bucket 93: 80% bucket 105: 80% Getting block 114 of 205 Reserving size (5249070) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 99: 80% bucket 106: 50% bucket 100: 70% bucket 91: 100% Sorting block of length 2216048 for bucket 91 (Using difference cover) bucket 95: 90% bucket 92: 100% Sorting block of length 3606363 for bucket 92 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3689549 for bucket 88 Sorting block time: 00:00:01 Returning block of 1284744 for bucket 89 Getting block 114 of 212 Reserving size (5249070) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 101: 90% bucket 86: 100% Sorting block of length 3905190 for bucket 86 (Using difference cover) Getting block 115 of 205 Reserving size (5249070) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 99: 70% bucket 98: 90% bucket 110: 10% bucket 102: 60% Sorting block time: 00:00:02 Returning block of 3024791 for bucket 89 Getting block 116 of 205 Reserving size (5249070) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: bucket 111: 10% bucket 105: 60% bucket 96: 80% bucket 107: 70% bucket 110: 10% bucket 90: 90% bucket 103: 80% bucket 109: 30% bucket 103: 60% Sorting block time: 00:00:01 Returning block of 2216049 for bucket 91 bucket 90: 90% Getting block 115 of 212 Reserving size (5249070) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 98: 80% bucket 104: 90% bucket 108: 70% bucket 113: 10% bucket 108: 50% bucket 95: 100% Sorting block of length 3757159 for bucket 95 (Using difference cover) bucket 96: 100% Sorting block of length 4087069 for bucket 96 (Using difference cover) bucket 112: 20% bucket 111: 10% Sorting block time: 00:00:03 Returning block of 4240719 for bucket 94 bucket 113: 10% bucket 94: 90% bucket 106: 90% bucket 109: 40% Getting block 116 of 212 Reserving size (5249070) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: Sorting block time: 00:00:03 Returning block of 4727017 for bucket 88 bucket 116: 10% bucket 100: 80% bucket 112: 10% bucket 106: 60% Getting block 117 of 212 Reserving size (5249070) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: Sorting block time: 00:00:02 Returning block of 3606364 for bucket 92 bucket 101: 80% bucket 101: 100% Sorting block of length 3273161 for bucket 101 (Using difference cover) bucket 97: 80% bucket 100: 100% Sorting block of length 4565839 for bucket 100 (Using difference cover) bucket 104: 60% Sorting block time: 00:00:02 Returning block of 3905191 for bucket 86 Getting block 118 of 212 Reserving size (5249070) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: bucket 107: 50% bucket 110: 20% bucket 93: 90% Getting block 119 of 212 Reserving size (5249070) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: bucket 98: 100% Sorting block of length 3148396 for bucket 98 (Using difference cover) bucket 93: 90% bucket 114: 10% bucket 92: 100% Sorting block of length 4501654 for bucket 92 (Using difference cover) bucket 97: 90% bucket 102: 70% bucket 114: 10% bucket 105: 90% bucket 109: 40% bucket 110: 20% bucket 95: 100% Sorting block of length 4048614 for bucket 95 (Using difference cover) bucket 105: 70% bucket 102: 80% bucket 99: 90% bucket 96: 90% bucket 107: 80% bucket 113: 20% bucket 116: 20% bucket 99: 80% bucket 91: 100% Sorting block of length 4890091 for bucket 91 (Using difference cover) bucket 90: 100% Sorting block of length 3966832 for bucket 90 (Using difference cover) bucket 115: 10% bucket 113: 20% Sorting block time: 00:00:02 Returning block of 4087070 for bucket 96 bucket 98: 90% Getting block 120 of 212 Reserving size (5249070) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 106: 100% Sorting block of length 659233 for bucket 106 (Using difference cover) bucket 111: 20% bucket 115: 10% bucket 104: 100% Sorting block of length 2058501 for bucket 104 (Using difference cover) bucket 103: 70% Sorting block time: 00:00:03 Returning block of 3757160 for bucket 95 bucket 108: 80% Sorting block time: 00:00:01 Returning block of 659234 for bucket 106 Sorting block time: 00:00:03 Returning block of 3273162 for bucket 101 Getting block 117 of 205 Reserving size (5249070) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: bucket 112: 20% bucket 90: 100% Sorting block of length 3997708 for bucket 90 (Using difference cover) Getting block 121 of 212 Reserving size (5249070) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: Getting block 122 of 212 Reserving size (5249070) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 103: 90% bucket 112: 30% bucket 94: 100% Sorting block of length 5248520 for bucket 94 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3148397 for bucket 98 bucket 118: 10% bucket 116: 10% bucket 109: 50% bucket 93: 100% Sorting block of length 1107867 for bucket 93 (Using difference cover) bucket 111: 20% Sorting block time: 00:00:03 Returning block of 4565840 for bucket 100 Getting block 123 of 212 Reserving size (5249070) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 116: 30% bucket 110: 30% bucket 108: 60% Sorting block time: 00:00:02 Returning block of 4501655 for bucket 92 bucket 117: 10% Getting block 118 of 205 Reserving size (5249070) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: Getting block 119 of 205 Reserving size (5249070) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: bucket 97: 90% bucket 106: 70% bucket 97: 100% Sorting block of length 3110406 for bucket 97 (Using difference cover) bucket 104: 70% bucket 100: 90% bucket 109: 50% bucket 93: 100% Sorting block of length 2176355 for bucket 93 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1107868 for bucket 93 Getting block 120 of 205 Reserving size (5249070) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 114: 20% bucket 107: 60% Sorting block time: 00:00:02 Returning block of 4048615 for bucket 95 bucket 107: 90% bucket 114: 20% Sorting block time: 00:00:02 Returning block of 2058502 for bucket 104 Getting block 121 of 205 Reserving size (5249070) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 105: 100% Sorting block of length 4688123 for bucket 105 (Using difference cover) Getting block 122 of 205 Reserving size (5249070) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 113: 30% bucket 101: 90% bucket 102: 90% bucket 110: 30% bucket 102: 80% bucket 115: 20% bucket 96: 100% Sorting block of length 4425702 for bucket 96 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3966833 for bucket 90 Getting block 124 of 212 Reserving size (5249070) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 113: 30% bucket 119: 10% bucket 105: 80% bucket 115: 20% bucket 112: 30% bucket 99: 90% bucket 117: 10% bucket 118: 20% bucket 108: 90% bucket 103: 80% bucket 121: 10% bucket 120: 10% Sorting block time: 00:00:04 Returning block of 4890092 for bucket 91 Sorting block time: 00:00:03 Returning block of 3997709 for bucket 90 Sorting block time: 00:00:02 Returning block of 2176356 for bucket 93 bucket 116: 40% Getting block 123 of 205 Reserving size (5249070) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 112: 40% Getting block 124 of 205 Reserving size (5249070) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: Getting block 125 of 212 Reserving size (5249070) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: bucket 98: 100% Sorting block of length 5036548 for bucket 98 (Using difference cover) bucket 116: 20% bucket 109: 60% bucket 111: 30% bucket 110: 40% bucket 122: 10% bucket 99: 100% Sorting block of length 4438739 for bucket 99 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3110407 for bucket 97 bucket 111: 30% Getting block 125 of 205 Reserving size (5249070) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: bucket 103: 100% Sorting block of length 4680357 for bucket 103 (Using difference cover) bucket 117: 20% Sorting block time: 00:00:04 Returning block of 5248521 for bucket 94 bucket 119: 10% bucket 109: 60% bucket 118: 10% Getting block 126 of 205 Reserving size (5249070) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: bucket 123: 10% bucket 108: 70% bucket 104: 80% bucket 115: 30% bucket 107: 100% Sorting block of length 5245681 for bucket 107 (Using difference cover) bucket 106: 80% bucket 121: 10% bucket 97: 100% Sorting block of length 2485207 for bucket 97 (Using difference cover) bucket 100: 100% Sorting block of length 2332646 for bucket 100 (Using difference cover) bucket 120: 10% bucket 102: 100% Sorting block of length 3606950 for bucket 102 (Using difference cover) bucket 114: 30% bucket 107: 70% bucket 120: 20% bucket 114: 30% bucket 110: 40% bucket 122: 10% Sorting block time: 00:00:04 Returning block of 4688124 for bucket 105 bucket 102: 90% bucket 99: 100% Sorting block of length 3164919 for bucket 99 (Using difference cover) bucket 101: 100% Sorting block of length 5098517 for bucket 101 (Using difference cover) bucket 113: 40% bucket 121: 20% bucket 119: 20% bucket 112: 50% Getting block 127 of 205 Reserving size (5249070) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: Sorting block time: 00:00:03 Returning block of 4425703 for bucket 96 bucket 113: 40% bucket 108: 100% Sorting block of length 1850301 for bucket 108 (Using difference cover) Getting block 128 of 205 Reserving size (5249070) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: bucket 115: 30% bucket 112: 40% bucket 103: 90% Sorting block time: 00:00:01 Returning block of 2485208 for bucket 97 bucket 116: 30% bucket 105: 90% Getting block 126 of 212 Reserving size (5249070) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: bucket 118: 30% Sorting block time: 00:00:03 Returning block of 4438740 for bucket 99 bucket 116: 50% bucket 124: 10% bucket 124: 10% bucket 123: 10% bucket 115: 40% bucket 117: 20% Getting block 129 of 205 Reserving size (5249070) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: Sorting block time: 00:00:02 Returning block of 2332647 for bucket 100 Getting block 127 of 212 Reserving size (5249070) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 109: 70% bucket 110: 50% bucket 109: 70% bucket 111: 40% bucket 125: 10% bucket 122: 20% Sorting block time: 00:00:03 Returning block of 4680358 for bucket 103 Sorting block time: 00:00:02 Returning block of 1850302 for bucket 108 bucket 123: 20% Getting block 130 of 205 Reserving size (5249070) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: Sorting block time: 00:00:04 Returning block of 5036549 for bucket 98 bucket 117: 30% Getting block 131 of 205 Reserving size (5249070) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 126: 10% bucket 119: 20% bucket 118: 20% bucket 120: 20% Getting block 132 of 205 Reserving size (5249070) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 111: 40% Sorting block time: 00:00:02 Returning block of 3164920 for bucket 99 bucket 125: 10% bucket 114: 40% bucket 115: 50% Getting block 128 of 212 Reserving size (5249070) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: bucket 108: 80% bucket 121: 20% Sorting block time: 00:00:03 Returning block of 3606951 for bucket 102 bucket 122: 20% bucket 104: 90% bucket 113: 50% bucket 114: 40% Getting block 133 of 205 Reserving size (5249070) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 127: 10% Sorting block time: 00:00:04 Returning block of 5245682 for bucket 107 bucket 110: 50% bucket 106: 90% bucket 116: 60% Getting block 134 of 205 Reserving size (5249070) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 107: 80% bucket 119: 30% bucket 115: 40% bucket 121: 30% bucket 113: 50% bucket 120: 30% bucket 126: 10% bucket 128: 10% bucket 105: 100% Sorting block of length 3519856 for bucket 105 (Using difference cover) bucket 103: 100% Sorting block of length 4372913 for bucket 103 (Using difference cover) bucket 112: 60% bucket 124: 20% bucket 129: 10% bucket 117: 30% Sorting block time: 00:00:04 Returning block of 5098518 for bucket 101 bucket 116: 40% bucket 124: 20% bucket 112: 50% bucket 102: 100% Sorting block of length 4353270 for bucket 102 (Using difference cover) bucket 125: 20% bucket 109: 80% bucket 127: 10% Getting block 135 of 205 Reserving size (5249070) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 118: 40% bucket 123: 20% bucket 115: 60% bucket 128: 10% bucket 122: 30% bucket 123: 30% bucket 109: 80% bucket 126: 20% bucket 110: 60% bucket 130: 10% bucket 111: 50% bucket 131: 10% bucket 117: 40% bucket 114: 50% bucket 108: 90% bucket 132: 10% bucket 120: 30% bucket 119: 30% bucket 118: 30% bucket 124: 30% bucket 125: 20% bucket 121: 30% bucket 110: 60% bucket 104: 100% Sorting block of length 2322834 for bucket 104 (Using difference cover) bucket 133: 10% bucket 120: 40% bucket 115: 70% bucket 124: 30% bucket 113: 60% bucket 127: 20% bucket 128: 20% bucket 111: 50% bucket 116: 70% Sorting block time: 00:00:03 Returning block of 3519857 for bucket 105 bucket 119: 40% bucket 122: 30% Getting block 129 of 212 Reserving size (5249070) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: Sorting block time: 00:00:03 Returning block of 4372914 for bucket 103 bucket 121: 40% bucket 113: 60% bucket 125: 30% bucket 114: 50% bucket 109: 90% Getting block 130 of 212 Reserving size (5249070) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: Sorting block time: 00:00:02 Returning block of 4353271 for bucket 102 bucket 135: 10% bucket 129: 20% bucket 116: 50% bucket 127: 20% Getting block 131 of 212 Reserving size (5249070) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 134: 10% bucket 128: 20% bucket 107: 90% bucket 112: 60% bucket 123: 30% bucket 117: 40% bucket 112: 70% bucket 106: 100% Sorting block of length 2932090 for bucket 106 (Using difference cover) bucket 115: 50% bucket 126: 20% bucket 109: 90% Sorting block time: 00:00:01 Returning block of 2322835 for bucket 104 Getting block 132 of 212 Reserving size (5249070) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 124: 40% bucket 118: 50% bucket 110: 70% bucket 115: 80% bucket 122: 40% bucket 130: 20% bucket 123: 40% bucket 126: 30% bucket 132: 20% bucket 111: 60% bucket 114: 60% bucket 120: 40% bucket 117: 50% bucket 131: 20% bucket 110: 70% bucket 124: 40% bucket 108: 100% Sorting block of length 4389187 for bucket 108 (Using difference cover) bucket 121: 40% bucket 119: 40% bucket 120: 50% bucket 133: 20% bucket 116: 80% bucket 118: 40% bucket 134: 20% bucket 119: 50% bucket 113: 70% bucket 128: 30% bucket 127: 30% Sorting block time: 00:00:02 Returning block of 2932091 for bucket 106 bucket 113: 70% Getting block 133 of 212 Reserving size (5249070) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 111: 60% bucket 122: 40% bucket 125: 30% bucket 121: 50% bucket 125: 40% bucket 109: 100% Sorting block of length 2938739 for bucket 109 (Using difference cover) bucket 115: 90% bucket 129: 10% bucket 116: 60% bucket 112: 80% bucket 130: 10% bucket 135: 20% bucket 129: 30% bucket 127: 30% bucket 131: 10% bucket 126: 40% bucket 123: 40% bucket 126: 30% bucket 117: 50% bucket 112: 70% bucket 114: 60% bucket 115: 60% bucket 109: 100% Sorting block of length 3934787 for bucket 109 (Using difference cover) bucket 107: 100% Sorting block of length 3421601 for bucket 107 (Using difference cover) bucket 128: 30% bucket 124: 50% bucket 110: 80% bucket 114: 70% bucket 122: 50% bucket 118: 60% bucket 132: 30% bucket 130: 30% bucket 111: 70% bucket 123: 50% bucket 121: 50% bucket 115: 100% Sorting block of length 2733553 for bucket 115 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2938740 for bucket 109 bucket 132: 10% bucket 117: 60% Sorting block time: 00:00:02 Returning block of 4389188 for bucket 108 Getting block 134 of 212 Reserving size (5249070) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 134: 30% Getting block 135 of 212 Reserving size (5249070) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 110: 80% bucket 124: 50% bucket 120: 50% bucket 116: 90% bucket 113: 80% bucket 131: 30% bucket 113: 80% bucket 133: 30% bucket 120: 60% bucket 128: 40% bucket 119: 50% bucket 116: 70% bucket 127: 40% bucket 122: 50% bucket 118: 50% bucket 129: 40% bucket 119: 60% bucket 117: 60% bucket 125: 50% Sorting block time: 00:00:02 Returning block of 2733554 for bucket 115 bucket 129: 20% bucket 112: 90% bucket 121: 60% Getting block 136 of 205 Reserving size (5249070) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: Sorting block time: 00:00:03 Returning block of 3421602 for bucket 107 Sorting block time: 00:00:03 Returning block of 3934788 for bucket 109 bucket 127: 40% bucket 133: 10% bucket 135: 30% Getting block 136 of 212 Reserving size (5249070) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: Getting block 137 of 205 Reserving size (5249070) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 123: 50% bucket 125: 40% bucket 126: 50% bucket 110: 90% bucket 126: 40% bucket 115: 70% bucket 114: 70% bucket 131: 20% bucket 111: 70% bucket 114: 80% bucket 130: 40% bucket 132: 40% bucket 118: 70% bucket 124: 60% bucket 112: 80% bucket 130: 20% bucket 121: 60% bucket 122: 60% bucket 113: 90% bucket 134: 10% bucket 123: 60% bucket 117: 70% bucket 131: 40% bucket 135: 10% bucket 134: 40% bucket 127: 50% bucket 128: 50% bucket 124: 60% bucket 111: 80% bucket 120: 60% bucket 116: 100% Sorting block of length 3400502 for bucket 116 (Using difference cover) bucket 128: 40% bucket 116: 80% bucket 126: 60% bucket 117: 70% bucket 120: 70% bucket 113: 90% bucket 118: 60% bucket 133: 20% bucket 110: 90% bucket 122: 60% bucket 133: 40% bucket 123: 60% bucket 119: 60% bucket 121: 70% bucket 135: 40% bucket 132: 20% bucket 137: 10% bucket 112: 100% Sorting block of length 2987962 for bucket 112 (Using difference cover) bucket 129: 30% bucket 129: 50% bucket 125: 60% bucket 113: 100% Sorting block of length 5030466 for bucket 113 (Using difference cover) bucket 127: 50% bucket 125: 50% bucket 124: 70% bucket 115: 80% bucket 110: 100% Sorting block of length 2461016 for bucket 110 (Using difference cover) bucket 114: 80% bucket 136: 10% bucket 123: 70% bucket 126: 50% bucket 130: 50% bucket 117: 80% bucket 132: 50% bucket 111: 80% bucket 136: 10% bucket 119: 70% bucket 122: 70% bucket 118: 80% bucket 131: 50% Sorting block time: 00:00:02 Returning block of 3400503 for bucket 116 bucket 124: 70% bucket 114: 90% bucket 134: 20% Getting block 138 of 205 Reserving size (5249070) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 121: 70% bucket 130: 30% bucket 112: 90% bucket 127: 60% bucket 134: 50% bucket 131: 30% bucket 128: 60% bucket 135: 20% bucket 135: 50% bucket 117: 80% bucket 111: 90% Sorting block time: 00:00:02 Returning block of 2987963 for bucket 112 bucket 120: 80% bucket 120: 70% bucket 126: 70% Getting block 137 of 212 Reserving size (5249070) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 128: 50% Sorting block time: 00:00:01 Returning block of 2461017 for bucket 110 bucket 116: 90% bucket 113: 100% Sorting block of length 2958404 for bucket 113 (Using difference cover) bucket 118: 70% bucket 133: 30% Getting block 138 of 212 Reserving size (5249070) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 122: 70% bucket 123: 70% bucket 133: 50% bucket 125: 70% bucket 137: 20% bucket 119: 70% bucket 121: 80% bucket 110: 100% Sorting block of length 4773358 for bucket 110 (Using difference cover) bucket 136: 20% bucket 131: 60% bucket 129: 40% bucket 124: 80% bucket 130: 60% bucket 132: 60% bucket 132: 30% bucket 123: 80% bucket 129: 60% bucket 117: 90% bucket 115: 90% bucket 127: 60% bucket 112: 100% Sorting block of length 4678203 for bucket 112 (Using difference cover) bucket 114: 90% Sorting block time: 00:00:04 Returning block of 5030467 for bucket 113 bucket 122: 80% bucket 130: 40% bucket 121: 80% bucket 138: 10% Sorting block time: 00:00:02 Returning block of 2958405 for bucket 113 bucket 128: 70% Getting block 139 of 205 Reserving size (5249070) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 135: 60% bucket 136: 20% Getting block 139 of 212 Reserving size (5249070) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 134: 60% bucket 117: 90% bucket 126: 60% bucket 111: 90% bucket 127: 70% bucket 118: 90% bucket 126: 80% bucket 119: 80% bucket 137: 10% bucket 111: 100% Sorting block of length 2051023 for bucket 111 (Using difference cover) bucket 124: 80% bucket 134: 30% bucket 114: 100% Sorting block of length 3881044 for bucket 114 (Using difference cover) bucket 120: 80% bucket 125: 60% bucket 135: 30% bucket 125: 80% bucket 118: 80% bucket 133: 60% bucket 137: 30% bucket 119: 80% bucket 122: 80% bucket 116: 100% Sorting block of length 2845623 for bucket 116 (Using difference cover) bucket 138: 10% bucket 136: 30% bucket 120: 90% bucket 131: 40% bucket 133: 40% bucket 128: 60% bucket 123: 80% Sorting block time: 00:00:03 Returning block of 4773359 for bucket 110 bucket 132: 70% Sorting block time: 00:00:01 Returning block of 2051024 for bucket 111 bucket 114: 100% Sorting block of length 1192269 for bucket 114 (Using difference cover) bucket 130: 70% Getting block 140 of 205 Reserving size (5249070) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: Getting block 141 of 205 Reserving size (5249070) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 129: 50% bucket 124: 90% bucket 115: 100% Sorting block of length 4873112 for bucket 115 (Using difference cover) bucket 131: 70% Sorting block time: 00:00:03 Returning block of 4678204 for bucket 112 bucket 129: 70% bucket 134: 70% Getting block 142 of 205 Reserving size (5249070) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 123: 90% bucket 117: 100% Sorting block of length 2531330 for bucket 117 (Using difference cover) bucket 128: 80% bucket 121: 90% bucket 127: 70% bucket 117: 100% Sorting block of length 4149694 for bucket 117 (Using difference cover) bucket 127: 80% Sorting block time: 00:00:01 Returning block of 1192270 for bucket 114 bucket 139: 10% Getting block 140 of 212 Reserving size (5249070) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: bucket 122: 90% bucket 121: 90% bucket 118: 100% Sorting block of length 5203283 for bucket 118 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3881045 for bucket 114 bucket 126: 90% bucket 132: 40% bucket 119: 90% bucket 139: 10% bucket 135: 70% Getting block 143 of 205 Reserving size (5249070) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 130: 50% bucket 136: 30% bucket 125: 90% bucket 126: 70% bucket 120: 90% Sorting block time: 00:00:02 Returning block of 2845624 for bucket 116 bucket 138: 20% bucket 134: 40% bucket 118: 90% Getting block 141 of 212 Reserving size (5249070) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 137: 20% bucket 111: 100% Sorting block of length 4752232 for bucket 111 (Using difference cover) bucket 119: 90% bucket 125: 70% bucket 137: 40% bucket 133: 70% bucket 120: 100% Sorting block of length 2790629 for bucket 120 (Using difference cover) bucket 135: 40% Sorting block time: 00:00:02 Returning block of 2531331 for bucket 117 bucket 138: 20% bucket 124: 100% Sorting block of length 4021839 for bucket 124 (Using difference cover) Getting block 144 of 205 Reserving size (5249070) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 124: 90% bucket 131: 50% bucket 122: 90% bucket 140: 10% bucket 141: 10% bucket 123: 90% bucket 128: 90% bucket 130: 80% bucket 128: 70% bucket 133: 50% bucket 136: 40% bucket 132: 80% bucket 129: 60% bucket 131: 80% Sorting block time: 00:00:03 Returning block of 4873113 for bucket 115 bucket 127: 90% bucket 134: 80% bucket 129: 80% bucket 123: 100% Sorting block of length 2497678 for bucket 123 (Using difference cover) bucket 139: 20% Getting block 142 of 212 Reserving size (5249070) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 142: 10% Sorting block time: 00:00:03 Returning block of 4149695 for bucket 117 bucket 121: 100% Sorting block of length 3421979 for bucket 121 (Using difference cover) bucket 122: 100% Sorting block of length 3324851 for bucket 122 (Using difference cover) Getting block 143 of 212 Reserving size (5249070) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 121: 100% Sorting block of length 4481369 for bucket 121 (Using difference cover) bucket 135: 80% bucket 139: 20% bucket 126: 100% Sorting block of length 3851847 for bucket 126 (Using difference cover) bucket 143: 10% bucket 127: 80% bucket 140: 10% Sorting block time: 00:00:02 Returning block of 2790630 for bucket 120 Getting block 144 of 212 Reserving size (5249070) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 138: 30% bucket 130: 60% bucket 125: 100% Sorting block of length 4170618 for bucket 125 (Using difference cover) bucket 119: 100% Sorting block of length 3027155 for bucket 119 (Using difference cover) bucket 134: 50% bucket 118: 100% Sorting block of length 3202587 for bucket 118 (Using difference cover) bucket 120: 100% Sorting block of length 4945080 for bucket 120 (Using difference cover) bucket 126: 80% Sorting block time: 00:00:04 Returning block of 5203284 for bucket 118 bucket 141: 10% bucket 132: 50% bucket 119: 100% Sorting block of length 4977089 for bucket 119 (Using difference cover) bucket 137: 30% bucket 133: 80% bucket 136: 40% bucket 140: 20% Getting block 145 of 212 Reserving size (5249070) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 137: 50% Sorting block time: 00:00:04 Returning block of 4752233 for bucket 111 bucket 141: 20% bucket 128: 100% Sorting block of length 3498206 for bucket 128 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4021840 for bucket 124 Getting block 146 of 212 Reserving size (5249070) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: bucket 123: 100% Sorting block of length 4732914 for bucket 123 (Using difference cover) bucket 144: 10% Getting block 145 of 205 Reserving size (5249070) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 122: 100% Sorting block of length 3018664 for bucket 122 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2497679 for bucket 123 Getting block 147 of 212 Reserving size (5249070) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 130: 90% bucket 138: 30% bucket 136: 50% bucket 131: 60% bucket 125: 80% bucket 124: 100% Sorting block of length 5019052 for bucket 124 (Using difference cover) bucket 139: 30% bucket 135: 50% Sorting block time: 00:00:02 Returning block of 3027156 for bucket 119 bucket 132: 90% bucket 131: 90% Getting block 146 of 205 Reserving size (5249070) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: Sorting block time: 00:00:03 Returning block of 3324852 for bucket 122 Sorting block time: 00:00:03 Returning block of 3421980 for bucket 121 bucket 127: 100% Sorting block of length 3813342 for bucket 127 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3851848 for bucket 126 bucket 134: 90% bucket 129: 90% bucket 128: 80% Getting block 148 of 212 Reserving size (5249070) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: Getting block 149 of 212 Reserving size (5249070) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: bucket 135: 90% Getting block 147 of 205 Reserving size (5249070) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 133: 60% Sorting block time: 00:00:02 Returning block of 3202588 for bucket 118 bucket 142: 20% Getting block 148 of 205 Reserving size (5249070) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 129: 70% bucket 143: 20% bucket 142: 10% Sorting block time: 00:00:04 Returning block of 4481370 for bucket 121 bucket 140: 30% bucket 127: 90% bucket 139: 30% bucket 143: 10% Sorting block time: 00:00:03 Returning block of 4170619 for bucket 125 Getting block 149 of 205 Reserving size (5249070) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: Sorting block time: 00:00:02 Returning block of 3018665 for bucket 122 bucket 133: 90% Getting block 150 of 205 Reserving size (5249070) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: Getting block 151 of 205 Reserving size (5249070) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 140: 20% Sorting block time: 00:00:02 Returning block of 3498207 for bucket 128 bucket 137: 60% Getting block 152 of 205 Reserving size (5249070) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: Sorting block time: 00:00:03 Returning block of 4945081 for bucket 120 bucket 138: 40% bucket 134: 60% bucket 144: 10% Getting block 153 of 205 Reserving size (5249070) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 130: 70% bucket 141: 20% bucket 132: 60% bucket 141: 30% bucket 145: 10% bucket 137: 40% Sorting block time: 00:00:04 Returning block of 4977090 for bucket 119 bucket 144: 20% Getting block 150 of 212 Reserving size (5249070) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 126: 90% bucket 147: 10% bucket 136: 60% Sorting block time: 00:00:03 Returning block of 4732915 for bucket 123 bucket 130: 100% Sorting block of length 5051445 for bucket 130 (Using difference cover) bucket 138: 40% bucket 146: 10% bucket 145: 10% Getting block 154 of 205 Reserving size (5249070) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 129: 100% Sorting block of length 2081067 for bucket 129 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3813343 for bucket 127 bucket 136: 50% Getting block 155 of 205 Reserving size (5249070) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: bucket 139: 40% bucket 140: 40% Sorting block time: 00:00:03 Returning block of 5019053 for bucket 124 bucket 134: 100% Sorting block of length 4460485 for bucket 134 (Using difference cover) bucket 132: 100% Sorting block of length 3799524 for bucket 132 (Using difference cover) bucket 135: 100% Sorting block of length 1479589 for bucket 135 (Using difference cover) bucket 125: 90% bucket 131: 70% Getting block 151 of 212 Reserving size (5249070) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 131: 100% Sorting block of length 1970805 for bucket 131 (Using difference cover) bucket 146: 10% bucket 135: 60% bucket 149: 10% bucket 148: 10% bucket 128: 90% bucket 142: 30% bucket 147: 10% bucket 143: 30% bucket 133: 70% bucket 129: 80% bucket 133: 100% Sorting block of length 4264564 for bucket 133 (Using difference cover) bucket 142: 20% bucket 127: 100% Sorting block of length 3351736 for bucket 127 (Using difference cover) bucket 152: 10% bucket 149: 10% Sorting block time: 00:00:02 Returning block of 2081068 for bucket 129 bucket 139: 40% Getting block 156 of 205 Reserving size (5249070) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 138: 50% Sorting block time: 00:00:01 Returning block of 1479590 for bucket 135 bucket 148: 10% bucket 137: 70% Getting block 157 of 205 Reserving size (5249070) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 143: 20% bucket 150: 10% bucket 140: 30% bucket 151: 10% Sorting block time: 00:00:01 Returning block of 1970806 for bucket 131 bucket 136: 70% Getting block 158 of 205 Reserving size (5249070) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: bucket 134: 70% bucket 132: 70% bucket 153: 10% bucket 140: 50% bucket 145: 20% bucket 137: 50% bucket 141: 40% bucket 141: 30% bucket 144: 20% bucket 139: 50% bucket 147: 20% bucket 144: 30% bucket 154: 10% bucket 145: 20% bucket 130: 80% bucket 150: 10% Sorting block time: 00:00:03 Returning block of 3799525 for bucket 132 bucket 138: 50% bucket 126: 100% Sorting block of length 4799182 for bucket 126 (Using difference cover) Getting block 159 of 205 Reserving size (5249070) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: Sorting block time: 00:00:04 Returning block of 5051446 for bucket 130 bucket 142: 40% bucket 146: 20% bucket 136: 60% Getting block 160 of 205 Reserving size (5249070) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: Sorting block time: 00:00:02 Returning block of 3351737 for bucket 127 Sorting block time: 00:00:03 Returning block of 4460486 for bucket 134 bucket 131: 80% bucket 146: 20% Getting block 152 of 212 Reserving size (5249070) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: bucket 148: 20% bucket 129: 90% bucket 155: 10% Getting block 161 of 205 Reserving size (5249070) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 143: 40% bucket 125: 100% Sorting block of length 1239902 for bucket 125 (Using difference cover) bucket 149: 20% Sorting block time: 00:00:02 Returning block of 4264565 for bucket 133 bucket 151: 10% bucket 128: 100% Sorting block of length 3427941 for bucket 128 (Using difference cover) Getting block 162 of 205 Reserving size (5249070) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 138: 60% bucket 136: 80% bucket 135: 70% bucket 157: 10% bucket 140: 40% bucket 156: 10% bucket 149: 20% bucket 152: 20% bucket 140: 60% bucket 147: 20% bucket 145: 30% bucket 137: 80% bucket 150: 20% Sorting block time: 00:00:01 Returning block of 1239903 for bucket 125 bucket 133: 80% Getting block 153 of 212 Reserving size (5249070) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 139: 50% bucket 151: 20% bucket 142: 30% bucket 143: 30% bucket 148: 20% bucket 139: 60% bucket 158: 10% bucket 144: 40% bucket 137: 60% bucket 141: 40% bucket 134: 80% bucket 132: 80% bucket 141: 50% bucket 154: 20% bucket 129: 100% Sorting block of length 3971018 for bucket 129 (Using difference cover) bucket 147: 30% bucket 144: 30% bucket 130: 90% bucket 150: 20% bucket 153: 20% Sorting block time: 00:00:03 Returning block of 4799183 for bucket 126 bucket 138: 60% Sorting block time: 00:00:02 Returning block of 3427942 for bucket 128 bucket 136: 70% bucket 159: 10% Getting block 154 of 212 Reserving size (5249070) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 131: 90% bucket 145: 30% Getting block 155 of 212 Reserving size (5249070) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: bucket 149: 30% bucket 148: 30% bucket 160: 10% bucket 140: 70% bucket 146: 30% bucket 152: 10% bucket 161: 10% bucket 155: 20% bucket 145: 40% bucket 146: 30% bucket 138: 70% bucket 156: 20% bucket 151: 20% bucket 143: 50% bucket 142: 50% bucket 136: 90% bucket 140: 50% bucket 157: 20% bucket 162: 10% bucket 149: 30% bucket 150: 30% bucket 147: 30% bucket 137: 90% bucket 139: 60% bucket 133: 90% bucket 141: 50% bucket 142: 40% Sorting block time: 00:00:03 Returning block of 3971019 for bucket 129 bucket 152: 30% bucket 143: 40% Getting block 156 of 212 Reserving size (5249070) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 141: 60% bucket 151: 30% bucket 153: 10% bucket 139: 70% bucket 132: 90% bucket 154: 30% bucket 135: 80% bucket 148: 30% bucket 137: 70% bucket 134: 90% bucket 144: 50% bucket 153: 30% bucket 150: 30% bucket 147: 40% bucket 158: 20% bucket 159: 20% bucket 156: 30% bucket 160: 20% bucket 131: 100% Sorting block of length 1709782 for bucket 131 (Using difference cover) bucket 137: 100% Sorting block of length 3707429 for bucket 137 (Using difference cover) bucket 145: 40% bucket 154: 10% bucket 138: 70% bucket 144: 40% bucket 146: 40% bucket 148: 40% bucket 161: 20% bucket 130: 100% Sorting block of length 4038336 for bucket 130 (Using difference cover) bucket 145: 50% bucket 138: 80% bucket 149: 40% bucket 146: 40% bucket 136: 100% Sorting block of length 4312247 for bucket 136 (Using difference cover) bucket 162: 20% bucket 155: 30% bucket 147: 40% bucket 142: 60% bucket 157: 30% bucket 149: 40% bucket 155: 10% bucket 152: 20% bucket 150: 40% bucket 140: 80% bucket 140: 60% bucket 156: 10% Sorting block time: 00:00:01 Returning block of 1709783 for bucket 131 bucket 143: 60% Getting block 157 of 212 Reserving size (5249070) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 151: 30% bucket 136: 80% bucket 141: 70% bucket 142: 50% bucket 152: 40% bucket 137: 80% bucket 133: 100% Sorting block of length 3839875 for bucket 133 (Using difference cover) bucket 139: 70% bucket 139: 80% bucket 141: 60% bucket 151: 40% bucket 154: 40% Sorting block time: 00:00:02 Returning block of 3707430 for bucket 137 bucket 143: 50% bucket 132: 100% Sorting block of length 5059566 for bucket 132 (Using difference cover) bucket 147: 50% Getting block 163 of 205 Reserving size (5249070) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: bucket 134: 100% Sorting block of length 4236027 for bucket 134 (Using difference cover) bucket 144: 60% bucket 159: 30% bucket 138: 80% bucket 138: 90% bucket 148: 40% bucket 160: 30% Sorting block time: 00:00:02 Returning block of 4038337 for bucket 130 bucket 153: 20% bucket 153: 40% bucket 146: 50% Sorting block time: 00:00:02 Returning block of 4312248 for bucket 136 bucket 150: 40% Getting block 158 of 212 Reserving size (5249070) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: bucket 135: 90% bucket 162: 30% bucket 156: 20% bucket 156: 40% Getting block 164 of 205 Reserving size (5249070) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 161: 30% bucket 144: 50% bucket 149: 50% bucket 154: 20% bucket 142: 70% bucket 158: 30% bucket 145: 50% bucket 155: 20% bucket 149: 50% bucket 147: 50% bucket 155: 40% bucket 145: 60% bucket 146: 50% bucket 157: 40% bucket 150: 50% bucket 140: 70% bucket 148: 50% Sorting block time: 00:00:02 Returning block of 3839876 for bucket 133 bucket 152: 30% Getting block 159 of 212 Reserving size (5249070) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 157: 10% bucket 140: 90% bucket 139: 90% bucket 143: 70% bucket 137: 90% bucket 152: 50% bucket 136: 90% bucket 142: 60% bucket 141: 80% bucket 151: 50% bucket 147: 60% bucket 141: 70% bucket 154: 50% bucket 139: 80% Sorting block time: 00:00:03 Returning block of 4236028 for bucket 134 bucket 143: 60% bucket 151: 40% Sorting block time: 00:00:04 Returning block of 5059567 for bucket 132 bucket 156: 30% Getting block 160 of 212 Reserving size (5249070) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 138: 100% Sorting block of length 3889999 for bucket 138 (Using difference cover) bucket 159: 40% Getting block 161 of 212 Reserving size (5249070) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 144: 70% bucket 163: 10% bucket 149: 60% bucket 160: 40% bucket 138: 90% bucket 144: 60% bucket 156: 50% bucket 158: 40% bucket 161: 40% bucket 153: 30% bucket 158: 10% bucket 135: 100% Sorting block of length 2137111 for bucket 135 (Using difference cover) bucket 153: 50% bucket 162: 40% bucket 150: 50% bucket 164: 10% bucket 142: 80% bucket 146: 60% bucket 145: 70% bucket 139: 100% Sorting block of length 4582307 for bucket 139 (Using difference cover) bucket 157: 50% bucket 154: 30% bucket 148: 50% bucket 155: 50% bucket 149: 60% bucket 156: 40% bucket 150: 60% bucket 140: 80% bucket 159: 10% bucket 148: 60% bucket 151: 60% bucket 155: 30% bucket 152: 40% bucket 137: 100% Sorting block of length 2104372 for bucket 137 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2137112 for bucket 135 Sorting block time: 00:00:02 Returning block of 3890000 for bucket 138 bucket 142: 70% bucket 136: 100% Sorting block of length 3344799 for bucket 136 (Using difference cover) Getting block 162 of 212 Reserving size (5249070) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 146: 60% bucket 151: 50% Getting block 165 of 205 Reserving size (5249070) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 145: 60% bucket 147: 70% bucket 144: 80% bucket 147: 60% bucket 149: 70% bucket 157: 20% bucket 152: 60% bucket 159: 50% bucket 139: 90% bucket 160: 10% bucket 143: 70% bucket 141: 80% bucket 143: 80% bucket 163: 20% bucket 154: 60% bucket 140: 100% Sorting block of length 4996188 for bucket 140 (Using difference cover) bucket 141: 90% bucket 158: 50% bucket 138: 100% Sorting block of length 4226035 for bucket 138 (Using difference cover) bucket 164: 20% Sorting block time: 00:00:02 Returning block of 2104373 for bucket 137 bucket 153: 60% Getting block 163 of 212 Reserving size (5249070) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: bucket 161: 50% bucket 161: 10% bucket 156: 50% bucket 144: 70% bucket 156: 60% bucket 162: 50% bucket 160: 50% bucket 142: 90% Sorting block time: 00:00:03 Returning block of 4582308 for bucket 139 bucket 153: 40% Getting block 166 of 205 Reserving size (5249070) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 157: 60% Sorting block time: 00:00:02 Returning block of 3344800 for bucket 136 bucket 158: 20% Getting block 164 of 212 Reserving size (5249070) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 150: 60% bucket 150: 70% bucket 145: 80% bucket 140: 90% bucket 159: 20% bucket 155: 60% bucket 148: 70% bucket 154: 40% bucket 149: 70% bucket 146: 70% bucket 165: 10% bucket 151: 70% bucket 152: 50% bucket 147: 80% bucket 142: 80% bucket 151: 60% bucket 146: 70% bucket 155: 40% bucket 149: 80% bucket 148: 60% bucket 144: 90% bucket 145: 70% bucket 139: 100% Sorting block of length 5059179 for bucket 139 (Using difference cover) bucket 144: 80% bucket 152: 70% bucket 141: 100% Sorting block of length 1018654 for bucket 141 (Using difference cover) bucket 162: 10% bucket 163: 10% bucket 143: 80% bucket 158: 60% bucket 141: 90% bucket 157: 30% bucket 159: 60% bucket 156: 70% Sorting block time: 00:00:03 Returning block of 4226036 for bucket 138 bucket 147: 70% Sorting block time: 00:00:04 Returning block of 4996189 for bucket 140 Sorting block time: 00:00:01 Returning block of 1018655 for bucket 141 Getting block 165 of 212 Reserving size (5249070) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: Getting block 167 of 205 Reserving size (5249070) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: bucket 154: 70% bucket 160: 20% bucket 153: 70% bucket 161: 60% Getting block 168 of 205 Reserving size (5249070) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 143: 90% bucket 161: 20% bucket 156: 60% bucket 162: 60% bucket 150: 70% bucket 166: 10% bucket 142: 100% Sorting block of length 4567997 for bucket 142 (Using difference cover) bucket 163: 30% bucket 160: 60% bucket 157: 70% bucket 151: 70% bucket 164: 30% bucket 164: 10% bucket 159: 30% bucket 150: 80% bucket 151: 80% bucket 148: 80% bucket 153: 50% bucket 146: 80% bucket 155: 70% bucket 140: 100% Sorting block of length 2581107 for bucket 140 (Using difference cover) bucket 145: 90% bucket 149: 80% bucket 147: 90% bucket 152: 80% bucket 146: 80% bucket 152: 60% bucket 158: 30% bucket 148: 70% bucket 159: 70% bucket 154: 50% bucket 149: 90% bucket 143: 100% Sorting block of length 4618245 for bucket 143 (Using difference cover) bucket 144: 100% Sorting block of length 4015774 for bucket 144 (Using difference cover) bucket 158: 70% bucket 165: 20% bucket 163: 20% bucket 145: 80% bucket 144: 90% bucket 155: 50% bucket 141: 100% Sorting block of length 5204693 for bucket 141 (Using difference cover) bucket 142: 90% bucket 143: 90% Sorting block time: 00:00:03 Returning block of 5059180 for bucket 139 bucket 162: 20% bucket 151: 80% bucket 167: 10% Getting block 166 of 212 Reserving size (5249070) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 165: 10% bucket 160: 30% bucket 168: 10% bucket 154: 80% bucket 156: 80% bucket 163: 40% bucket 162: 70% bucket 161: 30% bucket 157: 40% bucket 150: 90% bucket 147: 80% Sorting block time: 00:00:02 Returning block of 2581108 for bucket 140 bucket 153: 80% Sorting block time: 00:00:03 Returning block of 4567998 for bucket 142 Getting block 167 of 212 Reserving size (5249070) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: Getting block 169 of 205 Reserving size (5249070) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 150: 80% bucket 157: 80% bucket 156: 70% bucket 161: 70% bucket 152: 90% bucket 166: 20% bucket 145: 100% Sorting block of length 5229720 for bucket 145 (Using difference cover) bucket 159: 40% bucket 149: 90% bucket 146: 90% bucket 148: 90% bucket 151: 90% bucket 160: 70% bucket 159: 80% bucket 151: 90% bucket 146: 90% bucket 147: 100% Sorting block of length 3224958 for bucket 147 (Using difference cover) bucket 153: 60% bucket 152: 70% bucket 164: 40% bucket 155: 80% bucket 164: 20% bucket 158: 40% bucket 163: 30% bucket 165: 30% Sorting block time: 00:00:03 Returning block of 4015775 for bucket 144 Sorting block time: 00:00:03 Returning block of 4618246 for bucket 143 bucket 148: 80% Getting block 170 of 205 Reserving size (5249070) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 142: 100% Sorting block of length 4822751 for bucket 142 (Using difference cover) Getting block 171 of 205 Reserving size (5249070) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 149: 100% Sorting block of length 3599704 for bucket 149 (Using difference cover) bucket 145: 90% bucket 160: 40% bucket 165: 20% bucket 167: 20% bucket 163: 50% bucket 144: 100% Sorting block of length 1639872 for bucket 144 (Using difference cover) bucket 154: 60% bucket 166: 10% bucket 143: 100% Sorting block of length 3658580 for bucket 143 (Using difference cover) bucket 155: 60% Sorting block time: 00:00:04 Returning block of 5204694 for bucket 141 bucket 147: 90% bucket 150: 100% Sorting block of length 5018638 for bucket 150 (Using difference cover) bucket 158: 80% bucket 154: 90% Getting block 168 of 212 Reserving size (5249070) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: Sorting block time: 00:00:00 Returning block of 1639873 for bucket 144 Getting block 169 of 212 Reserving size (5249070) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 167: 10% bucket 151: 100% Sorting block of length 3693442 for bucket 151 (Using difference cover) bucket 162: 30% bucket 157: 90% bucket 157: 50% bucket 153: 90% bucket 162: 80% Sorting block time: 00:00:02 Returning block of 3224959 for bucket 147 bucket 168: 20% bucket 149: 100% Sorting block of length 1065298 for bucket 149 (Using difference cover) bucket 166: 30% bucket 169: 10% Getting block 170 of 212 Reserving size (5249070) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 161: 40% bucket 148: 100% Sorting block of length 5070387 for bucket 148 (Using difference cover) bucket 156: 90% Sorting block time: 00:00:03 Returning block of 5229721 for bucket 145 bucket 156: 80% bucket 150: 90% bucket 161: 80% Getting block 171 of 212 Reserving size (5249070) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 152: 100% Sorting block of length 4484639 for bucket 152 (Using difference cover) bucket 160: 80% Sorting block time: 00:00:01 Returning block of 1065299 for bucket 149 bucket 164: 50% bucket 151: 100% Sorting block of length 3516565 for bucket 151 (Using difference cover) Getting block 172 of 212 Reserving size (5249070) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: bucket 153: 70% bucket 152: 80% bucket 171: 10% bucket 159: 90% Sorting block time: 00:00:03 Returning block of 3599705 for bucket 149 bucket 159: 50% bucket 160: 50% bucket 155: 90% bucket 146: 100% Sorting block of length 4830957 for bucket 146 (Using difference cover) bucket 167: 30% Getting block 172 of 205 Reserving size (5249070) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: bucket 165: 40% bucket 163: 40% bucket 165: 30% bucket 145: 100% Sorting block of length 4511824 for bucket 145 (Using difference cover) bucket 146: 100% Sorting block of length 1802060 for bucket 146 (Using difference cover) bucket 158: 50% bucket 163: 60% bucket 164: 30% Sorting block time: 00:00:04 Returning block of 4822752 for bucket 142 Sorting block time: 00:00:03 Returning block of 3658581 for bucket 143 bucket 167: 20% Sorting block time: 00:00:02 Returning block of 3693443 for bucket 151 Getting block 173 of 212 Reserving size (5249070) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: bucket 148: 90% Getting block 174 of 212 Reserving size (5249070) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 170: 10% Getting block 175 of 212 Reserving size (5249070) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 158: 90% bucket 166: 20% bucket 154: 70% bucket 168: 10% Sorting block time: 00:00:03 Returning block of 5018639 for bucket 150 bucket 169: 10% Getting block 173 of 205 Reserving size (5249070) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: bucket 154: 100% Sorting block of length 4642112 for bucket 154 (Using difference cover) bucket 166: 40% bucket 157: 100% Sorting block of length 3789935 for bucket 157 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1802061 for bucket 146 bucket 156: 100% Sorting block of length 2753493 for bucket 156 (Using difference cover) Getting block 174 of 205 Reserving size (5249070) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 155: 70% bucket 169: 20% bucket 152: 90% bucket 162: 90% bucket 156: 90% bucket 147: 100% Sorting block of length 5011715 for bucket 147 (Using difference cover) bucket 159: 60% bucket 171: 10% bucket 157: 60% bucket 162: 40% Sorting block time: 00:00:02 Returning block of 3516566 for bucket 151 bucket 170: 10% bucket 153: 100% Sorting block of length 4780864 for bucket 153 (Using difference cover) bucket 172: 10% bucket 163: 70% Getting block 175 of 205 Reserving size (5249070) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 164: 60% bucket 165: 40% bucket 150: 100% Sorting block of length 4926133 for bucket 150 (Using difference cover) bucket 168: 30% Sorting block time: 00:00:04 Returning block of 5070388 for bucket 148 bucket 160: 90% Sorting block time: 00:00:03 Returning block of 4484640 for bucket 152 Getting block 176 of 212 Reserving size (5249070) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: Getting block 176 of 205 Reserving size (5249070) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: bucket 161: 50% bucket 165: 50% Sorting block time: 00:00:03 Returning block of 4830958 for bucket 146 bucket 161: 90% bucket 167: 40% bucket 153: 80% bucket 172: 10% Getting block 177 of 212 Reserving size (5249070) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 155: 100% Sorting block of length 4915242 for bucket 155 (Using difference cover) bucket 160: 60% bucket 163: 50% Sorting block time: 00:00:02 Returning block of 2753494 for bucket 156 bucket 167: 30% bucket 159: 100% Sorting block of length 3959706 for bucket 159 (Using difference cover) Getting block 177 of 205 Reserving size (5249070) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 173: 10% bucket 170: 20% bucket 158: 100% Sorting block of length 5021320 for bucket 158 (Using difference cover) bucket 164: 40% bucket 174: 10% Sorting block time: 00:00:04 Returning block of 4511825 for bucket 145 bucket 171: 20% bucket 166: 50% bucket 173: 10% Getting block 178 of 205 Reserving size (5249070) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: bucket 158: 60% bucket 175: 10% bucket 166: 30% bucket 168: 20% bucket 163: 80% bucket 169: 20% bucket 148: 100% Sorting block of length 4683015 for bucket 148 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3789936 for bucket 157 bucket 154: 80% Getting block 179 of 205 Reserving size (5249070) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: Sorting block time: 00:00:03 Returning block of 4642113 for bucket 154 bucket 171: 20% bucket 165: 50% bucket 152: 100% Sorting block of length 3981311 for bucket 152 (Using difference cover) Getting block 180 of 205 Reserving size (5249070) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 159: 70% bucket 156: 100% Sorting block of length 3653351 for bucket 156 (Using difference cover) bucket 172: 20% Sorting block time: 00:00:03 Returning block of 5011716 for bucket 147 Sorting block time: 00:00:02 Returning block of 4780865 for bucket 153 bucket 168: 40% Sorting block time: 00:00:02 Returning block of 4926134 for bucket 150 bucket 157: 70% bucket 170: 20% bucket 169: 30% bucket 174: 10% Getting block 181 of 205 Reserving size (5249070) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: Getting block 182 of 205 Reserving size (5249070) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 155: 80% Getting block 178 of 212 Reserving size (5249070) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: bucket 162: 50% bucket 177: 10% bucket 176: 10% bucket 175: 10% bucket 162: 100% Sorting block of length 4814689 for bucket 162 (Using difference cover) bucket 165: 60% bucket 161: 100% Sorting block of length 4707868 for bucket 161 (Using difference cover) bucket 170: 30% bucket 163: 60% bucket 164: 70% bucket 167: 40% bucket 163: 90% bucket 164: 50% bucket 153: 90% bucket 160: 100% Sorting block of length 5134304 for bucket 160 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3959707 for bucket 159 bucket 176: 10% bucket 172: 20% bucket 160: 70% Sorting block time: 00:00:04 Returning block of 4915243 for bucket 155 bucket 173: 20% bucket 177: 10% Sorting block time: 00:00:03 Returning block of 5021321 for bucket 158 Getting block 183 of 205 Reserving size (5249070) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: bucket 174: 20% bucket 166: 60% Getting block 184 of 205 Reserving size (5249070) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 171: 30% bucket 178: 10% Getting block 185 of 205 Reserving size (5249070) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 161: 60% bucket 168: 30% bucket 167: 50% bucket 173: 20% Sorting block time: 00:00:03 Returning block of 3653352 for bucket 156 bucket 166: 40% Sorting block time: 00:00:03 Returning block of 4683016 for bucket 148 Getting block 179 of 212 Reserving size (5249070) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 168: 50% Getting block 186 of 205 Reserving size (5249070) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: Sorting block time: 00:00:03 Returning block of 3981312 for bucket 152 bucket 171: 30% bucket 179: 10% Getting block 180 of 212 Reserving size (5249070) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 175: 20% bucket 165: 60% bucket 158: 70% bucket 182: 10% bucket 180: 10% bucket 169: 30% bucket 163: 100% Sorting block of length 2930343 for bucket 163 (Using difference cover) bucket 169: 40% bucket 172: 30% bucket 181: 10% bucket 170: 30% bucket 177: 20% bucket 154: 90% bucket 159: 80% bucket 178: 10% bucket 176: 20% bucket 162: 60% bucket 164: 60% Sorting block time: 00:00:03 Returning block of 4814690 for bucket 162 bucket 163: 70% Sorting block time: 00:00:03 Returning block of 4707869 for bucket 161 bucket 160: 80% bucket 155: 90% bucket 170: 40% Getting block 187 of 205 bucket 157: 80% Reserving size (5249070) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: bucket 184: 10% bucket 167: 50% Getting block 188 of 205 Reserving size (5249070) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 166: 70% bucket 174: 20% bucket 175: 20% bucket 165: 70% bucket 176: 20% bucket 174: 30% bucket 173: 30% bucket 153: 100% Sorting block of length 3583665 for bucket 153 (Using difference cover) bucket 168: 40% bucket 164: 80% Sorting block time: 00:00:02 Returning block of 2930344 for bucket 163 bucket 178: 20% bucket 185: 10% Getting block 189 of 205 Reserving size (5249070) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 171: 40% bucket 182: 20% bucket 161: 70% bucket 172: 30% bucket 171: 40% bucket 166: 50% bucket 186: 10% bucket 165: 70% bucket 175: 30% bucket 177: 20% bucket 167: 60% Sorting block time: 00:00:04 Returning block of 5134305 for bucket 160 bucket 183: 10% bucket 172: 40% bucket 169: 50% Getting block 190 of 205 Reserving size (5249070) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 167: 60% bucket 179: 10% bucket 180: 10% bucket 177: 30% bucket 169: 40% bucket 158: 80% bucket 168: 60% bucket 180: 20% bucket 179: 20% bucket 176: 30% bucket 170: 40% bucket 178: 20% bucket 154: 100% Sorting block of length 4651343 for bucket 154 (Using difference cover) bucket 189: 10% bucket 187: 10% bucket 164: 70% bucket 163: 80% Sorting block time: 00:00:02 Returning block of 3583666 for bucket 153 bucket 160: 90% bucket 181: 20% bucket 162: 70% bucket 185: 20% bucket 168: 50% bucket 173: 30% bucket 175: 30% Getting block 181 of 212 Reserving size (5249070) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: bucket 184: 20% bucket 155: 100% Sorting block of length 2057547 for bucket 155 (Using difference cover) bucket 174: 40% bucket 159: 90% bucket 182: 30% bucket 174: 30% bucket 166: 80% bucket 173: 40% bucket 176: 30% bucket 170: 50% bucket 188: 10% bucket 157: 90% bucket 166: 60% bucket 164: 90% bucket 169: 60% bucket 171: 50% bucket 178: 30% bucket 168: 70% bucket 165: 80% bucket 165: 80% bucket 175: 40% bucket 171: 50% bucket 172: 40% bucket 186: 20% bucket 190: 10% bucket 183: 20% Sorting block time: 00:00:01 Returning block of 2057548 for bucket 155 bucket 161: 80% bucket 189: 20% Getting block 182 of 212 Reserving size (5249070) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 172: 50% bucket 167: 70% bucket 180: 20% bucket 169: 50% bucket 167: 70% bucket 179: 30% bucket 176: 40% bucket 180: 30% bucket 158: 90% bucket 170: 50% bucket 177: 40% bucket 177: 30% bucket 179: 20% bucket 187: 20% bucket 163: 90% bucket 178: 30% Sorting block time: 00:00:03 Returning block of 4651344 for bucket 154 bucket 181: 10% bucket 160: 100% Sorting block of length 4923441 for bucket 160 (Using difference cover) bucket 181: 30% bucket 164: 80% bucket 173: 50% bucket 185: 30% bucket 168: 60% bucket 184: 30% Getting block 183 of 212 Reserving size (5249070) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: bucket 173: 40% bucket 162: 80% bucket 174: 50% bucket 170: 60% bucket 159: 100% Sorting block of length 4913286 for bucket 159 (Using difference cover) bucket 182: 40% bucket 174: 40% bucket 166: 90% bucket 175: 40% bucket 189: 30% bucket 166: 70% bucket 172: 60% bucket 164: 100% Sorting block of length 2984424 for bucket 164 (Using difference cover) bucket 176: 40% bucket 157: 100% Sorting block of length 2496018 for bucket 157 (Using difference cover) bucket 165: 90% bucket 188: 20% bucket 171: 60% bucket 171: 60% bucket 169: 70% bucket 165: 90% bucket 167: 80% bucket 168: 80% bucket 172: 50% bucket 180: 30% bucket 175: 50% bucket 180: 40% bucket 183: 30% bucket 161: 90% bucket 182: 10% bucket 169: 60% bucket 186: 30% bucket 167: 80% bucket 183: 10% bucket 178: 40% bucket 170: 60% bucket 179: 40% bucket 176: 50% bucket 158: 100% Sorting block of length 4623061 for bucket 158 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2496019 for bucket 157 bucket 189: 40% Getting block 184 of 212 Reserving size (5249070) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 190: 20% bucket 163: 100% Sorting block of length 3026906 for bucket 163 (Using difference cover) bucket 173: 60% bucket 182: 50% bucket 177: 50% bucket 181: 20% bucket 168: 70% bucket 184: 40% Sorting block time: 00:00:02 Returning block of 2984425 for bucket 164 bucket 185: 40% bucket 187: 30% Getting block 191 of 205 Reserving size (5249070) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: bucket 174: 60% bucket 178: 40% Sorting block time: 00:00:04 Returning block of 4923442 for bucket 160 bucket 177: 40% bucket 171: 70% bucket 179: 30% bucket 166: 100% Sorting block of length 3494867 for bucket 166 (Using difference cover) Getting block 185 of 212 Reserving size (5249070) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 181: 40% Sorting block time: 00:00:03 Returning block of 4913287 for bucket 159 bucket 170: 70% Getting block 186 of 212 Reserving size (5249070) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: bucket 166: 80% bucket 175: 50% bucket 174: 50% bucket 173: 50% bucket 164: 90% bucket 165: 100% Sorting block of length 2820859 for bucket 165 (Using difference cover) bucket 167: 90% bucket 162: 90% bucket 183: 20% bucket 165: 100% Sorting block of length 5180735 for bucket 165 (Using difference cover) bucket 172: 70% Sorting block time: 00:00:02 Returning block of 3026907 for bucket 163 bucket 176: 50% bucket 175: 60% bucket 186: 40% Getting block 187 of 212 Reserving size (5249070) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: bucket 169: 70% bucket 189: 50% bucket 171: 70% bucket 188: 30% bucket 180: 50% bucket 169: 80% bucket 183: 40% bucket 182: 20% Sorting block time: 00:00:03 Returning block of 4623062 for bucket 158 bucket 170: 70% bucket 177: 60% bucket 179: 50% bucket 168: 90% bucket 172: 60% Getting block 188 of 212 Reserving size (5249070) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 161: 100% Sorting block of length 1847325 for bucket 161 (Using difference cover) bucket 180: 40% bucket 176: 60% bucket 184: 10% bucket 181: 30% bucket 184: 50% bucket 167: 90% bucket 178: 50% bucket 191: 10% Sorting block time: 00:00:02 Returning block of 3494868 for bucket 166 bucket 182: 60% bucket 173: 70% Getting block 192 of 205 Reserving size (5249070) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 185: 50% Sorting block time: 00:00:02 Returning block of 2820860 for bucket 165 bucket 190: 30% bucket 168: 80% bucket 187: 40% Sorting block time: 00:00:01 Returning block of 1847326 for bucket 161 Getting block 193 of 205 Reserving size (5249070) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: bucket 174: 70% Getting block 189 of 212 Reserving size (5249070) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 186: 10% bucket 175: 70% bucket 170: 80% bucket 185: 10% bucket 179: 40% bucket 166: 90% bucket 178: 50% bucket 171: 80% bucket 181: 50% bucket 175: 60% bucket 174: 60% bucket 173: 60% bucket 164: 100% Sorting block of length 5111423 for bucket 164 (Using difference cover) bucket 177: 70% bucket 177: 50% bucket 162: 100% Sorting block of length 5143111 for bucket 162 (Using difference cover) bucket 189: 60% bucket 180: 60% bucket 183: 50% bucket 176: 60% bucket 188: 40% bucket 186: 50% bucket 171: 80% bucket 178: 60% bucket 167: 100% Sorting block of length 5142675 for bucket 167 (Using difference cover) bucket 172: 70% bucket 172: 80% bucket 169: 80% bucket 183: 30% Sorting block time: 00:00:04 Returning block of 5180736 for bucket 165 bucket 182: 30% bucket 188: 10% Getting block 190 of 212 Reserving size (5249070) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 168: 100% Sorting block of length 5219877 for bucket 168 (Using difference cover) bucket 176: 70% bucket 175: 80% bucket 169: 90% bucket 185: 60% bucket 187: 10% bucket 168: 90% bucket 179: 60% bucket 190: 40% bucket 182: 70% bucket 192: 10% bucket 184: 60% bucket 167: 100% Sorting block of length 4990336 for bucket 167 (Using difference cover) bucket 170: 80% bucket 173: 80% bucket 187: 50% bucket 181: 40% bucket 193: 10% bucket 170: 90% bucket 184: 20% bucket 191: 20% bucket 180: 50% bucket 186: 20% bucket 181: 60% bucket 189: 10% bucket 174: 80% bucket 171: 90% bucket 185: 20% bucket 175: 70% bucket 166: 100% Sorting block of length 959732 for bucket 166 (Using difference cover) bucket 174: 70% bucket 178: 60% bucket 177: 60% bucket 189: 70% bucket 179: 50% Sorting block time: 00:00:03 Returning block of 5111424 for bucket 164 bucket 178: 70% bucket 173: 70% bucket 188: 50% bucket 172: 80% bucket 192: 20% bucket 180: 70% Getting block 191 of 212 Reserving size (5249070) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: Sorting block time: 00:00:01 Returning block of 959733 for bucket 166 Getting block 192 of 212 Reserving size (5249070) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 172: 90% bucket 186: 60% bucket 183: 60% bucket 170: 100% Sorting block of length 3181542 for bucket 170 (Using difference cover) bucket 177: 80% bucket 169: 90% Sorting block time: 00:00:03 Returning block of 5142676 for bucket 167 bucket 176: 70% bucket 190: 50% bucket 171: 90% bucket 191: 30% bucket 185: 70% bucket 179: 70% bucket 182: 80% bucket 169: 100% Sorting block of length 3317286 for bucket 169 (Using difference cover) Getting block 193 of 212 Reserving size (5249070) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: bucket 184: 70% bucket 176: 80% bucket 187: 60% Sorting block time: 00:00:04 Returning block of 5219878 for bucket 168 Sorting block time: 00:00:05 Returning block of 5143112 for bucket 162 bucket 188: 20% bucket 183: 40% bucket 175: 90% Getting block 194 of 212 Reserving size (5249070) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 193: 20% bucket 174: 90% bucket 180: 60% bucket 190: 10% bucket 186: 30% Sorting block time: 00:00:03 Returning block of 4990337 for bucket 167 Getting block 194 of 205 Reserving size (5249070) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 173: 90% bucket 187: 20% Getting block 195 of 205 Reserving size (5249070) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 182: 40% bucket 189: 80% bucket 181: 70% bucket 168: 100% Sorting block of length 4720339 for bucket 168 (Using difference cover) bucket 184: 30% bucket 189: 20% bucket 181: 50% bucket 175: 80% bucket 185: 30% bucket 178: 80% Sorting block time: 00:00:02 Returning block of 3181543 for bucket 170 bucket 171: 100% Sorting block of length 5232472 for bucket 171 (Using difference cover) bucket 172: 90% bucket 188: 60% Getting block 196 of 205 Reserving size (5249070) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 173: 80% Sorting block time: 00:00:02 Returning block of 3317287 for bucket 169 bucket 170: 90% bucket 183: 70% bucket 177: 90% bucket 174: 80% Getting block 197 of 205 Reserving size (5249070) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: bucket 191: 40% bucket 179: 60% bucket 192: 30% bucket 185: 80% bucket 186: 70% bucket 180: 80% bucket 184: 80% bucket 190: 60% bucket 176: 80% bucket 177: 70% bucket 169: 100% Sorting block of length 767033 for bucket 169 (Using difference cover) bucket 178: 70% bucket 192: 10% bucket 187: 70% bucket 171: 100% Sorting block of length 5238730 for bucket 171 (Using difference cover) bucket 179: 80% bucket 189: 90% bucket 182: 90% bucket 172: 100% Sorting block of length 3807263 for bucket 172 (Using difference cover) bucket 191: 10% bucket 193: 30% bucket 194: 10% Sorting block time: 00:00:01 Returning block of 767034 for bucket 169 Getting block 195 of 212 Reserving size (5249070) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 195: 10% bucket 194: 10% bucket 187: 30% bucket 190: 20% bucket 193: 10% bucket 188: 30% bucket 176: 90% bucket 180: 70% bucket 183: 50% bucket 186: 40% bucket 174: 100% Sorting block of length 4426032 for bucket 174 (Using difference cover) bucket 175: 90% bucket 173: 100% Sorting block of length 1581601 for bucket 173 (Using difference cover) bucket 175: 100% Sorting block of length 4101645 for bucket 175 (Using difference cover) bucket 196: 10% bucket 189: 30% Sorting block time: 00:00:04 Returning block of 4720340 for bucket 168 bucket 178: 90% bucket 197: 10% bucket 173: 90% Getting block 196 of 212 Reserving size (5249070) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 182: 50% bucket 188: 70% bucket 189: 100% Sorting block of length 5216439 for bucket 189 (Using difference cover) bucket 181: 60% bucket 185: 40% bucket 181: 80% bucket 190: 70% bucket 177: 100% Sorting block of length 4478068 for bucket 177 (Using difference cover) bucket 186: 80% bucket 172: 100% Sorting block of length 2987819 for bucket 172 (Using difference cover) bucket 184: 40% Sorting block time: 00:00:03 Returning block of 5232473 for bucket 171 bucket 174: 90% bucket 170: 100% Sorting block of length 5208224 for bucket 170 (Using difference cover) bucket 187: 80% bucket 183: 80% bucket 182: 100% Sorting block of length 2350885 for bucket 182 (Using difference cover) bucket 179: 90% bucket 179: 70% Sorting block time: 00:00:02 Returning block of 1581602 for bucket 173 bucket 191: 50% Getting block 197 of 212 Reserving size (5249070) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: bucket 180: 90% bucket 192: 40% bucket 192: 20% Getting block 198 of 205 Reserving size (5249070) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 178: 80% bucket 184: 90% Sorting block time: 00:00:03 Returning block of 3807264 for bucket 172 bucket 193: 40% bucket 176: 90% Getting block 198 of 212 Reserving size (5249070) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 185: 90% bucket 195: 20% bucket 194: 20% bucket 177: 80% bucket 187: 40% bucket 195: 10% bucket 194: 20% Sorting block time: 00:00:04 Returning block of 5238731 for bucket 171 bucket 190: 30% bucket 191: 20% Getting block 199 of 212 Reserving size (5249070) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: bucket 193: 20% Sorting block time: 00:00:01 Returning block of 2350886 for bucket 182 bucket 176: 100% Sorting block of length 3163943 for bucket 176 (Using difference cover) Getting block 199 of 205 Reserving size (5249070) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: Sorting block time: 00:00:02 Returning block of 4101646 for bucket 175 bucket 178: 100% Sorting block of length 4833070 for bucket 178 (Using difference cover) bucket 188: 40% bucket 183: 60% Getting block 200 of 212 Reserving size (5249070) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 186: 50% Sorting block time: 00:00:03 Returning block of 2987820 for bucket 172 bucket 188: 80% Sorting block time: 00:00:04 Returning block of 4426033 for bucket 174 bucket 180: 80% Getting block 200 of 205 Reserving size (5249070) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 196: 20% bucket 197: 20% Sorting block time: 00:00:03 Returning block of 5216440 for bucket 189 bucket 196: 10% bucket 189: 40% bucket 181: 90% bucket 183: 90% Getting block 201 of 212 Reserving size (5249070) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: bucket 192: 50% bucket 174: 100% Sorting block of length 4194266 for bucket 174 (Using difference cover) bucket 187: 90% bucket 175: 100% Sorting block of length 5160624 for bucket 175 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4478069 for bucket 177 Getting block 201 of 205 Reserving size (5249070) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: bucket 185: 50% bucket 173: 100% Sorting block of length 2395419 for bucket 173 (Using difference cover) Getting block 202 of 205 Reserving size (5249070) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 182: 60% bucket 181: 70% bucket 186: 90% bucket 184: 50% bucket 197: 10% bucket 180: 100% Sorting block of length 5033844 for bucket 180 (Using difference cover) bucket 184: 100% Sorting block of length 3888263 for bucket 184 (Using difference cover) bucket 190: 80% bucket 198: 10% bucket 179: 100% Sorting block of length 2973144 for bucket 179 (Using difference cover) bucket 185: 100% Sorting block of length 4073511 for bucket 185 (Using difference cover) bucket 193: 50% bucket 192: 30% bucket 177: 90% bucket 179: 80% bucket 199: 10% bucket 198: 10% bucket 191: 60% bucket 178: 90% Sorting block time: 00:00:03 Returning block of 3163944 for bucket 176 Sorting block time: 00:00:02 Returning block of 2395420 for bucket 173 bucket 194: 30% Getting block 202 of 212 Reserving size (5249070) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: Getting block 203 of 205 Reserving size (5249070) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: bucket 194: 30% bucket 187: 50% bucket 195: 30% bucket 190: 40% Sorting block time: 00:00:04 Returning block of 5208225 for bucket 170 bucket 199: 10% bucket 176: 100% Sorting block of length 4704822 for bucket 176 (Using difference cover) bucket 195: 20% Getting block 203 of 212 Reserving size (5249070) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: bucket 188: 90% bucket 197: 30% bucket 196: 30% bucket 200: 10% bucket 192: 60% Sorting block time: 00:00:04 Returning block of 4833071 for bucket 178 Sorting block time: 00:00:03 Returning block of 4194267 for bucket 174 bucket 191: 30% Getting block 204 of 205 Reserving size (5249070) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: bucket 183: 100% Sorting block of length 3032631 for bucket 183 (Using difference cover) bucket 196: 20% Sorting block time: 00:00:02 Returning block of 2973145 for bucket 179 bucket 180: 90% bucket 193: 30% bucket 201: 10% bucket 201: 10% Getting block 205 of 205 Reserving size (5249070) for bucket 205 Calculating Z arrays for bucket 205 Entering block accumulator loop for bucket 205: bucket 202: 10% Sorting block time: 00:00:02 Returning block of 3888264 for bucket 184 bucket 200: 10% bucket 187: 100% Sorting block of length 5086119 for bucket 187 (Using difference cover) bucket 189: 50% bucket 186: 100% Sorting block of length 3522105 for bucket 186 (Using difference cover) bucket 186: 60% bucket 199: 20% bucket 190: 90% bucket 197: 20% bucket 183: 70% Sorting block time: 00:00:03 Returning block of 4073512 for bucket 185 Sorting block time: 00:00:03 Returning block of 5033845 for bucket 180 bucket 193: 60% Sorting block time: 00:00:04 Returning block of 5160625 for bucket 175 bucket 198: 20% bucket 188: 50% bucket 181: 100% Sorting block of length 4118455 for bucket 181 (Using difference cover) bucket 185: 60% bucket 177: 100% Sorting block of length 4306713 for bucket 177 (Using difference cover) bucket 181: 80% bucket 191: 70% bucket 202: 10% Sorting block time: 00:00:02 Returning block of 4704823 for bucket 176 bucket 194: 40% bucket 192: 40% bucket 203: 10% bucket 184: 60% bucket 195: 40% bucket 187: 60% Sorting block time: 00:00:02 Returning block of 3032632 for bucket 183 bucket 194: 40% bucket 190: 50% bucket 205: 10% bucket 188: 100% Sorting block of length 4292950 for bucket 188 (Using difference cover) bucket 195: 30% bucket 182: 70% bucket 198: 20% bucket 200: 20% bucket 199: 20% bucket 178: 100% Sorting block of length 4908494 for bucket 178 (Using difference cover) bucket 197: 40% bucket 203: 10% bucket 199: 30% bucket 196: 40% bucket 192: 70% Sorting block time: 00:00:03 Returning block of 3522106 for bucket 186 bucket 204: 10% bucket 202: 20% bucket 205: 20% bucket 179: 90% bucket 198: 30% Sorting block time: 00:00:03 Returning block of 5086120 for bucket 187 bucket 201: 20% bucket 190: 100% Sorting block of length 2697937 for bucket 190 (Using difference cover) bucket 197: 30% bucket 191: 40% bucket 193: 40% bucket 181: 90% bucket 200: 20% Sorting block time: 00:00:02 Returning block of 4118456 for bucket 181 bucket 191: 80% bucket 196: 30% Sorting block time: 00:00:02 Returning block of 4306714 for bucket 177 bucket 201: 20% bucket 193: 70% bucket 203: 20% Getting block 204 of 212 Reserving size (5249070) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: bucket 183: 80% bucket 189: 60% bucket 185: 70% bucket 180: 100% Sorting block of length 4772377 for bucket 180 (Using difference cover) bucket 188: 60% bucket 202: 20% bucket 190: 60% bucket 195: 50% bucket 186: 70% bucket 205: 30% bucket 197: 50% bucket 194: 50% bucket 192: 50% bucket 200: 30% bucket 198: 30% bucket 184: 70% bucket 195: 40% Sorting block time: 00:00:02 Returning block of 4292951 for bucket 188 bucket 187: 70% bucket 201: 30% bucket 202: 30% bucket 199: 40% bucket 204: 20% Sorting block time: 00:00:03 Returning block of 4908495 for bucket 178 bucket 192: 80% bucket 198: 40% Sorting block time: 00:00:02 Returning block of 2697938 for bucket 190 bucket 199: 30% bucket 196: 50% bucket 194: 50% Getting block 205 of 212 Reserving size (5249070) for bucket 205 Calculating Z arrays for bucket 205 Entering block accumulator loop for bucket 205: bucket 205: 40% bucket 203: 20% bucket 203: 30% bucket 197: 40% bucket 182: 80% bucket 193: 50% bucket 179: 100% Sorting block of length 3345345 for bucket 179 (Using difference cover) bucket 200: 30% bucket 195: 60% bucket 196: 40% bucket 201: 40% bucket 188: 70% bucket 181: 100% Sorting block of length 2358668 for bucket 181 (Using difference cover) bucket 191: 90% bucket 189: 70% bucket 197: 60% bucket 193: 80% bucket 200: 40% bucket 191: 50% bucket 202: 40% bucket 201: 30% bucket 204: 10% bucket 185: 80% bucket 194: 60% bucket 192: 60% bucket 205: 50% bucket 199: 40% Sorting block time: 00:00:03 Returning block of 4772378 for bucket 180 bucket 196: 60% bucket 183: 90% bucket 204: 30% bucket 202: 30% Getting block 206 of 212 Reserving size (5249070) for bucket 206 Calculating Z arrays for bucket 206 Entering block accumulator loop for bucket 206: bucket 203: 40% bucket 190: 70% bucket 186: 80% bucket 195: 50% bucket 184: 80% bucket 187: 80% bucket 182: 90% Sorting block time: 00:00:01 Returning block of 2358669 for bucket 181 bucket 198: 40% Sorting block time: 00:00:01 Returning block of 3345346 for bucket 179 bucket 198: 50% bucket 192: 90% bucket 193: 60% Getting block 207 of 212 Reserving size (5249070) for bucket 207 Calculating Z arrays for bucket 207 Entering block accumulator loop for bucket 207: bucket 203: 30% bucket 205: 10% Getting block 208 of 212 Reserving size (5249070) for bucket 208 Calculating Z arrays for bucket 208 Entering block accumulator loop for bucket 208: bucket 195: 70% bucket 194: 60% bucket 199: 50% bucket 205: 60% bucket 197: 50% bucket 200: 50% bucket 201: 50% bucket 196: 70% bucket 202: 50% bucket 191: 100% Sorting block of length 5248736 for bucket 191 (Using difference cover) bucket 196: 50% bucket 194: 70% bucket 188: 80% bucket 197: 70% bucket 200: 40% bucket 193: 90% bucket 189: 80% bucket 201: 40% bucket 191: 60% bucket 199: 50% bucket 204: 20% bucket 185: 90% bucket 208: 10% bucket 205: 70% bucket 205: 20% bucket 204: 40% bucket 192: 70% bucket 184: 90% bucket 183: 100% Sorting block of length 5074877 for bucket 183 (Using difference cover) bucket 207: 10% bucket 203: 50% bucket 206: 10% bucket 186: 90% bucket 199: 60% bucket 195: 80% bucket 195: 60% bucket 196: 80% bucket 192: 100% Sorting block of length 5066715 for bucket 192 (Using difference cover) bucket 194: 70% bucket 198: 60% bucket 196: 60% bucket 182: 100% Sorting block of length 3089921 for bucket 182 (Using difference cover) bucket 203: 40% bucket 202: 40% bucket 187: 90% bucket 200: 60% bucket 190: 80% bucket 193: 70% bucket 201: 60% bucket 198: 50% bucket 197: 60% bucket 205: 80% Sorting block time: 00:00:02 Returning block of 5248737 for bucket 191 bucket 202: 60% bucket 194: 80% bucket 193: 100% Sorting block of length 3511788 for bucket 193 (Using difference cover) bucket 197: 80% bucket 204: 50% bucket 205: 90% bucket 201: 50% bucket 200: 70% bucket 196: 90% bucket 199: 70% Sorting block time: 00:00:02 Returning block of 3089922 for bucket 182 bucket 195: 90% bucket 200: 50% bucket 199: 60% bucket 202: 70% bucket 189: 90% Getting block 209 of 212 Reserving size (5249070) for bucket 209 Calculating Z arrays for bucket 209 Entering block accumulator loop for bucket 209: bucket 185: 100% Sorting block of length 4176771 for bucket 185 (Using difference cover) bucket 198: 70% bucket 206: 20% bucket 188: 90% bucket 207: 20% bucket 201: 70% bucket 191: 70% bucket 184: 100% Sorting block of length 4927027 for bucket 184 (Using difference cover) bucket 208: 20% Sorting block time: 00:00:03 Returning block of 5074878 for bucket 183 bucket 203: 60% bucket 192: 80% Sorting block time: 00:00:03 Returning block of 5066716 for bucket 192 bucket 205: 30% Getting block 210 of 212 Reserving size (5249070) for bucket 210 Calculating Z arrays for bucket 210 Entering block accumulator loop for bucket 210: bucket 203: 50% bucket 204: 30% bucket 202: 50% bucket 196: 70% bucket 198: 60% Sorting block time: 00:00:01 Returning block of 3511789 for bucket 193 bucket 194: 90% bucket 205: 100% Sorting block of length 2377300 for bucket 205 (Using difference cover) bucket 190: 90% bucket 186: 100% Sorting block of length 4433972 for bucket 186 (Using difference cover) bucket 187: 100% Sorting block of length 3126506 for bucket 187 (Using difference cover) bucket 193: 80% bucket 195: 70% bucket 197: 70% bucket 194: 80% bucket 204: 60% bucket 199: 70% Sorting block time: 00:00:02 Returning block of 4176772 for bucket 185 Getting block 211 of 212 Reserving size (5249070) for bucket 211 Calculating Z arrays for bucket 211 Entering block accumulator loop for bucket 211: bucket 201: 60% bucket 200: 60% Sorting block time: 00:00:01 Returning block of 2377301 for bucket 205 bucket 198: 80% bucket 202: 80% bucket 189: 100% Sorting block of length 2128178 for bucket 189 (Using difference cover) bucket 209: 10% bucket 199: 80% bucket 206: 30% bucket 191: 80% bucket 201: 80% bucket 200: 80% bucket 195: 100% Sorting block of length 3472927 for bucket 195 (Using difference cover) bucket 198: 70% bucket 197: 90% bucket 196: 100% Sorting block of length 4280220 for bucket 196 (Using difference cover) bucket 192: 90% bucket 188: 100% Sorting block of length 5127167 for bucket 188 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3126507 for bucket 187 bucket 202: 60% Getting block 212 of 212 Reserving size (5249070) for bucket 212 Calculating Z arrays for bucket 212 Entering block accumulator loop for bucket 212: bucket 205: 40% bucket 207: 30% bucket 203: 70% Sorting block time: 00:00:04 Returning block of 4927028 for bucket 184 bucket 194: 100% Sorting block of length 3315360 for bucket 194 (Using difference cover) bucket 204: 70% bucket 190: 100% Sorting block of length 4646135 for bucket 190 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4433973 for bucket 186 Sorting block time: 00:00:01 Returning block of 2128179 for bucket 189 bucket 197: 80% bucket 208: 30% bucket 210: 10% bucket 199: 80% Sorting block time: 00:00:02 Returning block of 3472928 for bucket 195 bucket 204: 40% bucket 196: 80% bucket 195: 80% Sorting block time: 00:00:02 Returning block of 4280221 for bucket 196 bucket 203: 60% bucket 211: 10% bucket 201: 90% bucket 194: 90% Sorting block time: 00:00:01 Returning block of 3315361 for bucket 194 bucket 198: 90% bucket 193: 90% bucket 197: 100% Sorting block of length 4765861 for bucket 197 (Using difference cover) bucket 202: 90% bucket 200: 90% bucket 203: 80% bucket 201: 70% bucket 199: 90% Sorting block time: 00:00:03 Returning block of 5127168 for bucket 188 Sorting block time: 00:00:02 Returning block of 4646136 for bucket 190 bucket 192: 100% Sorting block of length 4323862 for bucket 192 (Using difference cover) bucket 212: 10% bucket 204: 80% bucket 198: 80% bucket 202: 70% bucket 205: 50% Sorting block time: 00:00:02 Returning block of 4765862 for bucket 197 bucket 197: 90% bucket 200: 100% Sorting block of length 4319350 for bucket 200 (Using difference cover) bucket 206: 40% bucket 200: 70% bucket 201: 100% Sorting block of length 2740032 for bucket 201 (Using difference cover) bucket 198: 100% Sorting block of length 1419315 for bucket 198 (Using difference cover) bucket 191: 90% bucket 199: 90% bucket 195: 90% Sorting block time: 00:00:02 Returning block of 4323863 for bucket 192 bucket 202: 100% Sorting block of length 4036884 for bucket 202 (Using difference cover) bucket 209: 20% bucket 211: 20% bucket 203: 90% bucket 199: 100% Sorting block of length 4417789 for bucket 199 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1419316 for bucket 198 bucket 204: 90% Sorting block time: 00:00:01 Returning block of 2740033 for bucket 201 bucket 207: 40% bucket 210: 20% bucket 201: 80% bucket 208: 40% bucket 204: 50% bucket 196: 90% Sorting block time: 00:00:02 Returning block of 4319351 for bucket 200 Sorting block time: 00:00:01 Returning block of 4036885 for bucket 202 bucket 198: 90% bucket 202: 80% bucket 203: 100% Sorting block of length 3674026 for bucket 203 (Using difference cover) bucket 203: 70% Sorting block time: 00:00:01 Returning block of 4417790 for bucket 199 bucket 205: 60% bucket 212: 20% bucket 204: 100% Sorting block of length 3234647 for bucket 204 (Using difference cover) bucket 193: 100% Sorting block of length 3691576 for bucket 193 (Using difference cover) bucket 197: 100% Sorting block of length 3664917 for bucket 197 (Using difference cover) bucket 194: 100% Sorting block of length 3790758 for bucket 194 (Using difference cover) bucket 199: 100% Sorting block of length 2553718 for bucket 199 (Using difference cover) bucket 195: 100% Sorting block of length 5032593 for bucket 195 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3674027 for bucket 203 Sorting block time: 00:00:02 Returning block of 3234648 for bucket 204 bucket 201: 90% bucket 200: 80% bucket 206: 50% bucket 191: 100% Sorting block of length 4392287 for bucket 191 (Using difference cover) bucket 211: 30% bucket 209: 30% bucket 198: 100% Sorting block of length 3085497 for bucket 198 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2553719 for bucket 199 Sorting block time: 00:00:01 Returning block of 3691577 for bucket 193 bucket 212: 30% bucket 202: 90% bucket 203: 80% Sorting block time: 00:00:01 Returning block of 3790759 for bucket 194 Sorting block time: 00:00:01 Returning block of 3664918 for bucket 197 bucket 210: 30% bucket 205: 70% bucket 207: 50% Sorting block time: 00:00:02 Returning block of 5032594 for bucket 195 Sorting block time: 00:00:01 Returning block of 4392288 for bucket 191 Sorting block time: 00:00:01 Returning block of 3085498 for bucket 198 bucket 208: 50% bucket 204: 60% bucket 196: 100% Sorting block of length 2895942 for bucket 196 (Using difference cover) bucket 201: 100% Sorting block of length 1687133 for bucket 201 (Using difference cover) bucket 212: 40% Sorting block time: 00:00:02 Returning block of 2895943 for bucket 196 Sorting block time: 00:00:01 Returning block of 1687134 for bucket 201 bucket 211: 40% bucket 202: 100% Sorting block of length 5099610 for bucket 202 (Using difference cover) bucket 203: 90% bucket 205: 80% bucket 200: 90% bucket 206: 60% bucket 212: 50% bucket 209: 40% bucket 208: 60% bucket 210: 40% bucket 207: 60% Sorting block time: 00:00:02 Returning block of 5099611 for bucket 202 bucket 211: 50% bucket 204: 70% bucket 203: 100% Sorting block of length 3865393 for bucket 203 (Using difference cover) bucket 205: 90% bucket 212: 60% bucket 208: 70% Sorting block time: 00:00:02 Returning block of 3865394 for bucket 203 bucket 200: 100% Sorting block of length 4211743 for bucket 200 (Using difference cover) bucket 206: 70% bucket 209: 50% bucket 211: 60% bucket 205: 100% Sorting block of length 2619236 for bucket 205 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4211744 for bucket 200 bucket 212: 70% bucket 210: 50% bucket 207: 70% bucket 204: 80% bucket 208: 80% Sorting block time: 00:00:01 Returning block of 2619237 for bucket 205 bucket 209: 60% bucket 212: 80% bucket 211: 70% bucket 206: 80% bucket 212: 90% bucket 207: 80% bucket 210: 60% bucket 208: 90% bucket 204: 90% bucket 211: 80% bucket 212: 100% Sorting block of length 4955850 for bucket 212 (Using difference cover) bucket 209: 70% bucket 206: 90% bucket 207: 90% bucket 210: 70% bucket 211: 90% bucket 208: 100% Sorting block of length 1062725 for bucket 208 (Using difference cover) bucket 204: 100% Sorting block of length 4865997 for bucket 204 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1062726 for bucket 208 Sorting block time: 00:00:02 Returning block of 4955851 for bucket 212 Sorting block time: 00:00:01 Returning block of 4865998 for bucket 204 bucket 209: 80% bucket 207: 100% Sorting block of length 2533078 for bucket 207 (Using difference cover) bucket 211: 100% Sorting block of length 4829944 for bucket 211 (Using difference cover) bucket 206: 100% Sorting block of length 2773264 for bucket 206 (Using difference cover) bucket 210: 80% Sorting block time: 00:00:01 Returning block of 2533079 for bucket 207 Sorting block time: 00:00:01 Returning block of 2773265 for bucket 206 Sorting block time: 00:00:01 Returning block of 4829945 for bucket 211 bucket 209: 90% bucket 210: 90% bucket 210: 100% Sorting block of length 4721103 for bucket 210 (Using difference cover) bucket 209: 100% Sorting block of length 4682897 for bucket 209 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4682898 for bucket 209 Sorting block time: 00:00:02 Returning block of 4721104 for bucket 210 Exited Ebwt loop fchr[A]: 0 fchr[C]: 391954798 fchr[G]: 524347498 fchr[T]: 524347498 fchr[$]: 783861161 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 266840223 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 195965296 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 783861161 bwtLen: 783861162 sz: 195965291 bwtSz: 195965291 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 48991323 offsSz: 195965292 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 4082611 numLines: 4082611 ebwtTotLen: 261287104 ebwtTotSz: 261287104 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:05:25 Exited Ebwt loop fchr[A]: 0 fchr[C]: 259567700 fchr[G]: 259567700 fchr[T]: 391954798 fchr[$]: 783861161 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 266840223 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 195965296 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 783861161 bwtLen: 783861162 sz: 195965291 bwtSz: 195965291 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 48991323 offsSz: 195965292 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 4082611 numLines: 4082611 ebwtTotLen: 261287104 ebwtTotSz: 261287104 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:06:16 Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-103_S27_L005_R1_001_val_1.fq.gz to EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-103_S27_L005_R1_001_val_1.fq.gz (20349659 sequences in total) Writing a G -> A converted version of the input file EPI-103_S27_L005_R2_001_val_2.fq.gz to EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-103_S27_L005_R2_001_val_2.fq.gz (20349659 sequences in total) Input files are EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1512:1956_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 NGTTTATATGTATGTATTATATTTGTGTAGGTATTGTATTTGATAAGGAT #<<>> Writing bisulfite mapping results to EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2303:16672:27349_1:N:0:ATCACG Scaffold_09 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far 20349659 reads; of these: 20349659 (100.00%) were paired; of these: 13093446 (64.34%) aligned concordantly 0 times 3361315 (16.52%) aligned concordantly exactly 1 time 3894898 (19.14%) aligned concordantly >1 times 35.66% overall alignment rate 20349659 reads; of these: 20349659 (100.00%) were paired; of these: 13027775 (64.02%) aligned concordantly 0 times 3373694 (16.58%) aligned concordantly exactly 1 time 3948190 (19.40%) aligned concordantly >1 times 35.98% overall alignment rate Processed 20349659 sequences in total Successfully deleted the temporary files EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 20349659 Number of paired-end alignments with a unique best hit: 9095592 Mapping efficiency: 44.7% Sequence pairs with no alignments under any condition: 9572011 Sequence pairs did not map uniquely: 1682056 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4509438 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4586153 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 289949317 Total methylated C's in CpG context: 9619421 Total methylated C's in CHG context: 1310642 Total methylated C's in CHH context: 2350411 Total methylated C's in Unknown context: 40612 Total unmethylated C's in CpG context: 31065297 Total unmethylated C's in CHG context: 59905410 Total unmethylated C's in CHH context: 185698136 Total unmethylated C's in Unknown context: 609374 C methylated in CpG context: 23.6% C methylated in CHG context: 2.1% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.2% Bismark completed in 0d 1h 15m 14s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-104_S28_L005_R1_001_val_1.fq.gz to EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-104_S28_L005_R1_001_val_1.fq.gz (30015261 sequences in total) Writing a G -> A converted version of the input file EPI-104_S28_L005_R2_001_val_2.fq.gz to EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-104_S28_L005_R2_001_val_2.fq.gz (30015261 sequences in total) Input files are EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1112:1988_1:N:0:CGATGT/1 99 Scaffold_05_CT_converted 17340906 1 101M = 17341304 497 NGGTGGTAGTTATTAAGTATGTATATGTATTAAAAATTGAAATGAAAAATTATTTTATTAGTTTTTGAAATATTTTGGTATTATATTTAGAGGTGTTTGTG #<>> Writing bisulfite mapping results to EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1202:6821:3657_1:N:0:CGATGT Scaffold_09 2 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far 30015261 reads; of these: 30015261 (100.00%) were paired; of these: 18948145 (63.13%) aligned concordantly 0 times 5093125 (16.97%) aligned concordantly exactly 1 time 5973991 (19.90%) aligned concordantly >1 times 36.87% overall alignment rate 30015261 reads; of these: 30015261 (100.00%) were paired; of these: 18888567 (62.93%) aligned concordantly 0 times 5102104 (17.00%) aligned concordantly exactly 1 time 6024590 (20.07%) aligned concordantly >1 times 37.07% overall alignment rate Processed 30015261 sequences in total Successfully deleted the temporary files EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 30015261 Number of paired-end alignments with a unique best hit: 13633936 Mapping efficiency: 45.4% Sequence pairs with no alignments under any condition: 13665400 Sequence pairs did not map uniquely: 2715925 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6781130 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6852805 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 418448650 Total methylated C's in CpG context: 15436769 Total methylated C's in CHG context: 2036052 Total methylated C's in CHH context: 3597610 Total methylated C's in Unknown context: 67853 Total unmethylated C's in CpG context: 41191940 Total unmethylated C's in CHG context: 85561381 Total unmethylated C's in CHH context: 270624898 Total unmethylated C's in Unknown context: 900361 C methylated in CpG context: 27.3% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 7.0% Bismark completed in 0d 1h 52m 4s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-111_S29_L005_R1_001_val_1.fq.gz to EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-111_S29_L005_R1_001_val_1.fq.gz (27014996 sequences in total) Writing a G -> A converted version of the input file EPI-111_S29_L005_R2_001_val_2.fq.gz to EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-111_S29_L005_R2_001_val_2.fq.gz (27014996 sequences in total) Input files are EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1222:1965_1:N:0:TTAGGC/1 99 Scaffold_02_CT_converted 52423574 6 101M = 52423755 280 NTGATGAGTGATTTATAATGTTTTGTAGGTTTATTAAAAGATTGTGTTTGTGTTTGTAATTTTTTTGATATATTGTTAATTAAAGTTGGGATGGTTGGATT #<>> Writing bisulfite mapping results to EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2305:8726:65045_1:N:0:TTAGGC Scaffold_14 2 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far 27014996 reads; of these: 27014996 (100.00%) were paired; of these: 17004362 (2701499662.94 reads; of these:%) aligned concordantly 0 times 270149964645643 ( (17.20%) aligned concordantly exactly 1 time 5364991 (100.0019.86%%) were paired; of these:) aligned concordantly >1 times 37.0616931638% ( overall alignment rate62.67 %) aligned concordantly 0 times 4662317 (17.26%) aligned concordantly exactly 1 time 5421041 (20.07%) aligned concordantly >1 times 37.33% overall alignment rate Processed 27014996 sequences in total Successfully deleted the temporary files EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27014996 Number of paired-end alignments with a unique best hit: 12312883 Mapping efficiency: 45.6% Sequence pairs with no alignments under any condition: 12235438 Sequence pairs did not map uniquely: 2466675 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6118719 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6194163 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 377453061 Total methylated C's in CpG context: 13097257 Total methylated C's in CHG context: 1893893 Total methylated C's in CHH context: 2999476 Total methylated C's in Unknown context: 59372 Total unmethylated C's in CpG context: 39327878 Total unmethylated C's in CHG context: 76742866 Total unmethylated C's in CHH context: 243391691 Total unmethylated C's in Unknown context: 784343 C methylated in CpG context: 25.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 7.0% Bismark completed in 0d 1h 41m 46s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-113_S30_L005_R1_001_val_1.fq.gz to EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-113_S30_L005_R1_001_val_1.fq.gz (26302191 sequences in total) Writing a G -> A converted version of the input file EPI-113_S30_L005_R2_001_val_2.fq.gz to EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-113_S30_L005_R2_001_val_2.fq.gz (26302191 sequences in total) Input files are EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1442:1956_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 NTAGTATTTTTATTAGAAGAATTAGAAATATTAGTAATAGTAAATTATTAGGTAGTGATAATATTGTAAATGAGTAATTAAAGTATTTATTATATGTGATG #>> Writing bisulfite mapping results to EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16931:96627_1:N:0:TGACCA Scaffold_13 44396777 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far 26302191 reads; of these: 26302191 (100.00%) were paired; of these: 17013134 (64.68%) aligned concordantly 0 times 4367646 (16.61%) aligned concordantly exactly 1 time 4921411 (18.71%) aligned concordantly >1 times 35.32% overall alignment rate 26302191 reads; of these: 26302191 (100.00%) were paired; of these: 16935818 (64.39%) aligned concordantly 0 times 4415733 (16.79%) aligned concordantly exactly 1 time 4950640 (18.82%) aligned concordantly >1 times 35.61% overall alignment rate Processed 26302191 sequences in total Successfully deleted the temporary files EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 26302191 Number of paired-end alignments with a unique best hit: 11581686 Mapping efficiency: 44.0% Sequence pairs with no alignments under any condition: 12489960 Sequence pairs did not map uniquely: 2230545 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5744513 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5837172 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 359357698 Total methylated C's in CpG context: 12471829 Total methylated C's in CHG context: 1771590 Total methylated C's in CHH context: 2827755 Total methylated C's in Unknown context: 53715 Total unmethylated C's in CpG context: 37593518 Total unmethylated C's in CHG context: 73195958 Total unmethylated C's in CHH context: 231497048 Total unmethylated C's in Unknown context: 768555 C methylated in CpG context: 24.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.5% Bismark completed in 0d 1h 35m 41s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-119_S31_L005_R1_001_val_1.fq.gz to EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-119_S31_L005_R1_001_val_1.fq.gz (28905983 sequences in total) Writing a G -> A converted version of the input file EPI-119_S31_L005_R2_001_val_2.fq.gz to EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-119_S31_L005_R2_001_val_2.fq.gz (28905983 sequences in total) Input files are EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1132:1973_1:N:0:ACAGTG/1 99 Scaffold_12_CT_converted 4017483 2 93M = 4017483 -93 NTGGTGAAAATTTTGAAAATTGTTTAATAATGGTGTAAAATATTAATTTATATATTATTTTAGTAATTAGGGTGAAATATTTTGAAAGTAAGA #<>> Writing bisulfite mapping results to EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2302:14681:37197_1:N:0:ACAGTG Scaffold_16 2 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1304:7949:12013_1:N:0:ACAGTG Scaffold_16 2 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1215:10856:17476_1:N:0:ACAGTG Scaffold_16 2 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far 28905983 reads; of these: 28905983 (100.00%) were paired; of these: 19005598 (65.75%) aligned concordantly 0 times 4722302 (16.34%) aligned concordantly exactly 1 time 5178083 (17.91%) aligned concordantly >1 times 34.25% overall alignment rate 28905983 reads; of these: 28905983 (100.00%) were paired; of these: 19154447 (66.26%) aligned concordantly 0 times 4636303 (16.04%) aligned concordantly exactly 1 time 5115233 (17.70%) aligned concordantly >1 times 33.74% overall alignment rate Processed 28905983 sequences in total Successfully deleted the temporary files EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28905983 Number of paired-end alignments with a unique best hit: 12331889 Mapping efficiency: 42.7% Sequence pairs with no alignments under any condition: 14292877 Sequence pairs did not map uniquely: 2281217 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6078960 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6252926 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 389840146 Total methylated C's in CpG context: 12477704 Total methylated C's in CHG context: 1827358 Total methylated C's in CHH context: 3035063 Total methylated C's in Unknown context: 49011 Total unmethylated C's in CpG context: 45041606 Total unmethylated C's in CHG context: 80081549 Total unmethylated C's in CHH context: 247376866 Total unmethylated C's in Unknown context: 795814 C methylated in CpG context: 21.7% C methylated in CHG context: 2.2% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 5.8% Bismark completed in 0d 1h 42m 48s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-120_S32_L005_R1_001_val_1.fq.gz to EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-120_S32_L005_R1_001_val_1.fq.gz (24140505 sequences in total) Writing a G -> A converted version of the input file EPI-120_S32_L005_R2_001_val_2.fq.gz to EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-120_S32_L005_R2_001_val_2.fq.gz (24140505 sequences in total) Input files are EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1140:1995_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 NGTATTTGGTTATATTTTAATATTAAATTTTGATTAAAATAGTTGTTGAAAATTGATTAGTATTATTTAGGAAGTATAGAAGTGTTAATATAAAGTTAATT #<>> Writing bisulfite mapping results to EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2203:1403:16239_1:N:0:GCCAAT Scaffold_09 2 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2110:13197:92900_1:N:0:GCCAAT Scaffold_09 3 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2102:12972:86705_1:N:0:GCCAAT Scaffold_09 2 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far 24140505 reads; of these: 24140505 (100.00%) were paired; of these: 15202444 (62.97%) aligned concordantly 0 times 4175808 (17.30%) aligned concordantly exactly 1 time 4762253 (19.73%) aligned concordantly >1 times 37.03% overall alignment rate 24140505 reads; of these: 24140505 (100.00%) were paired; of these: 15252082 (63.18%) aligned concordantly 0 times 4174115 (17.29%) aligned concordantly exactly 1 time 4714308 (19.53%) aligned concordantly >1 times 36.82% overall alignment rate Processed 24140505 sequences in total Successfully deleted the temporary files EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24140505 Number of paired-end alignments with a unique best hit: 11050083 Mapping efficiency: 45.8% Sequence pairs with no alignments under any condition: 10973461 Sequence pairs did not map uniquely: 2116961 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5486119 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5563961 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 343610405 Total methylated C's in CpG context: 11964980 Total methylated C's in CHG context: 1672574 Total methylated C's in CHH context: 2746920 Total methylated C's in Unknown context: 46814 Total unmethylated C's in CpG context: 35958013 Total unmethylated C's in CHG context: 69824544 Total unmethylated C's in CHH context: 221443374 Total unmethylated C's in Unknown context: 719473 C methylated in CpG context: 25.0% C methylated in CHG context: 2.3% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.1% Bismark completed in 0d 1h 30m 38s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-127_S33_L005_R1_001_val_1.fq.gz to EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-127_S33_L005_R1_001_val_1.fq.gz (22262118 sequences in total) Writing a G -> A converted version of the input file EPI-127_S33_L005_R2_001_val_2.fq.gz to EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-127_S33_L005_R2_001_val_2.fq.gz (22262118 sequences in total) Input files are EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1259:1963_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 NTATTTATTTTTATATATTATTAAAAATTTATATTTTTATTATTAAAAATATAAATTTATATATTATTAATAATTTATTTTTATATTTTATTAATAAT #<>> Writing bisulfite mapping results to EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2302:15297:83758_1:N:0:CAGATC Scaffold_09 1 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far 22262118 reads; of these: 22262118 (100.00%) were paired; of these: 14211965 (63.84%) aligned concordantly 0 times 3770814 (16.94%) aligned concordantly exactly 1 time 4279339 (19.22%) aligned concordantly >1 times 36.16% overall alignment rate 22262118 reads; of these: 22262118 (100.00%) were paired; of these: 14293314 (64.20%) aligned concordantly 0 times 3750672 (16.85%) aligned concordantly exactly 1 time 4218132 (18.95%) aligned concordantly >1 times 35.80% overall alignment rate Processed 22262118 sequences in total Successfully deleted the temporary files EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22262118 Number of paired-end alignments with a unique best hit: 9986595 Mapping efficiency: 44.9% Sequence pairs with no alignments under any condition: 10417464 Sequence pairs did not map uniquely: 1858059 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4954421 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5032173 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 314010295 Total methylated C's in CpG context: 11042968 Total methylated C's in CHG context: 1520028 Total methylated C's in CHH context: 2541364 Total methylated C's in Unknown context: 47519 Total unmethylated C's in CpG context: 33055152 Total unmethylated C's in CHG context: 64128787 Total unmethylated C's in CHH context: 201721996 Total unmethylated C's in Unknown context: 647317 C methylated in CpG context: 25.0% C methylated in CHG context: 2.3% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.8% Bismark completed in 0d 1h 22m 1s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-128_S34_L005_R1_001_val_1.fq.gz to EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-128_S34_L005_R1_001_val_1.fq.gz (24557803 sequences in total) Writing a G -> A converted version of the input file EPI-128_S34_L005_R2_001_val_2.fq.gz to EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-128_S34_L005_R2_001_val_2.fq.gz (24557803 sequences in total) Input files are EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1617:1971_1:N:0:ACTTGA/1 99 Scaffold_07_CT_converted 39044038 2 98M = 39044221 281 NGAGATTATTTAATATAGATATGTGTTTAAGGTTTTGGTAGATATTGTTAATTATGATTATTGAGGTTATTTAATATAGATATGTTTTAAAGGTTTGG #<<>> Writing bisulfite mapping results to EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2107:9857:95864_1:N:0:ACTTGA Scaffold_16 2 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1116:4355:21006_1:N:0:ACTTGA Scaffold_16 2 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far 24557803 reads; of these: 24557803 (100.00%) were paired; of these: 15716613 (64.00%) aligned concordantly 0 times 4172368 (16.99%) aligned concordantly exactly 1 time 4668822 (19.01%) aligned concordantly >1 times 36.00% overall alignment rate 24557803 reads; of these: 24557803 (100.00%) were paired; of these: 15638441 (63.68%) aligned concordantly 0 times 4202494 (17.11%) aligned concordantly exactly 1 time 4716868 (19.21%) aligned concordantly >1 times 36.32% overall alignment rate Processed 24557803 sequences in total Successfully deleted the temporary files EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24557803 Number of paired-end alignments with a unique best hit: 11023912 Mapping efficiency: 44.9% Sequence pairs with no alignments under any condition: 11430018 Sequence pairs did not map uniquely: 2103873 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5468345 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5555565 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 342815591 Total methylated C's in CpG context: 12084385 Total methylated C's in CHG context: 1712206 Total methylated C's in CHH context: 2665031 Total methylated C's in Unknown context: 47752 Total unmethylated C's in CpG context: 36262181 Total unmethylated C's in CHG context: 69681804 Total unmethylated C's in CHH context: 220409984 Total unmethylated C's in Unknown context: 723863 C methylated in CpG context: 25.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.2% Bismark completed in 0d 1h 31m 5s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-135_S35_L005_R1_001_val_1.fq.gz to EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-135_S35_L005_R1_001_val_1.fq.gz (28731808 sequences in total) Writing a G -> A converted version of the input file EPI-135_S35_L005_R2_001_val_2.fq.gz to EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-135_S35_L005_R2_001_val_2.fq.gz (28731808 sequences in total) Input files are EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1469:1995_1:N:0:GATCAG/1 99 Scaffold_02_CT_converted 52412008 1 97M = 52412014 104 NTGTATTTGTTATATTTTTAAAATAAATTAAAATTTTAATTATTTGTTTATTTTGTTTTTTTGGAATTTTGAGTGTATATGTATTATATAATTTATT #<>> Writing bisulfite mapping results to EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1106:4844:54933_1:N:0:GATCAG Scaffold_16 2 Processed 28000000 sequence pairs so far 28731808 reads; of these: 28731808 (100.00%) were paired; of these: 18174330 (63.26%) aligned concordantly 0 times 4818195 (16.77%) aligned concordantly exactly 1 time 5739283 (19.98%) aligned concordantly >1 times 36.74% overall alignment rate 28731808 reads; of these: 28731808 (100.00%) were paired; of these: 18095326 (62.98%) aligned concordantly 0 times 4833538 (16.82%) aligned concordantly exactly 1 time 5802944 (20.20%) aligned concordantly >1 times 37.02% overall alignment rate Processed 28731808 sequences in total Successfully deleted the temporary files EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28731808 Number of paired-end alignments with a unique best hit: 12720631 Mapping efficiency: 44.3% Sequence pairs with no alignments under any condition: 13210078 Sequence pairs did not map uniquely: 2801099 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6307893 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6412737 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 379885177 Total methylated C's in CpG context: 14174074 Total methylated C's in CHG context: 2097825 Total methylated C's in CHH context: 3204273 Total methylated C's in Unknown context: 64166 Total unmethylated C's in CpG context: 39497431 Total unmethylated C's in CHG context: 77915331 Total unmethylated C's in CHH context: 242996243 Total unmethylated C's in Unknown context: 785379 C methylated in CpG context: 26.4% C methylated in CHG context: 2.6% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 7.6% Bismark completed in 0d 1h 43m 17s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-136_S36_L005_R1_001_val_1.fq.gz to EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-136_S36_L005_R1_001_val_1.fq.gz (27792315 sequences in total) Writing a G -> A converted version of the input file EPI-136_S36_L005_R2_001_val_2.fq.gz to EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-136_S36_L005_R2_001_val_2.fq.gz (27792315 sequences in total) Input files are EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1242:1980_1:N:0:TAGCTT/1 99 Scaffold_11_CT_converted 30489349 0 100M = 30489366 109 NATGGTTGGATTATTTTATAGTTAAAATATTATGAGGTGTATTGATTGTTTTATTTTGAGATGTTGTGTAGATATTGTTTTAATGGGGTGTAGTGTTTTT #<>> Writing bisulfite mapping results to EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1205:15387:22738_1:N:0:TAGCTT Scaffold_13 44396778 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far 27792315 reads; of these: 27792315 (100.00%) were paired; of these: 17640819 (63.47%) aligned concordantly 0 times 4583263 (16.49%) aligned concordantly exactly 1 time 5568233 (20.04%) aligned concordantly >1 times 36.53% overall alignment rate 27792315 reads; of these: 27792315 (100.00%) were paired; of these: 17566832 (63.21%) aligned concordantly 0 times 4600321 (16.55%) aligned concordantly exactly 1 time 5625162 (20.24%) aligned concordantly >1 times 36.79% overall alignment rate Processed 27792315 sequences in total Successfully deleted the temporary files EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27792315 Number of paired-end alignments with a unique best hit: 12229034 Mapping efficiency: 44.0% Sequence pairs with no alignments under any condition: 12912342 Sequence pairs did not map uniquely: 2650939 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6066303 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6162730 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 371098859 Total methylated C's in CpG context: 12526554 Total methylated C's in CHG context: 1883224 Total methylated C's in CHH context: 2923602 Total methylated C's in Unknown context: 54090 Total unmethylated C's in CpG context: 39735089 Total unmethylated C's in CHG context: 76137777 Total unmethylated C's in CHH context: 237892613 Total unmethylated C's in Unknown context: 810936 C methylated in CpG context: 24.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.3% Bismark completed in 0d 1h 38m 18s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-143_S37_L005_R1_001_val_1.fq.gz to EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-143_S37_L005_R1_001_val_1.fq.gz (21160872 sequences in total) Writing a G -> A converted version of the input file EPI-143_S37_L005_R2_001_val_2.fq.gz to EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-143_S37_L005_R2_001_val_2.fq.gz (21160872 sequences in total) Input files are EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1205:1956_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 NGAAGGAAAATGAATTGATAGTATTATAAGGTTTAAATTTGTTATTATTTTTATAATTTGTATTATTTTTATTATTATGTTATATTTTTATAAATAAATTT #<>> Writing bisulfite mapping results to EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2115:10166:97532_1:N:0:GGCTAC Scaffold_09 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far 21160872 reads; of these: 21160872 (100.00%) were paired; of these: 13590247 (64.22%) aligned concordantly 0 times 3523727 (16.65%) aligned concordantly exactly 1 time 4046898 (19.12%) aligned concordantly >1 times 35.78% overall alignment rate 21160872 reads; of these: 21160872 (100.00%) were paired; of these: 13649084 (64.50%) aligned concordantly 0 times 3511297 (16.59%) aligned concordantly exactly 1 time 4000491 (18.91%) aligned concordantly >1 times 35.50% overall alignment rate Processed 21160872 sequences in total Successfully deleted the temporary files EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 21160872 Number of paired-end alignments with a unique best hit: 9316819 Mapping efficiency: 44.0% Sequence pairs with no alignments under any condition: 10036514 Sequence pairs did not map uniquely: 1807539 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4624000 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4692818 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 288290011 Total methylated C's in CpG context: 10342749 Total methylated C's in CHG context: 1387455 Total methylated C's in CHH context: 2413979 Total methylated C's in Unknown context: 44158 Total unmethylated C's in CpG context: 29588909 Total unmethylated C's in CHG context: 58728884 Total unmethylated C's in CHH context: 185828035 Total unmethylated C's in Unknown context: 610790 C methylated in CpG context: 25.9% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 6.7% Bismark completed in 0d 1h 16m 22s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-145_S38_L005_R1_001_val_1.fq.gz to EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-145_S38_L005_R1_001_val_1.fq.gz (25314513 sequences in total) Writing a G -> A converted version of the input file EPI-145_S38_L005_R2_001_val_2.fq.gz to EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-145_S38_L005_R2_001_val_2.fq.gz (25314513 sequences in total) Input files are EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1386:1965_1:N:0:CTTGTA/1 99 Scaffold_01_CT_converted 61447290 40 97M = 61447296 105 NTGGGTAAGTAAAGATATAATATTGTAAGTATTATTATGTATATAAGTTTTATATTTTTTTTTTGAGGGTTGAAGTGTTATTATTTTGATATATATT #<>> Writing bisulfite mapping results to EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2203:7305:92572_1:N:0:CTTGTA Scaffold_16 3 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1106:12531:67820_1:N:0:CTTGTA Scaffold_16 1 Processed 25000000 sequence pairs so far 25314513 reads; of these: 25314513 (100.00%) were paired; of these: 16271826 (64.28%) aligned concordantly 0 times 4267243 (16.86%) aligned concordantly exactly 1 time 4775444 (18.86%) aligned concordantly >1 times 35.72% overall alignment rate 25314513 reads; of these: 25314513 (100.00%) were paired; of these: 16361226 (64.63%) aligned concordantly 0 times 4230313 (16.71%) aligned concordantly exactly 1 time 4722974 (18.66%) aligned concordantly >1 times 35.37% overall alignment rate Processed 25314513 sequences in total Successfully deleted the temporary files EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 25314513 Number of paired-end alignments with a unique best hit: 11191276 Mapping efficiency: 44.2% Sequence pairs with no alignments under any condition: 11992514 Sequence pairs did not map uniquely: 2130723 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5539947 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5651327 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 346932784 Total methylated C's in CpG context: 12322055 Total methylated C's in CHG context: 1693840 Total methylated C's in CHH context: 2773795 Total methylated C's in Unknown context: 48529 Total unmethylated C's in CpG context: 36498527 Total unmethylated C's in CHG context: 70595301 Total unmethylated C's in CHH context: 223049266 Total unmethylated C's in Unknown context: 722709 C methylated in CpG context: 25.2% C methylated in CHG context: 2.3% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.3% Bismark completed in 0d 1h 32m 26s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-151_S2_L002_R1_001_val_1.fq.gz to EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-151_S2_L002_R1_001_val_1.fq.gz (24505793 sequences in total) Writing a G -> A converted version of the input file EPI-151_S2_L002_R2_001_val_2.fq.gz to EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-151_S2_L002_R2_001_val_2.fq.gz (24505793 sequences in total) Input files are EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1928:2248_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TAGTAGAGGTTTATATGTATTTATGTTTGGTTAGAAAAGGTTTATATGTATTTATGTTTGGTTAGTAGAGGTTTATATGTATTTATGTTTGGTTA BBBBBFFBFFBBFBBBBFFF/B/FBBF>> Writing bisulfite mapping results to EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2114:2329:9695_1:N:0:ATCACG Scaffold_09 2 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far 24505793 reads; of these: 24505793 (100.00%) were paired; of these: 16362174 (66.77%) aligned concordantly 0 times 3586050 (14.63%) aligned concordantly exactly 1 time 4557569 (18.60%) aligned concordantly >1 times 33.23% overall alignment rate 24505793 reads; of these: 24505793 (100.00%) were paired; of these: 16471528 (67.21%) aligned concordantly 0 times 3553354 (14.50%) aligned concordantly exactly 1 time 4480911 (18.29%) aligned concordantly >1 times 32.79% overall alignment rate Processed 24505793 sequences in total Successfully deleted the temporary files EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24505793 Number of paired-end alignments with a unique best hit: 9915442 Mapping efficiency: 40.5% Sequence pairs with no alignments under any condition: 12555282 Sequence pairs did not map uniquely: 2035069 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4881878 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5033563 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 303264962 Total methylated C's in CpG context: 12323211 Total methylated C's in CHG context: 1414630 Total methylated C's in CHH context: 3533701 Total methylated C's in Unknown context: 52135 Total unmethylated C's in CpG context: 31194293 Total unmethylated C's in CHG context: 65160946 Total unmethylated C's in CHH context: 189638181 Total unmethylated C's in Unknown context: 646387 C methylated in CpG context: 28.3% C methylated in CHG context: 2.1% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 7.5% Bismark completed in 0d 1h 23m 8s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-152_S3_L002_R1_001_val_1.fq.gz to EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-152_S3_L002_R1_001_val_1.fq.gz (29855018 sequences in total) Writing a G -> A converted version of the input file EPI-152_S3_L002_R2_001_val_2.fq.gz to EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-152_S3_L002_R2_001_val_2.fq.gz (29855018 sequences in total) Input files are EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1155:2233_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 AATGGNTATGAAAATGTAATAAAGGAAGAGATATGAAAATGTAATAAAGGAANATTTATGANAATGTATTGTGGGAAGTGATATGAAAATGTAATATG BBBBB#B>> Writing bisulfite mapping results to EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 29855018 reads; of these: 29855018 (100.00%) were paired; of these: 20215536 (67.71%) aligned concordantly 0 times 4311215 (14.44%) aligned concordantly exactly 1 time 5328267 (17.85%) aligned concordantly >1 times 32.29% overall alignment rate 29855018 reads; of these: 29855018 (100.00%) were paired; of these: 20302194 (68.00%) aligned concordantly 0 times 4294798 (14.39%) aligned concordantly exactly 1 time 5258026 (17.61%) aligned concordantly >1 times 32.00% overall alignment rate Processed 29855018 sequences in total Successfully deleted the temporary files EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29855018 Number of paired-end alignments with a unique best hit: 11727816 Mapping efficiency: 39.3% Sequence pairs with no alignments under any condition: 15750735 Sequence pairs did not map uniquely: 2376467 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5811638 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5916178 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 358780662 Total methylated C's in CpG context: 14625118 Total methylated C's in CHG context: 1782524 Total methylated C's in CHH context: 4106805 Total methylated C's in Unknown context: 73648 Total unmethylated C's in CpG context: 34864391 Total unmethylated C's in CHG context: 74934034 Total unmethylated C's in CHH context: 228467790 Total unmethylated C's in Unknown context: 784418 C methylated in CpG context: 29.6% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 8.6% Bismark completed in 0d 1h 38m 18s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-153_S4_L002_R1_001_val_1.fq.gz to EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-153_S4_L002_R1_001_val_1.fq.gz (26009397 sequences in total) Writing a G -> A converted version of the input file EPI-153_S4_L002_R2_001_val_2.fq.gz to EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-153_S4_L002_R2_001_val_2.fq.gz (26009397 sequences in total) Input files are EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1785:2231_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 TGTTGNGATATATAATTGAAAATTGTTGAAAGTGTTATTAAATATAATGTAATAATAAATGATAAAGGGATGTAATGTTGTATATTAATTATTAT BBBBB#BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:2:2207:1785:2231_2:N:0:TTAGGC/2 141 * 0 0 * * 0 0 ATANNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNATTTATTATTACATTATATTTAATAACACTTTCAACAATTTTCAATTATATATCACAACA BBB############################B###BB<>> Writing bisulfite mapping results to EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1115:15676:64681_1:N:0:TTAGGC Scaffold_08 61151067 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2314:20445:24921_1:N:0:TTAGGC Scaffold_11 1 Processed 26000000 sequence pairs so far 26009397 reads; of these: 26009397 (100.00%) were paired; of these: 17425568 (67.00%) aligned concordantly 0 times 3786588 (14.56%) aligned concordantly exactly 1 time 4797241 (18.44%) aligned concordantly >1 times 33.00% overall alignment rate 26009397 reads; of these: 26009397 (100.00%) were paired; of these: 17345929 (66.69%) aligned concordantly 0 times 3790523 (14.57%) aligned concordantly exactly 1 time 4872945 (18.74%) aligned concordantly >1 times 33.31% overall alignment rate Processed 26009397 sequences in total Successfully deleted the temporary files EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 26009397 Number of paired-end alignments with a unique best hit: 10439073 Mapping efficiency: 40.1% Sequence pairs with no alignments under any condition: 13324084 Sequence pairs did not map uniquely: 2246240 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5162472 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5276599 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 313246619 Total methylated C's in CpG context: 12166335 Total methylated C's in CHG context: 1553054 Total methylated C's in CHH context: 3545799 Total methylated C's in Unknown context: 59307 Total unmethylated C's in CpG context: 33102077 Total unmethylated C's in CHG context: 67300222 Total unmethylated C's in CHH context: 195579132 Total unmethylated C's in Unknown context: 676779 C methylated in CpG context: 26.9% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 8.1% Bismark completed in 0d 1h 25m 41s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-154_S5_L002_R1_001_val_1.fq.gz to EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-154_S5_L002_R1_001_val_1.fq.gz (25226760 sequences in total) Writing a G -> A converted version of the input file EPI-154_S5_L002_R2_001_val_2.fq.gz to EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-154_S5_L002_R2_001_val_2.fq.gz (25226760 sequences in total) Input files are EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2191:2242_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 ATGTANATTAAGAGTTAAATTATGTAGATGTAGATTAAAAGTTAAATTATGTATAGGTAGATTAAGAGTTAAATTAAGTAGATGTAGATTAAGAGTTTAAT BBBBB#>> Writing bisulfite mapping results to EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far 25226760 reads; of these: 25226760 (100.00%) were paired; of these: 17487663 (69.32%) aligned concordantly 0 times 3441962 (13.64%) aligned concordantly exactly 1 time 4297135 (17.03%) aligned concordantly >1 times 30.68% overall alignment rate 25226760 reads; of these: 25226760 (100.00%) were paired; of these: 17561189 (69.61%) aligned concordantly 0 times 3444557 (13.65%) aligned concordantly exactly 1 time 4221014 (16.73%) aligned concordantly >1 times 30.39% overall alignment rate Processed 25226760 sequences in total Successfully deleted the temporary files EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 25226760 Number of paired-end alignments with a unique best hit: 9405544 Mapping efficiency: 37.3% Sequence pairs with no alignments under any condition: 13904236 Sequence pairs did not map uniquely: 1916980 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4637602 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4767942 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 285373397 Total methylated C's in CpG context: 11306006 Total methylated C's in CHG context: 1298778 Total methylated C's in CHH context: 3449101 Total methylated C's in Unknown context: 62682 Total unmethylated C's in CpG context: 28242299 Total unmethylated C's in CHG context: 60128621 Total unmethylated C's in CHH context: 180948592 Total unmethylated C's in Unknown context: 625876 C methylated in CpG context: 28.6% C methylated in CHG context: 2.1% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 9.1% Bismark completed in 0d 1h 19m 56s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-159_S6_L002_R1_001_val_1.fq.gz to EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-159_S6_L002_R1_001_val_1.fq.gz (15453987 sequences in total) Writing a G -> A converted version of the input file EPI-159_S6_L002_R2_001_val_2.fq.gz to EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-159_S6_L002_R2_001_val_2.fq.gz (15453987 sequences in total) Input files are EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1469:2230_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 GGTTANTGAAGTGTATATAGTTATATTGTAAATTAATGGTTGAGTGAGTTTTNTTTTTTATTAGGTAATATTTTAAGGGAATGGTTGTTTGTAAATATTGG BBBBB#BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFF#<>> Writing bisulfite mapping results to EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far 15453987 reads; of these: 15453987 (100.00%) were paired; of these: 10169665 (65.81%) aligned concordantly 0 times 2347488 (15.19%) aligned concordantly exactly 1 time 2936834 (19.00%) aligned concordantly >1 times 34.19% overall alignment rate 15453987 reads; of these: 15453987 (100.00%) were paired; of these: 10221296 (66.14%) aligned concordantly 0 times 2334749 (15.11%) aligned concordantly exactly 1 time 2897942 (18.75%) aligned concordantly >1 times 33.86% overall alignment rate Processed 15453987 sequences in total Successfully deleted the temporary files EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 15453987 Number of paired-end alignments with a unique best hit: 6380873 Mapping efficiency: 41.3% Sequence pairs with no alignments under any condition: 7739907 Sequence pairs did not map uniquely: 1333207 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3152381 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3228492 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 195385696 Total methylated C's in CpG context: 7804592 Total methylated C's in CHG context: 1021997 Total methylated C's in CHH context: 3443697 Total methylated C's in Unknown context: 54626 Total unmethylated C's in CpG context: 19140558 Total unmethylated C's in CHG context: 40545239 Total unmethylated C's in CHH context: 123429613 Total unmethylated C's in Unknown context: 431888 C methylated in CpG context: 29.0% C methylated in CHG context: 2.5% C methylated in CHH context: 2.7% C methylated in unknown context (CN or CHN): 11.2% Bismark completed in 0d 0h 52m 43s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-160_S7_L002_R1_001_val_1.fq.gz to EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-160_S7_L002_R1_001_val_1.fq.gz (31922572 sequences in total) Writing a G -> A converted version of the input file EPI-160_S7_L002_R2_001_val_2.fq.gz to EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-160_S7_L002_R2_001_val_2.fq.gz (31922572 sequences in total) Input files are EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1522:2231_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 GTATGNGTAATTAGGTGATTTTTTTTGATTTGATGTAGTTAGTGGATTGGGAATTGGTAA BBBBB#BBBFFBFFFFFFFFFFFFFFB/>> Writing bisulfite mapping results to EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1114:12011:63361_1:N:0:GCCAAT Scaffold_16 2 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far 31922572 reads; of these: 31922572 (100.00%) were paired; of these: 21498211 (67.34%) aligned concordantly 0 times 4482845 (14.04%) aligned concordantly exactly 1 time 5941516 (18.61%) aligned concordantly >1 times 32.66% overall alignment rate 31922572 reads; of these: 31922572 (100.00%) were paired; of these: 21367255 (66.93%) aligned concordantly 0 times 4496752 (14.09%) aligned concordantly exactly 1 time 6058565 (18.98%) aligned concordantly >1 times 33.07% overall alignment rate Processed 31922572 sequences in total Successfully deleted the temporary files EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 31922572 Number of paired-end alignments with a unique best hit: 12255649 Mapping efficiency: 38.4% Sequence pairs with no alignments under any condition: 16675995 Sequence pairs did not map uniquely: 2990928 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6034016 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6221632 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 356119849 Total methylated C's in CpG context: 13819770 Total methylated C's in CHG context: 1872039 Total methylated C's in CHH context: 4292886 Total methylated C's in Unknown context: 84309 Total unmethylated C's in CpG context: 37264731 Total unmethylated C's in CHG context: 75867945 Total unmethylated C's in CHH context: 223002478 Total unmethylated C's in Unknown context: 787408 C methylated in CpG context: 27.1% C methylated in CHG context: 2.4% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 9.7% Bismark completed in 0d 1h 40m 56s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-161_S8_L002_R1_001_val_1.fq.gz to EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-161_S8_L002_R1_001_val_1.fq.gz (24510805 sequences in total) Writing a G -> A converted version of the input file EPI-161_S8_L002_R2_001_val_2.fq.gz to EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-161_S8_L002_R2_001_val_2.fq.gz (24510805 sequences in total) Input files are EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2010:2229_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TGATANGTAGTATATGGTGTATGATATAGTA BBBBB#>> Writing bisulfite mapping results to EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2114:19616:68633_1:N:0:CAGATC Scaffold_16 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1112:4795:6211_1:N:0:CAGATC Scaffold_16 2 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far 24510805 reads; of these: 24510805 (100.00%) were paired; of these: 17297281 (70.57%) aligned concordantly 0 times 3166248 (12.92%) aligned concordantly exactly 1 time 4047276 (16.51%) aligned concordantly >1 times 29.43% overall alignment rate 24510805 reads; of these: 24510805 (100.00%) were paired; of these: 17217869 (70.25%) aligned concordantly 0 times 3175317 (12.95%) aligned concordantly exactly 1 time 4117619 (16.80%) aligned concordantly >1 times 29.75% overall alignment rate Processed 24510805 sequences in total Successfully deleted the temporary files EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24510805 Number of paired-end alignments with a unique best hit: 8593707 Mapping efficiency: 35.1% Sequence pairs with no alignments under any condition: 13929047 Sequence pairs did not map uniquely: 1988051 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4237007 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4356698 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 251244640 Total methylated C's in CpG context: 9311185 Total methylated C's in CHG context: 1241250 Total methylated C's in CHH context: 3334595 Total methylated C's in Unknown context: 63649 Total unmethylated C's in CpG context: 25878911 Total unmethylated C's in CHG context: 52710364 Total unmethylated C's in CHH context: 158768335 Total unmethylated C's in Unknown context: 546831 C methylated in CpG context: 26.5% C methylated in CHG context: 2.3% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 10.4% Bismark completed in 0d 1h 12m 16s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-162_S9_L002_R1_001_val_1.fq.gz to EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-162_S9_L002_R1_001_val_1.fq.gz (22769546 sequences in total) Writing a G -> A converted version of the input file EPI-162_S9_L002_R2_001_val_2.fq.gz to EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-162_S9_L002_R2_001_val_2.fq.gz (22769546 sequences in total) Input files are EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1238:2233_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 TGTTANTTATTTTAAAATTTGTTGATAAATTGTTTATTTTTAGGATAGTTTTTTTAGATATTGTTTTTTTTTGGTTTGAAAGGGTTATGAATAGTTTTTTT BBBBB#>> Writing bisulfite mapping results to EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far 22769546 reads; of these: 22769546 (100.00%) were paired; of these: 15616786 (68.59%) aligned concordantly 0 times 3009100 (13.22%) aligned concordantly exactly 1 time 4143660 (18.20%) aligned concordantly >1 times 31.41% overall alignment rate 22769546 reads; of these: 22769546 (100.00%) were paired; of these: 15681883 (68.87%) aligned concordantly 0 times 3024375 (13.28%) aligned concordantly exactly 1 time 4063288 (17.85%) aligned concordantly >1 times 31.13% overall alignment rate Processed 22769546 sequences in total Successfully deleted the temporary files EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22769546 Number of paired-end alignments with a unique best hit: 8267039 Mapping efficiency: 36.3% Sequence pairs with no alignments under any condition: 12467371 Sequence pairs did not map uniquely: 2035136 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4073674 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4193365 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 238005650 Total methylated C's in CpG context: 8810888 Total methylated C's in CHG context: 1190010 Total methylated C's in CHH context: 3285737 Total methylated C's in Unknown context: 56519 Total unmethylated C's in CpG context: 24654378 Total unmethylated C's in CHG context: 50555362 Total unmethylated C's in CHH context: 149509275 Total unmethylated C's in Unknown context: 528637 C methylated in CpG context: 26.3% C methylated in CHG context: 2.3% C methylated in CHH context: 2.2% C methylated in unknown context (CN or CHN): 9.7% Bismark completed in 0d 1h 7m 56s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-167_S10_L002_R1_001_val_1.fq.gz to EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-167_S10_L002_R1_001_val_1.fq.gz (24481250 sequences in total) Writing a G -> A converted version of the input file EPI-167_S10_L002_R2_001_val_2.fq.gz to EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-167_S10_L002_R2_001_val_2.fq.gz (24481250 sequences in total) Input files are EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1666:2232_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 TTGAANTTGTTGATTTATATGGGGATATGAATAATAAGTTTAATATTTAAGATGGAGAAGAAATAAGTGTAGAATTTTGGATAAAGGATAATTAAGTTAAT BBBBB#BBFFFFFF>> Writing bisulfite mapping results to EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far 24481250 reads; of these: 24481250 (100.00%) were paired; of these: 16118278 (65.84%) aligned concordantly 0 times 3811968 (15.57%) aligned concordantly exactly 1 time 4551004 (18.59%) aligned concordantly >1 times 34.16% overall alignment rate 24481250 reads; of these: 24481250 (100.00%) were paired; of these: 16050656 (65.56%) aligned concordantly 0 times 3801758 (15.53%) aligned concordantly exactly 1 time 4628836 (18.91%) aligned concordantly >1 times 34.44% overall alignment rate Processed 24481250 sequences in total Successfully deleted the temporary files EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24481250 Number of paired-end alignments with a unique best hit: 10438000 Mapping efficiency: 42.6% Sequence pairs with no alignments under any condition: 12046563 Sequence pairs did not map uniquely: 1996687 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5166645 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5271355 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 327276929 Total methylated C's in CpG context: 12357096 Total methylated C's in CHG context: 2047643 Total methylated C's in CHH context: 6308688 Total methylated C's in Unknown context: 65277 Total unmethylated C's in CpG context: 31908920 Total unmethylated C's in CHG context: 67977563 Total unmethylated C's in CHH context: 206677019 Total unmethylated C's in Unknown context: 705078 C methylated in CpG context: 27.9% C methylated in CHG context: 2.9% C methylated in CHH context: 3.0% C methylated in unknown context (CN or CHN): 8.5% Bismark completed in 0d 1h 26m 14s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-168_S11_L002_R1_001_val_1.fq.gz to EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-168_S11_L002_R1_001_val_1.fq.gz (22688467 sequences in total) Writing a G -> A converted version of the input file EPI-168_S11_L002_R2_001_val_2.fq.gz to EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-168_S11_L002_R2_001_val_2.fq.gz (22688467 sequences in total) Input files are EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1424:2239_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 GTGATNTATAATGTATTATTGAAAGTTAATAGTTTATTTAAGTTTTTGGTATTTTTTGATTTAGGTTTAATTATTTTGTTATGTGGGTTTGTGATTTG BBBBB#B>> Writing bisulfite mapping results to EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far 22688467 reads; of these: 22688467 (100.00%) were paired; of these: 15440681 (68.06%) aligned concordantly 0 times 3190562 (14.06%) aligned concordantly exactly 1 time 4057224 (17.88%) aligned concordantly >1 times 31.94% overall alignment rate 22688467 reads; of these: 22688467 (100.00%) were paired; of these: 15321747 (67.53%) aligned concordantly 0 times 3226165 (14.22%) aligned concordantly exactly 1 time 4140555 (18.25%) aligned concordantly >1 times 32.47% overall alignment rate Processed 22688467 sequences in total Successfully deleted the temporary files EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22688467 Number of paired-end alignments with a unique best hit: 8967128 Mapping efficiency: 39.5% Sequence pairs with no alignments under any condition: 11891374 Sequence pairs did not map uniquely: 1829965 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4393790 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4573338 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 278794431 Total methylated C's in CpG context: 10658385 Total methylated C's in CHG context: 1268483 Total methylated C's in CHH context: 3535297 Total methylated C's in Unknown context: 54743 Total unmethylated C's in CpG context: 29012483 Total unmethylated C's in CHG context: 59889529 Total unmethylated C's in CHH context: 174430254 Total unmethylated C's in Unknown context: 615881 C methylated in CpG context: 26.9% C methylated in CHG context: 2.1% C methylated in CHH context: 2.0% C methylated in unknown context (CN or CHN): 8.2% Bismark completed in 0d 1h 15m 54s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-169_S12_L002_R1_001_val_1.fq.gz to EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-169_S12_L002_R1_001_val_1.fq.gz (21392200 sequences in total) Writing a G -> A converted version of the input file EPI-169_S12_L002_R2_001_val_2.fq.gz to EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-169_S12_L002_R2_001_val_2.fq.gz (21392200 sequences in total) Input files are EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1452:2231_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 TGGTANGAGGTTGTGTGATTAGTATAAAGGTGTTTAGAGTTATTAAGTGGATTGGATTGGAGTTTGGATTGGTTTTGTATTAATAAAAGTGTTTTTTTTGT BBBBB#<>> Writing bisulfite mapping results to EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2205:7072:26521_1:N:0:GGCTAC Scaffold_09 1 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1306:7118:3504_1:N:0:GGCTAC Scaffold_16 2 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1208:9887:13727_1:N:0:GGCTAC Scaffold_16 2 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1114:15881:53162_1:N:0:GGCTAC Scaffold_10 1 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far 21392200 reads; of these: 21392200 (100.00%) were paired; of these: 14178782 (66.28%) aligned concordantly 0 times 3054776 (14.28%) aligned concordantly exactly 1 time 4158642 (19.44%) aligned concordantly >1 times 33.72% overall alignment rate 21392200 reads; of these: 21392200 (100.00%) were paired; of these: 14275451 (66.73%) aligned concordantly 0 times 3039394 (14.21%) aligned concordantly exactly 1 time 4077355 (19.06%) aligned concordantly >1 times 33.27% overall alignment rate Processed 21392200 sequences in total Successfully deleted the temporary files EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 21392200 Number of paired-end alignments with a unique best hit: 8408059 Mapping efficiency: 39.3% Sequence pairs with no alignments under any condition: 10932504 Sequence pairs did not map uniquely: 2051637 Sequence pairs which were discarded because genomic sequence could not be extracted: 4 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4126394 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4281661 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 245148711 Total methylated C's in CpG context: 9715161 Total methylated C's in CHG context: 1293014 Total methylated C's in CHH context: 3765782 Total methylated C's in Unknown context: 64209 Total unmethylated C's in CpG context: 25600954 Total unmethylated C's in CHG context: 52728521 Total unmethylated C's in CHH context: 152045279 Total unmethylated C's in Unknown context: 533680 C methylated in CpG context: 27.5% C methylated in CHG context: 2.4% C methylated in CHH context: 2.4% C methylated in unknown context (CN or CHN): 10.7% Bismark completed in 0d 1h 8m 43s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-170_S13_L002_R1_001_val_1.fq.gz to EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-170_S13_L002_R1_001_val_1.fq.gz (27996279 sequences in total) Writing a G -> A converted version of the input file EPI-170_S13_L002_R2_001_val_2.fq.gz to EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-170_S13_L002_R2_001_val_2.fq.gz (27996279 sequences in total) Input files are EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2244:2228_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 TTGTTNAGTTTGTTTAAGTTATTTTGATTTGTTAAAAAATATGGTAG BBBBB#<>> Writing bisulfite mapping results to EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2107:18595:54334_1:N:0:CTTGTA Scaffold_16 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2111:5981:74801_1:N:0:CTTGTA Scaffold_16 3 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1316:10202:11032_1:N:0:CTTGTA Scaffold_16 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1314:12592:63283_1:N:0:CTTGTA Scaffold_15 3 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2213:8607:54584_1:N:0:CTTGTA Scaffold_09 2 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2312:8356:27499_1:N:0:CTTGTA Scaffold_15 3 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2312:6036:58634_1:N:0:CTTGTA Scaffold_15 3 27996279 reads; of these: 27996279 (100.00%) were paired; of these: 19276145 (68.85%) aligned concordantly 0 times 3764638 (13.45%) aligned concordantly exactly 1 time 4955496 (17.70%) aligned concordantly >1 times 31.15% overall alignment rate 27996279 reads; of these: 27996279 (100.00%) were paired; of these: 19163557 (68.45%) aligned concordantly 0 times 3776883 (13.49%) aligned concordantly exactly 1 time 5055839 (18.06%) aligned concordantly >1 times 31.55% overall alignment rate Processed 27996279 sequences in total Successfully deleted the temporary files EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27996279 Number of paired-end alignments with a unique best hit: 10233767 Mapping efficiency: 36.6% Sequence pairs with no alignments under any condition: 15243065 Sequence pairs did not map uniquely: 2519447 Sequence pairs which were discarded because genomic sequence could not be extracted: 7 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5017772 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5215988 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 295230497 Total methylated C's in CpG context: 10743620 Total methylated C's in CHG context: 1476561 Total methylated C's in CHH context: 3272606 Total methylated C's in Unknown context: 54419 Total unmethylated C's in CpG context: 31907626 Total unmethylated C's in CHG context: 62815831 Total unmethylated C's in CHH context: 185014253 Total unmethylated C's in Unknown context: 638215 C methylated in CpG context: 25.2% C methylated in CHG context: 2.3% C methylated in CHH context: 1.7% C methylated in unknown context (CN or CHN): 7.9% Bismark completed in 0d 1h 23m 52s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-175_S14_L003_R1_001_val_1.fq.gz to EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-175_S14_L003_R1_001_val_1.fq.gz (24654280 sequences in total) Writing a G -> A converted version of the input file EPI-175_S14_L003_R2_001_val_2.fq.gz to EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-175_S14_L003_R2_001_val_2.fq.gz (24654280 sequences in total) Input files are EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:1436:2247_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 AAGAANATGTGTTTGTATGTTGGAAGTTTGTTTAGTGTGG BBBBB#>> Writing bisulfite mapping results to EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1308:2082:73549_1:N:0:ATCACG Scaffold_09 1 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far 24654280 reads; of these: 24654280 (100.00%) were paired; of these: 16285716 (66.06%) aligned concordantly 0 times 3719776 (15.09%) aligned concordantly exactly 1 time 4648788 (18.86%) aligned concordantly >1 times 33.94% overall alignment rate 24654280 reads; of these: 24654280 (100.00%) were paired; of these: 16219919 (65.79%) aligned concordantly 0 times 3719837 (15.09%) aligned concordantly exactly 1 time 4714524 (19.12%) aligned concordantly >1 times 34.21% overall alignment rate Processed 24654280 sequences in total Successfully deleted the temporary files EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24654280 Number of paired-end alignments with a unique best hit: 10209530 Mapping efficiency: 41.4% Sequence pairs with no alignments under any condition: 12327982 Sequence pairs did not map uniquely: 2116768 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5041243 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5168286 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 309993582 Total methylated C's in CpG context: 11855544 Total methylated C's in CHG context: 1437285 Total methylated C's in CHH context: 3685251 Total methylated C's in Unknown context: 57157 Total unmethylated C's in CpG context: 31961048 Total unmethylated C's in CHG context: 65204352 Total unmethylated C's in CHH context: 195850102 Total unmethylated C's in Unknown context: 677780 C methylated in CpG context: 27.1% C methylated in CHG context: 2.2% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 7.8% Bismark completed in 0d 1h 24m 48s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-176_S15_L003_R1_001_val_1.fq.gz to EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-176_S15_L003_R1_001_val_1.fq.gz (36345555 sequences in total) Writing a G -> A converted version of the input file EPI-176_S15_L003_R2_001_val_2.fq.gz to EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-176_S15_L003_R2_001_val_2.fq.gz (36345555 sequences in total) Input files are EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4405:2246_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 TGTGGNGTAGATGAAGATGTTTGATATGTTGTAGAATATGTAGTTGTAGAGTGTTATTGTGAAGGTGATGTATGTTGTTATTATTGAGAG BBBBB#B>> Writing bisulfite mapping results to EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1102:4573:54620_1:N:0:CGATGT Scaffold_16 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1103:17389:25945_1:N:0:CGATGT Scaffold_02 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1104:15612:91578_1:N:0:CGATGT Scaffold_16 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2201:12506:83456_1:N:0:CGATGT Scaffold_08 61151062 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2205:13682:89946_1:N:0:CGATGT Scaffold_09 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2109:14625:56631_1:N:0:CGATGT Scaffold_08 61151062 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1208:8738:55944_1:N:0:CGATGT Scaffold_16 2 Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far 36345555 reads; of these: 36345555 (100.00%) were paired; of these: 25018491 (68.84%) aligned concordantly 0 times 5092475 (14.01%) aligned concordantly exactly 1 time 6234589 (17.15%) aligned concordantly >1 times 31.16% overall alignment rate 36345555 reads; of these: 36345555 (100.00%) were paired; of these: 25118626 (69.11%) aligned concordantly 0 times 5091930 (14.01%) aligned concordantly exactly 1 time 6134999 (16.88%) aligned concordantly >1 times 30.89% overall alignment rate Processed 36345555 sequences in total Successfully deleted the temporary files EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 36345555 Number of paired-end alignments with a unique best hit: 13724724 Mapping efficiency: 37.8% Sequence pairs with no alignments under any condition: 19810124 Sequence pairs did not map uniquely: 2810707 Sequence pairs which were discarded because genomic sequence could not be extracted: 7 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6759192 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6965525 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 415508402 Total methylated C's in CpG context: 15449887 Total methylated C's in CHG context: 1795361 Total methylated C's in CHH context: 4293575 Total methylated C's in Unknown context: 73998 Total unmethylated C's in CpG context: 44600919 Total unmethylated C's in CHG context: 86098830 Total unmethylated C's in CHH context: 263269830 Total unmethylated C's in Unknown context: 887032 C methylated in CpG context: 25.7% C methylated in CHG context: 2.0% C methylated in CHH context: 1.6% C methylated in unknown context (CN or CHN): 7.7% Bismark completed in 0d 1h 54m 30s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-181_S16_L003_R1_001_val_1.fq.gz to EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-181_S16_L003_R1_001_val_1.fq.gz (27212918 sequences in total) Writing a G -> A converted version of the input file EPI-181_S16_L003_R2_001_val_2.fq.gz to EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-181_S16_L003_R2_001_val_2.fq.gz (27212918 sequences in total) Input files are EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:3117:2249_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 GTTAGNGTTTAAAATATATGTATATTGAATATGTAGTAATTATATAGATAAAGTTTTATTGGTTATAAAATAGGGATGTTTTTAGTTTTGTTGAGTAT BBBBB#>> Writing bisulfite mapping results to EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1316:13789:41230_1:N:0:TTAGGC Scaffold_16 2 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far 27212918 reads; of these: 27212918 (100.00%) were paired; of these: 18517573 (68.05%) aligned concordantly 0 times 3909659 (14.37%) aligned concordantly exactly 1 time 4785686 (17.59%) aligned concordantly >1 times 31.95% overall alignment rate 27212918 reads; of these: 27212918 (100.00%) were paired; of these: 18377954 (67.53%) aligned concordantly 0 times 3966469 (14.58%) aligned concordantly exactly 1 time 4868495 (17.89%) aligned concordantly >1 times 32.47% overall alignment rate Processed 27212918 sequences in total Successfully deleted the temporary files EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27212918 Number of paired-end alignments with a unique best hit: 10790981 Mapping efficiency: 39.7% Sequence pairs with no alignments under any condition: 14282015 Sequence pairs did not map uniquely: 2139922 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5313318 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5477662 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 336107175 Total methylated C's in CpG context: 13211112 Total methylated C's in CHG context: 1652081 Total methylated C's in CHH context: 3893943 Total methylated C's in Unknown context: 60101 Total unmethylated C's in CpG context: 34596724 Total unmethylated C's in CHG context: 71273976 Total unmethylated C's in CHH context: 211479339 Total unmethylated C's in Unknown context: 733272 C methylated in CpG context: 27.6% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 7.6% Bismark completed in 0d 1h 29m 19s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-182_S17_L003_R1_001_val_1.fq.gz to EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-182_S17_L003_R1_001_val_1.fq.gz (31499315 sequences in total) Writing a G -> A converted version of the input file EPI-182_S17_L003_R2_001_val_2.fq.gz to EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-182_S17_L003_R2_001_val_2.fq.gz (31499315 sequences in total) Input files are EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:2786:2250_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 TGATTNTATTATGGAAATATTGTTTAGTTTAGTAGAAATATTTTTTGGAGTTGTTGTGA BBBBB#<>> Writing bisulfite mapping results to EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far 31499315 reads; of these: 31499315 (100.00%) were paired; of these: 20717975 (65.77%) aligned concordantly 0 times 4809206 (15.27%) aligned concordantly exactly 1 time 5972134 (18.96%) aligned concordantly >1 times 34.23% overall alignment rate 31499315 reads; of these: 31499315 (100.00%) were paired; of these: 20639641 (65.52%) aligned concordantly 0 times 4805807 (15.26%) aligned concordantly exactly 1 time 6053867 (19.22%) aligned concordantly >1 times 34.48% overall alignment rate Processed 31499315 sequences in total Successfully deleted the temporary files EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 31499315 Number of paired-end alignments with a unique best hit: 13143700 Mapping efficiency: 41.7% Sequence pairs with no alignments under any condition: 15672601 Sequence pairs did not map uniquely: 2683014 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6520043 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6623657 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 407184402 Total methylated C's in CpG context: 14617019 Total methylated C's in CHG context: 1959865 Total methylated C's in CHH context: 4544903 Total methylated C's in Unknown context: 72663 Total unmethylated C's in CpG context: 40997905 Total unmethylated C's in CHG context: 84917152 Total unmethylated C's in CHH context: 260147558 Total unmethylated C's in Unknown context: 900486 C methylated in CpG context: 26.3% C methylated in CHG context: 2.3% C methylated in CHH context: 1.7% C methylated in unknown context (CN or CHN): 7.5% Bismark completed in 0d 1h 47m 33s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-184_S18_L003_R1_001_val_1.fq.gz to EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-184_S18_L003_R1_001_val_1.fq.gz (20689148 sequences in total) Writing a G -> A converted version of the input file EPI-184_S18_L003_R2_001_val_2.fq.gz to EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-184_S18_L003_R2_001_val_2.fq.gz (20689148 sequences in total) Input files are EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:2159:2247_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 GAATANGGAAATGGGTAGGATGTAGGTTATAAAGGAAATTGGGTTAATAATGTGAATAGAGAAATGGGTAGGAGGTAGGTTATAAAGGAAATTGGGT BBBBB#B>> Writing bisulfite mapping results to EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2211:18307:25265_1:N:0:ACAGTG Scaffold_09 2 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2204:5160:88396_1:N:0:ACAGTG Scaffold_08 61151067 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far 20689148 reads; of these: 20689148 (100.00%) were paired; of these: 13581727 (65.65%) aligned concordantly 0 times 3064795 (14.81%) aligned concordantly exactly 1 time 4042626 (19.54%) aligned concordantly >1 times 34.35% overall alignment rate 20689148 reads; of these: 20689148 (100.00%) were paired; of these: 13516815 (65.33%) aligned concordantly 0 times 3053788 (14.76%) aligned concordantly exactly 1 time 4118545 (19.91%) aligned concordantly >1 times 34.67% overall alignment rate Processed 20689148 sequences in total Successfully deleted the temporary files EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 20689148 Number of paired-end alignments with a unique best hit: 8444730 Mapping efficiency: 40.8% Sequence pairs with no alignments under any condition: 10305796 Sequence pairs did not map uniquely: 1938622 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4167553 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4277175 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 251839676 Total methylated C's in CpG context: 9669457 Total methylated C's in CHG context: 1217679 Total methylated C's in CHH context: 3983200 Total methylated C's in Unknown context: 60694 Total unmethylated C's in CpG context: 25706227 Total unmethylated C's in CHG context: 53487968 Total unmethylated C's in CHH context: 157775145 Total unmethylated C's in Unknown context: 557312 C methylated in CpG context: 27.3% C methylated in CHG context: 2.2% C methylated in CHH context: 2.5% C methylated in unknown context (CN or CHN): 9.8% Bismark completed in 0d 1h 8m 12s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-185_S19_L003_R1_001_val_1.fq.gz to EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-185_S19_L003_R1_001_val_1.fq.gz (11003725 sequences in total) Writing a G -> A converted version of the input file EPI-185_S19_L003_R2_001_val_2.fq.gz to EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-185_S19_L003_R2_001_val_2.fq.gz (11003725 sequences in total) Input files are EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4218:2247_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 GGGGANGGAGAGTTATAGGTAGTTGTAGTGGATATGTTGTGGGATTGAGGATGTTGTGTTGTGTTTTATGGTTTTGGGTTGTTGTTGTAGAGTTGAATTTG BBBBB#B>> Writing bisulfite mapping results to EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far 11003725 reads; of these: 11003725 (100.00%) were paired; of these: 7568004 (68.78%) aligned concordantly 0 times 1482121 (13.47%) aligned concordantly exactly 1 time 1953600 (17.75%) aligned concordantly >1 times 31.22% overall alignment rate 11003725 reads; of these: 11003725 (100.00%) were paired; of these: 7619058 (69.24%) aligned concordantly 0 times 1471639 (13.37%) aligned concordantly exactly 1 time 1913028 (17.39%) aligned concordantly >1 times 30.76% overall alignment rate Processed 11003725 sequences in total Successfully deleted the temporary files EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 11003725 Number of paired-end alignments with a unique best hit: 4103253 Mapping efficiency: 37.3% Sequence pairs with no alignments under any condition: 6008199 Sequence pairs did not map uniquely: 892273 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2013443 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2089810 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 125649607 Total methylated C's in CpG context: 4647874 Total methylated C's in CHG context: 682027 Total methylated C's in CHH context: 3288445 Total methylated C's in Unknown context: 50440 Total unmethylated C's in CpG context: 13300931 Total unmethylated C's in CHG context: 26446504 Total unmethylated C's in CHH context: 77283826 Total unmethylated C's in Unknown context: 276168 C methylated in CpG context: 25.9% C methylated in CHG context: 2.5% C methylated in CHH context: 4.1% C methylated in unknown context (CN or CHN): 15.4% Bismark completed in 0d 0h 34m 1s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-187_S20_L003_R1_001_val_1.fq.gz to EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-187_S20_L003_R1_001_val_1.fq.gz (22734395 sequences in total) Writing a G -> A converted version of the input file EPI-187_S20_L003_R2_001_val_2.fq.gz to EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-187_S20_L003_R2_001_val_2.fq.gz (22734395 sequences in total) Input files are EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:5270:2246_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TAATANATAATTATTTTAGATAATAAGGTTGGAAAAATTGTTGAAATATGGGTTTATTTTTTGTTTTATTGTTTGTAAATTTAGTGTTGAGTTATTGT BBBBB#BBBFFFFFFFFBFFFFFFBBFFF>> Writing bisulfite mapping results to EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2312:4165:2931_1:N:0:CAGATC Scaffold_09 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2204:7022:13811_1:N:0:CAGATC Scaffold_16 1 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2112:6280:50513_1:N:0:CAGATC Scaffold_16 2 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1111:19003:88210_1:N:0:CAGATC Scaffold_16 2 Processed 22000000 sequence pairs so far 22734395 reads; of these: 22734395 (100.00%) were paired; of these: 14659250 (64.48%) aligned concordantly 0 times 3540890 (15.58%) aligned concordantly exactly 1 time 4534255 (19.94%) aligned concordantly >1 times 35.52% overall alignment rate 22734395 reads; of these: 22734395 (100.00%) were paired; of these: 14778776 (65.01%) aligned concordantly 0 times 3507484 (15.43%) aligned concordantly exactly 1 time 4448135 (19.57%) aligned concordantly >1 times 34.99% overall alignment rate Processed 22734395 sequences in total Successfully deleted the temporary files EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22734395 Number of paired-end alignments with a unique best hit: 9655534 Mapping efficiency: 42.5% Sequence pairs with no alignments under any condition: 10981695 Sequence pairs did not map uniquely: 2097166 Sequence pairs which were discarded because genomic sequence could not be extracted: 4 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4757885 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4897645 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 292287685 Total methylated C's in CpG context: 12549941 Total methylated C's in CHG context: 1572027 Total methylated C's in CHH context: 3841851 Total methylated C's in Unknown context: 60882 Total unmethylated C's in CpG context: 29075423 Total unmethylated C's in CHG context: 62324170 Total unmethylated C's in CHH context: 182924273 Total unmethylated C's in Unknown context: 633983 C methylated in CpG context: 30.1% C methylated in CHG context: 2.5% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 8.8% Bismark completed in 0d 1h 18m 45s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-188_S21_L003_R1_001_val_1.fq.gz to EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-188_S21_L003_R1_001_val_1.fq.gz (21488138 sequences in total) Writing a G -> A converted version of the input file EPI-188_S21_L003_R2_001_val_2.fq.gz to EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-188_S21_L003_R2_001_val_2.fq.gz (21488138 sequences in total) Input files are EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:6853:2249_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AGTTGNGGGTAAGAGAGAGTTTTTTTGGAAAATTTTGATATTTTAAAAGTTAAATAATGTATTATAGTAAGTTTTATAGTGTATGAGGGG BBBBB#>> Writing bisulfite mapping results to EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2205:11759:30686_1:N:0:ACTTGA Scaffold_16 1 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far 21488138 reads; of these: 21488138 (100.00%) were paired; of these: 13990818 (65.11%) aligned concordantly 0 times 3141180 (14.62%) aligned concordantly exactly 1 time 4356140 (20.27%) aligned concordantly >1 times 34.89% overall alignment rate 21488138 reads; of these: 21488138 (100.00%) were paired; of these: 14059030 (65.43%) aligned concordantly 0 times 3145929 (14.64%) aligned concordantly exactly 1 time 4283179 (19.93%) aligned concordantly >1 times 34.57% overall alignment rate Processed 21488138 sequences in total Successfully deleted the temporary files EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 21488138 Number of paired-end alignments with a unique best hit: 8423411 Mapping efficiency: 39.2% Sequence pairs with no alignments under any condition: 10776872 Sequence pairs did not map uniquely: 2287855 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4160590 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4262820 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 235029500 Total methylated C's in CpG context: 8853859 Total methylated C's in CHG context: 1292583 Total methylated C's in CHH context: 3088082 Total methylated C's in Unknown context: 52541 Total unmethylated C's in CpG context: 25257864 Total unmethylated C's in CHG context: 49422337 Total unmethylated C's in CHH context: 147114775 Total unmethylated C's in Unknown context: 499727 C methylated in CpG context: 26.0% C methylated in CHG context: 2.5% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 9.5% Bismark completed in 0d 1h 7m 51s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-193_S22_L003_R1_001_val_1.fq.gz to EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-193_S22_L003_R1_001_val_1.fq.gz (26770469 sequences in total) Writing a G -> A converted version of the input file EPI-193_S22_L003_R2_001_val_2.fq.gz to EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-193_S22_L003_R2_001_val_2.fq.gz (26770469 sequences in total) Input files are EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:3001:2249_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 ATTGTNTATAATTTTGGTATAGTTTTATGTAGTTGGGGATATTTAGGGATATTGTATATAATTTTGGTATAGTTTTGTAAAGTTAGGGATATTTAGGG /B/BB#//>> Writing bisulfite mapping results to EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far 26770469 reads; of these: 26770469 (100.00%) were paired; of these: 17323811 (64.71%) aligned concordantly 0 times 3958282 (14.79%) aligned concordantly exactly 1 time 5488376 (20.50%) aligned concordantly >1 times 35.29% overall alignment rate 26770469 reads; of these: 26770469 (100.00%) were paired; of these: 17401826 (65.00%) aligned concordantly 0 times 3983428 (14.88%) aligned concordantly exactly 1 time 5385215 (20.12%) aligned concordantly >1 times 35.00% overall alignment rate Processed 26770469 sequences in total Successfully deleted the temporary files EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 26770469 Number of paired-end alignments with a unique best hit: 10697352 Mapping efficiency: 40.0% Sequence pairs with no alignments under any condition: 13242455 Sequence pairs did not map uniquely: 2830662 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5278754 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5418598 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 301211333 Total methylated C's in CpG context: 12254387 Total methylated C's in CHG context: 1506836 Total methylated C's in CHH context: 3959201 Total methylated C's in Unknown context: 62246 Total unmethylated C's in CpG context: 30734018 Total unmethylated C's in CHG context: 63666955 Total unmethylated C's in CHH context: 189089936 Total unmethylated C's in Unknown context: 644527 C methylated in CpG context: 28.5% C methylated in CHG context: 2.3% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 8.8% Bismark completed in 0d 1h 25m 52s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-194_S23_L003_R1_001_val_1.fq.gz to EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-194_S23_L003_R1_001_val_1.fq.gz (27459153 sequences in total) Writing a G -> A converted version of the input file EPI-194_S23_L003_R2_001_val_2.fq.gz to EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-194_S23_L003_R2_001_val_2.fq.gz (27459153 sequences in total) Input files are EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4438:2247_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 TTAGTNATTAAGGGGTTGTGTGTTTGAATTTTTTGTTTGGTAATAGTTTTTGTGATGATTGATATATGATATTGTGTTTTATTATTATTTGTTTTTTA BBBBB#BBB>> Writing bisulfite mapping results to EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far 27459153 reads; of these: 27459153 (100.00%) were paired; of these: 18108485 (65.95%) aligned concordantly 0 times 4245947 (15.46%) aligned concordantly exactly 1 time 5104721 (18.59%) aligned concordantly >1 times 34.05% overall alignment rate 27459153 reads; of these: 27459153 (100.00%) were paired; of these: 17993725 (65.53%) aligned concordantly 0 times 4268412 (15.54%) aligned concordantly exactly 1 time 5197016 (18.93%) aligned concordantly >1 times 34.47% overall alignment rate Processed 27459153 sequences in total Successfully deleted the temporary files EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27459153 Number of paired-end alignments with a unique best hit: 11624042 Mapping efficiency: 42.3% Sequence pairs with no alignments under any condition: 13557404 Sequence pairs did not map uniquely: 2277707 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5726606 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5897436 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 360459395 Total methylated C's in CpG context: 15208121 Total methylated C's in CHG context: 1730704 Total methylated C's in CHH context: 4696700 Total methylated C's in Unknown context: 66894 Total unmethylated C's in CpG context: 35095565 Total unmethylated C's in CHG context: 75921624 Total unmethylated C's in CHH context: 227806681 Total unmethylated C's in Unknown context: 771714 C methylated in CpG context: 30.2% C methylated in CHG context: 2.2% C methylated in CHH context: 2.0% C methylated in unknown context (CN or CHN): 8.0% Bismark completed in 0d 1h 36m 35s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-199_S24_L003_R1_001_val_1.fq.gz to EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-199_S24_L003_R1_001_val_1.fq.gz (15913069 sequences in total) Writing a G -> A converted version of the input file EPI-199_S24_L003_R2_001_val_2.fq.gz to EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-199_S24_L003_R2_001_val_2.fq.gz (15913069 sequences in total) Input files are EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:3720:2249_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 ATTAGNTTTTTATATTTAAGGAGATTGAGAGATATATTGTGAATTTTGAAAGAAAATTGAAAGAGGTTATTGAAGAAAGAGGTATGTG BBBBB#BB>> Writing bisulfite mapping results to EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far 15913069 reads; of these: 15913069 (100.00%) were paired; of these: 10515513 (66.08%) aligned concordantly 0 times 2317383 (14.56%) aligned concordantly exactly 1 time 3080173 (1591306919.36 reads; of these:%) aligned concordantly >1 times 33.9215913069% ( overall alignment rate 100.00%) were paired; of these: 10578681 (66.48%) aligned concordantly 0 times 2317757 (14.57%) aligned concordantly exactly 1 time 3016631 (18.96%) aligned concordantly >1 times 33.52% overall alignment rate Processed 15913069 sequences in total Successfully deleted the temporary files EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 15913069 Number of paired-end alignments with a unique best hit: 6267321 Mapping efficiency: 39.4% Sequence pairs with no alignments under any condition: 8113691 Sequence pairs did not map uniquely: 1532057 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3085988 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3181333 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 181304638 Total methylated C's in CpG context: 8091308 Total methylated C's in CHG context: 993527 Total methylated C's in CHH context: 3522698 Total methylated C's in Unknown context: 63898 Total unmethylated C's in CpG context: 17646077 Total unmethylated C's in CHG context: 38210008 Total unmethylated C's in CHH context: 112841020 Total unmethylated C's in Unknown context: 386634 C methylated in CpG context: 31.4% C methylated in CHG context: 2.5% C methylated in CHH context: 3.0% C methylated in unknown context (CN or CHN): 14.2% Bismark completed in 0d 0h 50m 59s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-200_S25_L003_R1_001_val_1.fq.gz to EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-200_S25_L003_R1_001_val_1.fq.gz (25100695 sequences in total) Writing a G -> A converted version of the input file EPI-200_S25_L003_R2_001_val_2.fq.gz to EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-200_S25_L003_R2_001_val_2.fq.gz (25100695 sequences in total) Input files are EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4688:2247_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 GTATGNTGTTTATGTGTTTTAGAGGTGGAGTATTGGATTAATGATAA BBBBB#BBFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:3:1107:4688:2247_2:N:0:CTTGTA/2 141 * 0 0 * * 0 0 TTANCANNNNNNNNNNNNNNNNNCTNTNNNNNACATAAACACCATAC BBB#BB#################B<#B#####BBBFFFFFFFFFFFF YT:Z:UP YF:Z:NS Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4688:2247_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 GTATGNTGTTTATGTGTTTTAGAGGTGGAGTATTGGATTAATGATAA BBBBB#BBFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:3:1107:4688:2247_2:N:0:CTTGTA/2 141 * 0 0 * * 0 0 TTANCANNNNNNNNNNNNNNNNNCTNTNNNNNACATAAACACCATAC BBB#BB#################B<#B#####BBBFFFFFFFFFFFF YT:Z:UP YF:Z:NS >>> Writing bisulfite mapping results to EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2101:4656:49942_1:N:0:CTTGTA Scaffold_09 2 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far 25100695 reads; of these: 25100695 (100.00%) were paired; of these: 15917679 (63.42%) aligned concordantly 0 times 3833844 (2510069515.27 reads; of these:%) aligned concordantly exactly 1 time 5349172 (2510069521.31 (%) aligned concordantly >1 times 36.58% overall alignment rate 100.00%) were paired; of these: 16002055 (63.75%) aligned concordantly 0 times 3838624 (15.29%) aligned concordantly exactly 1 time 5260016 (20.96%) aligned concordantly >1 times 36.25% overall alignment rate Processed 25100695 sequences in total Successfully deleted the temporary files EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 25100695 Number of paired-end alignments with a unique best hit: 10396122 Mapping efficiency: 41.4% Sequence pairs with no alignments under any condition: 11933311 Sequence pairs did not map uniquely: 2771262 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5128955 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5267166 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 292335065 Total methylated C's in CpG context: 12585999 Total methylated C's in CHG context: 1652750 Total methylated C's in CHH context: 4231978 Total methylated C's in Unknown context: 79283 Total unmethylated C's in CpG context: 28671686 Total unmethylated C's in CHG context: 61623093 Total unmethylated C's in CHH context: 183569559 Total unmethylated C's in Unknown context: 639910 C methylated in CpG context: 30.5% C methylated in CHG context: 2.6% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 11.0% Bismark completed in 0d 1h 23m 22s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-205_S26_L004_R1_001_val_1.fq.gz to EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-205_S26_L004_R1_001_val_1.fq.gz (16541499 sequences in total) Writing a G -> A converted version of the input file EPI-205_S26_L004_R2_001_val_2.fq.gz to EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-205_S26_L004_R2_001_val_2.fq.gz (16541499 sequences in total) Input files are EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1391:2218_1:N:0:ATCACG/1 99 Scaffold_03_CT_converted 56130216 1 45M = 56130216 -45 GATGTAGGTTGTGGTTGATGGAGAAATATTGGAAGTAGTATTTGT BBBBB/FFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2207:16029:91165_1:N:0:ATCACG Scaffold_16 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2213:13737:21109_1:N:0:ATCACG Scaffold_16 2 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1211:7255:87113_1:N:0:ATCACG Scaffold_16 2 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far 16541499 reads; of these: 16541499 (100.00%) were paired; of these: 10853410 (65.61%) aligned concordantly 0 times 2354083 (14.23%) aligned concordantly exactly 1 time 3334006 (20.16%) aligned concordantly >1 times 34.39% overall alignment rate 16541499 reads; of these: 16541499 (100.00%) were paired; of these: 10794891 (65.26%) aligned concordantly 0 times 2351357 (14.21%) aligned concordantly exactly 1 time 3395251 (20.53%) aligned concordantly >1 times 34.74% overall alignment rate Processed 16541499 sequences in total Successfully deleted the temporary files EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 16541499 Number of paired-end alignments with a unique best hit: 6323593 Mapping efficiency: 38.2% Sequence pairs with no alignments under any condition: 8364655 Sequence pairs did not map uniquely: 1853251 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3111821 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3211769 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 172098082 Total methylated C's in CpG context: 7352466 Total methylated C's in CHG context: 973752 Total methylated C's in CHH context: 2227658 Total methylated C's in Unknown context: 41273 Total unmethylated C's in CpG context: 18563469 Total unmethylated C's in CHG context: 36797171 Total unmethylated C's in CHH context: 106183566 Total unmethylated C's in Unknown context: 362805 C methylated in CpG context: 28.4% C methylated in CHG context: 2.6% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 10.2% Bismark completed in 0d 0h 50m 30s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-206_S27_L004_R1_001_val_1.fq.gz to EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-206_S27_L004_R1_001_val_1.fq.gz (20931018 sequences in total) Writing a G -> A converted version of the input file EPI-206_S27_L004_R2_001_val_2.fq.gz to EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-206_S27_L004_R2_001_val_2.fq.gz (20931018 sequences in total) Input files are EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1645:2233_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 TTATATGAGGTGGTGGTTATATTTTGATTTAATTTGAGGTTTTTTTTATTAATATGATTGG BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2103:6353:16906_1:N:0:CGATGT Scaffold_16 1 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1211:14006:58140_1:N:0:CGATGT Scaffold_16 1 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far 20931018 reads; of these: 20931018 (100.00%) were paired; of these: 13187170 (63.00%) aligned concordantly 0 times 3187504 (15.23%) aligned concordantly exactly 1 time 4556344 (2093101821.77 reads; of these:%) aligned concordantly >1 times 37.0020931018% ( overall alignment rate 100.00%) were paired; of these: 13310092 (63.59%) aligned concordantly 0 times 3167100 (15.13%) aligned concordantly exactly 1 time 4453826 (21.28%) aligned concordantly >1 times 36.41% overall alignment rate Processed 20931018 sequences in total Successfully deleted the temporary files EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 20931018 Number of paired-end alignments with a unique best hit: 8694089 Mapping efficiency: 41.5% Sequence pairs with no alignments under any condition: 9860951 Sequence pairs did not map uniquely: 2375978 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4266342 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4427745 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 247081316 Total methylated C's in CpG context: 10213182 Total methylated C's in CHG context: 1350781 Total methylated C's in CHH context: 3265902 Total methylated C's in Unknown context: 56380 Total unmethylated C's in CpG context: 26443083 Total unmethylated C's in CHG context: 53493463 Total unmethylated C's in CHH context: 152314905 Total unmethylated C's in Unknown context: 526689 C methylated in CpG context: 27.9% C methylated in CHG context: 2.5% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 9.7% Bismark completed in 0d 1h 9m 0s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-208_S28_L004_R1_001_val_1.fq.gz to EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-208_S28_L004_R1_001_val_1.fq.gz (29146503 sequences in total) Writing a G -> A converted version of the input file EPI-208_S28_L004_R2_001_val_2.fq.gz to EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-208_S28_L004_R2_001_val_2.fq.gz (29146503 sequences in total) Input files are EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1156:2191_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 ATGTTTTATTTTTTAGANATAATAGGTTAANNNTNTNNNNTGTAGTATTTAGNGGTTNGNNNGGAAGAGTATATGTTTGAATTTTAGTTATTTAGGTATTT BBBBBFF>> Writing bisulfite mapping results to EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2305:8854:87586_1:N:0:TTAGGC Scaffold_08 61151067 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1313:10573:73734_1:N:0:TTAGGC Scaffold_10 1 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1201:5663:17431_1:N:0:TTAGGC Scaffold_09 2 Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1112:15304:52396_1:N:0:TTAGGC Scaffold_10 1 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 29146503 reads; of these: 29146503 (100.00%) were paired; of these: 18935303 (64.97%) aligned concordantly 0 times 4124381 (14.15%) aligned concordantly exactly 1 time 6086819 (20.88%) aligned concordantly >1 times 35.03% overall alignment rate 29146503 reads; of these: 29146503 (100.00%) were paired; of these: 18852155 (64.68%) aligned concordantly 0 times 4094007 (14.05%) aligned concordantly exactly 1 time 6200341 (21.27%) aligned concordantly >1 times 35.32% overall alignment rate Processed 29146503 sequences in total Successfully deleted the temporary files EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29146503 Number of paired-end alignments with a unique best hit: 11240949 Mapping efficiency: 38.6% Sequence pairs with no alignments under any condition: 14550345 Sequence pairs did not map uniquely: 3355209 Sequence pairs which were discarded because genomic sequence could not be extracted: 4 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5552476 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5688469 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 311618922 Total methylated C's in CpG context: 11403965 Total methylated C's in CHG context: 1731400 Total methylated C's in CHH context: 3248557 Total methylated C's in Unknown context: 54196 Total unmethylated C's in CpG context: 33743386 Total unmethylated C's in CHG context: 67489106 Total unmethylated C's in CHH context: 194002508 Total unmethylated C's in Unknown context: 680321 C methylated in CpG context: 25.3% C methylated in CHG context: 2.5% C methylated in CHH context: 1.6% C methylated in unknown context (CN or CHN): 7.4% Bismark completed in 0d 1h 29m 33s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-209_S29_L004_R1_001_val_1.fq.gz to EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-209_S29_L004_R1_001_val_1.fq.gz (29638248 sequences in total) Writing a G -> A converted version of the input file EPI-209_S29_L004_R2_001_val_2.fq.gz to EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-209_S29_L004_R2_001_val_2.fq.gz (29638248 sequences in total) Input files are EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1317:2220_1:N:0:TGACCA/1 99 Scaffold_10_CT_converted 32311949 42 87M = 32311949 -87 TAAAGGTATTGGATTAGTTATTGTTGTATGAGTAAAGAATGTATATAATAAATATGATTTTAAATAGTTTTAGTTGATATATTAGGT BB>> Writing bisulfite mapping results to EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2207:11600:61311_1:N:0:TGACCA Scaffold_09 1 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2312:14878:45622_1:N:0:TGACCA Scaffold_09 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1209:21220:77577_1:N:0:TGACCA Scaffold_09 1 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1102:10195:40194_1:N:0:TGACCA Scaffold_16 3 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1114:18083:94909_1:N:0:TGACCA Scaffold_09 2 Processed 29000000 sequence pairs so far 29638248 reads; of these: 29638248 (100.00%) were paired; of these: 19174450 (64.69%) aligned concordantly 0 times 4514082 (15.23%) aligned concordantly exactly 1 time 5949716 (20.07%) aligned concordantly >1 times 35.31% overall alignment rate 29638248 reads; of these: 29638248 (100.00%) were paired; of these: 19011220 (64.14%) aligned concordantly 0 times 4547140 (15.34%) aligned concordantly exactly 1 time 6079888 (20.51%) aligned concordantly >1 times 35.86% overall alignment rate Processed 29638248 sequences in total Successfully deleted the temporary files EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29638248 Number of paired-end alignments with a unique best hit: 12390019 Mapping efficiency: 41.8% Sequence pairs with no alignments under any condition: 14317340 Sequence pairs did not map uniquely: 2930889 Sequence pairs which were discarded because genomic sequence could not be extracted: 5 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6084990 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6305024 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 367398872 Total methylated C's in CpG context: 15426958 Total methylated C's in CHG context: 1845531 Total methylated C's in CHH context: 4197293 Total methylated C's in Unknown context: 75507 Total unmethylated C's in CpG context: 38606002 Total unmethylated C's in CHG context: 78585196 Total unmethylated C's in CHH context: 228737892 Total unmethylated C's in Unknown context: 791989 C methylated in CpG context: 28.6% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 8.7% Bismark completed in 0d 1h 42m 48s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-214_S30_L004_R1_001_val_1.fq.gz to EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-214_S30_L004_R1_001_val_1.fq.gz (28660043 sequences in total) Writing a G -> A converted version of the input file EPI-214_S30_L004_R2_001_val_2.fq.gz to EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-214_S30_L004_R2_001_val_2.fq.gz (28660043 sequences in total) Input files are EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1228:2242_1:N:0:ACAGTG/1 99 Scaffold_18_CT_converted 25379951 1 41M = 25379951 -41 TAAGATGTATTTTTATAGTATAATGAAGTATATTTATTTTT BBBBBFFFFFFFFFFFFFFFFBBFFBFFFFFFFFFBFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:41 YS:i:0 YT:Z:CP D00743:144:CAAWNANXX:4:2315:1228:2242_2:N:0:ACAGTG/2 147 Scaffold_18_CT_converted 25379951 1 41M = 25379951 -41 TAAGATGTATTTTTATAGTATAATGAAGTATATTTATTTTT FFFFFFFFFFFFFFFFFFBFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2307:21282:95127_1:N:0:ACAGTG Scaffold_09 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2302:8005:16451_1:N:0:ACAGTG Scaffold_09 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2204:7409:50593_1:N:0:ACAGTG Scaffold_09 1 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2112:4091:16831_1:N:0:ACAGTG Scaffold_09 1 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1109:11354:68408_1:N:0:ACAGTG Scaffold_09 1 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1106:11751:57911_1:N:0:ACAGTG Scaffold_09 1 28660043 reads; of these:28660043 reads; of these: 28660043 ( 28660043 (100.00%) were paired; of these: 100.0019060313% () were paired; of these:66.50 % ) aligned concordantly 0 times18987602 ( 66.254198728% () aligned concordantly 0 times14.65 % ) aligned concordantly exactly 1 time4195301 ( 14.645401002% () aligned concordantly exactly 1 time18.85 % ) aligned concordantly >1 times5477140 (33.5019.11%% overall alignment rate) aligned concordantly >1 times 33.75% overall alignment rate Processed 28660043 sequences in total Successfully deleted the temporary files EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28660043 Number of paired-end alignments with a unique best hit: 11468074 Mapping efficiency: 40.0% Sequence pairs with no alignments under any condition: 14622941 Sequence pairs did not map uniquely: 2569028 Sequence pairs which were discarded because genomic sequence could not be extracted: 6 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5665121 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5802947 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 344103876 Total methylated C's in CpG context: 13048066 Total methylated C's in CHG context: 1676923 Total methylated C's in CHH context: 4069143 Total methylated C's in Unknown context: 63794 Total unmethylated C's in CpG context: 35864648 Total unmethylated C's in CHG context: 72383593 Total unmethylated C's in CHH context: 217061503 Total unmethylated C's in Unknown context: 751976 C methylated in CpG context: 26.7% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 7.8% Bismark completed in 0d 1h 39m 47s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-215_S31_L004_R1_001_val_1.fq.gz to EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-215_S31_L004_R1_001_val_1.fq.gz (21150005 sequences in total) Writing a G -> A converted version of the input file EPI-215_S31_L004_R2_001_val_2.fq.gz to EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-215_S31_L004_R2_001_val_2.fq.gz (21150005 sequences in total) Input files are EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1539:2240_1:N:0:GCCAAT/1 99 Scaffold_13_CT_converted 10986848 1 101M = 10986886 137 ATGGTAGTAGAGTGTTGGATTAATATTGGGGTTTGTATGTTTGAGTGTATGGTTTAGTAGTAGAGTGTTGGATTAATATTGGGGGTTGTATGTTTGAGTGT BBBBBFF>> Writing bisulfite mapping results to EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1305:3900:27082_1:N:0:GCCAAT Scaffold_09 1 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far 21150005 reads; of these: 21150005 (100.00%) were paired; of these: 13428551 (63.49%) aligned concordantly 0 times 3294139 (15.58%) aligned concordantly exactly 1 time 4427315 (20.93%) aligned concordantly >1 times 36.51% overall alignment rate 21150005 reads; of these: 21150005 (100.00%) were paired; of these: 13330719 (63.03%) aligned concordantly 0 times 3311858 (15.66%) aligned concordantly exactly 1 time 4507428 (21.31%) aligned concordantly >1 times 36.97% overall alignment rate Processed 21150005 sequences in total Successfully deleted the temporary files EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 21150005 Number of paired-end alignments with a unique best hit: 8898558 Mapping efficiency: 42.1% Sequence pairs with no alignments under any condition: 9932657 Sequence pairs did not map uniquely: 2318790 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4386310 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4512247 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 255324646 Total methylated C's in CpG context: 11359862 Total methylated C's in CHG context: 1449582 Total methylated C's in CHH context: 3434042 Total methylated C's in Unknown context: 63236 Total unmethylated C's in CpG context: 25363136 Total unmethylated C's in CHG context: 54116553 Total unmethylated C's in CHH context: 159601471 Total unmethylated C's in Unknown context: 546779 C methylated in CpG context: 30.9% C methylated in CHG context: 2.6% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 10.4% Bismark completed in 0d 1h 15m 54s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-220_S32_L004_R1_001_val_1.fq.gz to EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-220_S32_L004_R1_001_val_1.fq.gz (15670592 sequences in total) Writing a G -> A converted version of the input file EPI-220_S32_L004_R2_001_val_2.fq.gz to EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-220_S32_L004_R2_001_val_2.fq.gz (15670592 sequences in total) Input files are EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1490:2220_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TTTTTTGGTTGTTGTATGGTGTTGTTGTATAGTGTTGTGGTGTTGTTGTATGGTGTTGGTATATGGTGTTGTGGTGTTATGTATGGTGTTGTGGTGTTGGT BBBBBFFFFFFBFFFFFFF/BFFFFFBF/FFFFFFFFFFFBF>> Writing bisulfite mapping results to EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2116:14308:81928_1:N:0:CAGATC Scaffold_16 2 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far 15670592 reads; of these: 15670592 (100.00%) were paired; of these: 10271084 (65.54%) aligned concordantly 0 times 2353216 (15.02%) aligned concordantly exactly 1 time 3046292 (19.44%) aligned concordantly >1 times 34.46% overall alignment rate 15670592 reads; of these: 15670592 (100.00%) were paired; of these: 10197163 (65.07%) aligned concordantly 0 times 2371554 (15.13%) aligned concordantly exactly 1 time 3101875 (19.79%) aligned concordantly >1 times 34.93% overall alignment rate Processed 15670592 sequences in total Successfully deleted the temporary files EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 15670592 Number of paired-end alignments with a unique best hit: 6443741 Mapping efficiency: 41.1% Sequence pairs with no alignments under any condition: 7744109 Sequence pairs did not map uniquely: 1482742 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3171588 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3272152 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 192776371 Total methylated C's in CpG context: 7792143 Total methylated C's in CHG context: 1027385 Total methylated C's in CHH context: 3406922 Total methylated C's in Unknown context: 57729 Total unmethylated C's in CpG context: 19534468 Total unmethylated C's in CHG context: 40565305 Total unmethylated C's in CHH context: 120450148 Total unmethylated C's in Unknown context: 422486 C methylated in CpG context: 28.5% C methylated in CHG context: 2.5% C methylated in CHH context: 2.8% C methylated in unknown context (CN or CHN): 12.0% Bismark completed in 0d 0h 56m 49s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-221_S33_L004_R1_001_val_1.fq.gz to EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-221_S33_L004_R1_001_val_1.fq.gz (16300374 sequences in total) Writing a G -> A converted version of the input file EPI-221_S33_L004_R2_001_val_2.fq.gz to EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-221_S33_L004_R2_001_val_2.fq.gz (16300374 sequences in total) Input files are EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1412:2190_1:N:0:ACTTGA/1 99 Scaffold_13_CT_converted 41856358 2 98M = 41856393 133 ATTTTNTGTTTTATGTTTTATTTTTATTTTAGTGTTTGAAAAAATTTTGGAGAAAGGTAGATATTTTTTAGTGGTTGTAAAAAATATAAGTTGGATTG BBBBB#BBBBFFFFFFFFFFFFFFFFFFFFFBF7FFFFF>> Writing bisulfite mapping results to EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2211:4716:98965_1:N:0:ACTTGA Scaffold_09 2 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2103:13364:91695_1:N:0:ACTTGA Scaffold_16 2 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far 16300374 reads; of these: 16300374 (100.00%) were paired; of these: 10304625 (63.22%) aligned concordantly 0 times 2553714 (15.67%) aligned concordantly exactly 1 time 3442035 (21.12%) aligned concordantly >1 times 36.78% overall alignment rate 16300374 reads; of these: 16300374 (100.00%) were paired; of these: 10247311 (62.87%) aligned concordantly 0 times 2557704 (15.69%) aligned concordantly exactly 1 time 3495359 (21.44%) aligned concordantly >1 times 37.13% overall alignment rate Processed 16300374 sequences in total Successfully deleted the temporary files EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 16300374 Number of paired-end alignments with a unique best hit: 6871477 Mapping efficiency: 42.2% Sequence pairs with no alignments under any condition: 7612342 Sequence pairs did not map uniquely: 1816555 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3394540 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3476935 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 195629573 Total methylated C's in CpG context: 8208009 Total methylated C's in CHG context: 1115053 Total methylated C's in CHH context: 3356022 Total methylated C's in Unknown context: 59602 Total unmethylated C's in CpG context: 19626346 Total unmethylated C's in CHG context: 41123332 Total unmethylated C's in CHH context: 122200811 Total unmethylated C's in Unknown context: 418497 C methylated in CpG context: 29.5% C methylated in CHG context: 2.6% C methylated in CHH context: 2.7% C methylated in unknown context (CN or CHN): 12.5% Bismark completed in 0d 1h 1m 24s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-226_S34_L004_R1_001_val_1.fq.gz to EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-226_S34_L004_R1_001_val_1.fq.gz (11133150 sequences in total) Writing a G -> A converted version of the input file EPI-226_S34_L004_R2_001_val_2.fq.gz to EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-226_S34_L004_R2_001_val_2.fq.gz (11133150 sequences in total) Input files are EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1168:2235_1:N:0:GATCAG/1 99 Scaffold_09_CT_converted 21134968 1 84M = 21134968 -84 TTATATTATATTTTATANTGTGTAAAGTTGTNGTTAAGTGATTTATATTTGTNGTATTTTNNTTGTTATTGTTTATATAGTGGG BBBBBFFFFFFFFFFBF#BB>> Writing bisulfite mapping results to EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far 11133150 reads; of these: 11133150 (100.00%) were paired; of these: 7275943 (65.35%) aligned concordantly 0 times 1704164 (15.31%) aligned concordantly exactly 1 time 2153043 (19.34%) aligned concordantly >1 times 34.65% overall alignment rate 11133150 reads; of these: 11133150 (100.00%) were paired; of these: 7326692 (65.81%) aligned concordantly 0 times 1687118 (15.15%) aligned concordantly exactly 1 time 2119340 (19.04%) aligned concordantly >1 times 34.19% overall alignment rate Processed 11133150 sequences in total Successfully deleted the temporary files EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 11133150 Number of paired-end alignments with a unique best hit: 4644692 Mapping efficiency: 41.7% Sequence pairs with no alignments under any condition: 5510557 Sequence pairs did not map uniquely: 977901 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2290844 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2353848 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 142579752 Total methylated C's in CpG context: 6040169 Total methylated C's in CHG context: 756511 Total methylated C's in CHH context: 2622283 Total methylated C's in Unknown context: 41120 Total unmethylated C's in CpG context: 13986909 Total unmethylated C's in CHG context: 29876966 Total unmethylated C's in CHH context: 89296914 Total unmethylated C's in Unknown context: 314802 C methylated in CpG context: 30.2% C methylated in CHG context: 2.5% C methylated in CHH context: 2.9% C methylated in unknown context (CN or CHN): 11.6% Bismark completed in 0d 0h 42m 57s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-227_S35_L004_R1_001_val_1.fq.gz to EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-227_S35_L004_R1_001_val_1.fq.gz (13531234 sequences in total) Writing a G -> A converted version of the input file EPI-227_S35_L004_R2_001_val_2.fq.gz to EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-227_S35_L004_R2_001_val_2.fq.gz (13531234 sequences in total) Input files are EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1203:2205_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 TTTGTTTTTTTTTATATATAAATTATTAATTAAATAATTTAATTTTGTAAAANTTGTAAAANTATATAAATATTTATGTATTATTTTAATATTTTATAGTT BBBBB>> Writing bisulfite mapping results to EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1114:15289:101085_1:N:0:TAGCTT Scaffold_09 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1106:15612:24235_1:N:0:TAGCTT Scaffold_09 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1106:5390:26206_1:N:0:TAGCTT Scaffold_09 1 13531234 reads; of these: 13531234 (100.00%) were paired; of these: 8564398 (63.29%) aligned concordantly 0 times 2130788 (15.75%) aligned concordantly exactly 1 time 2836048 (20.96%) aligned concordantly >1 times 36.71% overall alignment rate 13531234 reads; of these: 13531234 (100.00%) were paired; of these: 8607387 (63.61%) aligned concordantly 0 times 2127294 (15.72%) aligned concordantly exactly 1 time 2796553 (20.67%) aligned concordantly >1 times 36.39% overall alignment rate Processed 13531234 sequences in total Successfully deleted the temporary files EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 13531234 Number of paired-end alignments with a unique best hit: 5777321 Mapping efficiency: 42.7% Sequence pairs with no alignments under any condition: 6365101 Sequence pairs did not map uniquely: 1388812 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2853863 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2923455 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 170387967 Total methylated C's in CpG context: 7151061 Total methylated C's in CHG context: 914187 Total methylated C's in CHH context: 3215757 Total methylated C's in Unknown context: 47223 Total unmethylated C's in CpG context: 16695256 Total unmethylated C's in CHG context: 35577795 Total unmethylated C's in CHH context: 106833911 Total unmethylated C's in Unknown context: 363445 C methylated in CpG context: 30.0% C methylated in CHG context: 2.5% C methylated in CHH context: 2.9% C methylated in unknown context (CN or CHN): 11.5% Bismark completed in 0d 0h 50m 49s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-229_S36_L004_R1_001_val_1.fq.gz to EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-229_S36_L004_R1_001_val_1.fq.gz (19891722 sequences in total) Writing a G -> A converted version of the input file EPI-229_S36_L004_R2_001_val_2.fq.gz to EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-229_S36_L004_R2_001_val_2.fq.gz (19891722 sequences in total) Input files are EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1979:2198_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 TGTATAGTATAGTTTAGTGTTGTGGTTAGTTTTAATATAGAAATATTAATTTTAATTTAATGTGATGTATTTAGAAAGTTTTAGAAAGTTTGTGGTAG B/BBBFFFF>> Writing bisulfite mapping results to EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2313:17038:73178_1:N:0:GGCTAC Scaffold_16 1 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far 19891722 reads; of these: 19891722 (100.00%) were paired; of these: 13000744 (65.36%) aligned concordantly 0 times 2936830 (14.76%) aligned concordantly exactly 1 time 3954148 (19.88%) aligned concordantly >1 times 34.64% overall alignment rate 19891722 reads; of these: 19891722 (100.00%) were paired; of these: 13119088 (65.95%) aligned concordantly 0 times 2905732 (14.61%) aligned concordantly exactly 1 time 3866902 (19.44%) aligned concordantly >1 times 34.05% overall alignment rate Processed 19891722 sequences in total Successfully deleted the temporary files EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 19891722 Number of paired-end alignments with a unique best hit: 8020238 Mapping efficiency: 40.3% Sequence pairs with no alignments under any condition: 9946231 Sequence pairs did not map uniquely: 1925253 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3928266 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4091971 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 234928287 Total methylated C's in CpG context: 9402130 Total methylated C's in CHG context: 1206978 Total methylated C's in CHH context: 3281401 Total methylated C's in Unknown context: 62587 Total unmethylated C's in CpG context: 24903264 Total unmethylated C's in CHG context: 50373954 Total unmethylated C's in CHH context: 145760560 Total unmethylated C's in Unknown context: 512946 C methylated in CpG context: 27.4% C methylated in CHG context: 2.3% C methylated in CHH context: 2.2% C methylated in unknown context (CN or CHN): 10.9% Bismark completed in 0d 1h 11m 21s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-230_S37_L004_R1_001_val_1.fq.gz to EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-230_S37_L004_R1_001_val_1.fq.gz (29439432 sequences in total) Writing a G -> A converted version of the input file EPI-230_S37_L004_R2_001_val_2.fq.gz to EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-230_S37_L004_R2_001_val_2.fq.gz (29439432 sequences in total) Input files are EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1161:2210_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 ATTTTGTATATGGTATANATTTAGTTTGATTNNTNANATNGGTGAATGATGTNGTATATNNNTTGTTTGATTGGTAAAATGGGTGAATGATGTTATATATG BBBBBFFFFFFFFFFFF#B<>> Writing bisulfite mapping results to EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1309:15438:42412_1:N:0:CTTGTA Scaffold_16 2 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1214:8602:31140_1:N:0:CTTGTA Scaffold_16 2 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1104:14877:71207_1:N:0:CTTGTA Scaffold_15 3 Processed 29000000 sequence pairs so far 29439432 reads; of these: 29439432 (100.00%) were paired; of these: 19816927 (67.31%) aligned concordantly 0 times 4140780 (14.07%) aligned concordantly exactly 1 time 5481725 (18.62%) aligned concordantly >1 times 32.69% overall alignment rate 29439432 reads; of these: 29439432 (100.00%) were paired; of these: 19725091 (67.00%) aligned concordantly 0 times 4124627 (14.01%) aligned concordantly exactly 1 time 5589714 (18.99%) aligned concordantly >1 times 33.00% overall alignment rate Processed 29439432 sequences in total Successfully deleted the temporary files EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29439432 Number of paired-end alignments with a unique best hit: 11206080 Mapping efficiency: 38.1% Sequence pairs with no alignments under any condition: 15456327 Sequence pairs did not map uniquely: 2777025 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5519967 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5686110 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 319285007 Total methylated C's in CpG context: 13011809 Total methylated C's in CHG context: 1476854 Total methylated C's in CHH context: 3593317 Total methylated C's in Unknown context: 73261 Total unmethylated C's in CpG context: 33278910 Total unmethylated C's in CHG context: 67397808 Total unmethylated C's in CHH context: 200526309 Total unmethylated C's in Unknown context: 692785 C methylated in CpG context: 28.1% C methylated in CHG context: 2.1% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 9.6% Bismark completed in 0d 1h 51m 6s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-41_S38_L005_R1_001_val_1.fq.gz to EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-41_S38_L005_R1_001_val_1.fq.gz (25055317 sequences in total) Writing a G -> A converted version of the input file EPI-41_S38_L005_R2_001_val_2.fq.gz to EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-41_S38_L005_R2_001_val_2.fq.gz (25055317 sequences in total) Input files are EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1186:2238_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 GTAGTNTTGGTTGGAATATATATTGTATTGTTATTTGTATTTGGTATATAAGNGGTATNGTNGTTGGTGTTTGGTGTGTAAGTAGTATTGTTGTTGGAGTT BBBBB#>> Writing bisulfite mapping results to EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:5:1203:12890:67154_1:N:0:ATCACG Scaffold_16 2 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:5:2309:19429:51893_1:N:0:ATCACG Scaffold_16 2 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far 25055317 reads; of these: 25055317 (100.00%) were paired; of these: 16350090 (65.26%) aligned concordantly 0 times 3786709 (15.11%) aligned concordantly exactly 1 time 4918518 (19.63%) aligned concordantly >1 times 34.74% overall alignment rate 25055317 reads; of these: 25055317 (100.00%) were paired; of these: 16269403 (64.93%) aligned concordantly 0 times 3783069 (15.10%) aligned concordantly exactly 1 time 5002845 (19.97%) aligned concordantly >1 times 35.07% overall alignment rate Processed 25055317 sequences in total Successfully deleted the temporary files EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 25055317 Number of paired-end alignments with a unique best hit: 10110534 Mapping efficiency: 40.4% Sequence pairs with no alignments under any condition: 12402840 Sequence pairs did not map uniquely: 2541943 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4993663 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5116869 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 290510503 Total methylated C's in CpG context: 12940226 Total methylated C's in CHG context: 1543391 Total methylated C's in CHH context: 4910085 Total methylated C's in Unknown context: 96039 Total unmethylated C's in CpG context: 28119492 Total unmethylated C's in CHG context: 60698341 Total unmethylated C's in CHH context: 182298968 Total unmethylated C's in Unknown context: 604385 C methylated in CpG context: 31.5% C methylated in CHG context: 2.5% C methylated in CHH context: 2.6% C methylated in unknown context (CN or CHN): 13.7% Bismark completed in 0d 1h 27m 13s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-42_S39_L005_R1_001_val_1.fq.gz to EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-42_S39_L005_R1_001_val_1.fq.gz (29623269 sequences in total) Writing a G -> A converted version of the input file EPI-42_S39_L005_R2_001_val_2.fq.gz to EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-42_S39_L005_R2_001_val_2.fq.gz (29623269 sequences in total) Input files are EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1597:2224_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 AGGTANTATGATGTGATGATGGGGTATGATGTGAAGATGGG BBBBB#BBFFFFFFFFFFFFFFFFBFFBFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:5:1107:1597:2224_2:N:0:CGATGT/2 141 * 0 0 * * 0 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNCCT ####################################<#<>> Writing bisulfite mapping results to EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 29623269 reads; of these: 29623269 (100.00%) were paired; of these: 18159622 (61.30%) aligned concordantly 0 times 4916719 (16.60%) aligned concordantly exactly 1 time 6546928 (22.10%) aligned concordantly >1 times 38.70% overall alignment rate 29623269 reads; of these: 29623269 (100.00%) were paired; of these: 18241307 (61.58%) aligned concordantly 0 times 4905564 (16.56%) aligned concordantly exactly 1 time 6476398 (21.86%) aligned concordantly >1 times 38.42% overall alignment rate Processed 29623269 sequences in total Successfully deleted the temporary files EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29623269 Number of paired-end alignments with a unique best hit: 13173399 Mapping efficiency: 44.5% Sequence pairs with no alignments under any condition: 13088150 Sequence pairs did not map uniquely: 3361720 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6518218 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6655181 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 371864315 Total methylated C's in CpG context: 17401813 Total methylated C's in CHG context: 2029825 Total methylated C's in CHH context: 4531660 Total methylated C's in Unknown context: 68790 Total unmethylated C's in CpG context: 35533244 Total unmethylated C's in CHG context: 78200824 Total unmethylated C's in CHH context: 234166949 Total unmethylated C's in Unknown context: 781521 C methylated in CpG context: 32.9% C methylated in CHG context: 2.5% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 8.1% Bismark completed in 0d 1h 48m 56s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-43_S40_L005_R1_001_val_1.fq.gz to EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-43_S40_L005_R1_001_val_1.fq.gz (22573555 sequences in total) Writing a G -> A converted version of the input file EPI-43_S40_L005_R2_001_val_2.fq.gz to EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-43_S40_L005_R2_001_val_2.fq.gz (22573555 sequences in total) Input files are EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1481:2240_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 TTTTAATATTAATATATTAAAATATAAAATTTTTATAATTATAATATATATAAATATTATAATATTAATATATTAATATAAAAATTTTATATAATTATAAT BBBBBFF>> Writing bisulfite mapping results to EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far 22573555 reads; of these: 22573555 (100.00%) were paired; of these: 13873582 (61.46%) aligned concordantly 0 times 3802013 (16.84%) aligned concordantly exactly 1 time 4897960 (21.70%) aligned concordantly >1 times 38.54% overall alignment rate 22573555 reads; of these: 22573555 (100.00%) were paired; of these: 13942903 (61.77%) aligned concordantly 0 times 3795765 (16.82%) aligned concordantly exactly 1 time 4834887 (21.42%) aligned concordantly >1 times 38.23% overall alignment rate Processed 22573555 sequences in total Successfully deleted the temporary files EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22573555 Number of paired-end alignments with a unique best hit: 10112774 Mapping efficiency: 44.8% Sequence pairs with no alignments under any condition: 10003930 Sequence pairs did not map uniquely: 2456851 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5003413 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5109361 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 291124282 Total methylated C's in CpG context: 12587981 Total methylated C's in CHG context: 1494744 Total methylated C's in CHH context: 5077384 Total methylated C's in Unknown context: 67963 Total unmethylated C's in CpG context: 28303550 Total unmethylated C's in CHG context: 60291324 Total unmethylated C's in CHH context: 183369299 Total unmethylated C's in Unknown context: 592883 C methylated in CpG context: 30.8% C methylated in CHG context: 2.4% C methylated in CHH context: 2.7% C methylated in unknown context (CN or CHN): 10.3% Bismark completed in 0d 1h 21m 27s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1217'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1217 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-44_S41_L005_R1_001_val_1.fq.gz to EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-44_S41_L005_R1_001_val_1.fq.gz (13762658 sequences in total) Writing a G -> A converted version of the input file EPI-44_S41_L005_R2_001_val_2.fq.gz to EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-44_S41_L005_R2_001_val_2.fq.gz (13762658 sequences in total) Input files are EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1348:2233_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AATTTNGGTGTATAGTTTAAGTTAGGAAAGTTTTTTTTATTAAATTGTTTTGTTATGTTTAAATAGATATTTTTTTGGTAGTAT BBBBB#/B>> Writing bisulfite mapping results to EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:5:1215:4007:34225_1:N:0:ACTTGA Scaffold_09 1 13762658 reads; of these: 13762658 (100.00%) were paired; of these: 8493354 (61.71%) aligned concordantly 0 times 2308211 (16.77%) aligned concordantly exactly 1 time 2961093 (21.52%) aligned concordantly >1 times 38.29% overall alignment rate 13762658 reads; of these: 13762658 (100.00%) were paired; of these: 8468686 (61.53%) aligned concordantly 0 times 2306213 (16.76%) aligned concordantly exactly 1 time 2987759 (21.71%) aligned concordantly >1 times 38.47% overall alignment rate Processed 13762658 sequences in total Successfully deleted the temporary files EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 13762658 Number of paired-end alignments with a unique best hit: 6084805 Mapping efficiency: 44.2% Sequence pairs with no alignments under any condition: 6118468 Sequence pairs did not map uniquely: 1559385 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3020647 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3064157 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 170813493 Total methylated C's in CpG context: 8105964 Total methylated C's in CHG context: 922535 Total methylated C's in CHH context: 2562650 Total methylated C's in Unknown context: 43087 Total unmethylated C's in CpG context: 16050613 Total unmethylated C's in CHG context: 35418280 Total unmethylated C's in CHH context: 107753451 Total unmethylated C's in Unknown context: 349691 C methylated in CpG context: 33.6% C methylated in CHG context: 2.5% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 11.0% Bismark completed in 0d 0h 48m 7s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam: 9095591 Total number duplicated alignments removed: 1259755 (13.85%) Duplicated alignments were found at: 632529 different position(s) Total count of deduplicated leftover sequences: 7835836 (86.15% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam: 13633935 Total number duplicated alignments removed: 2020190 (14.82%) Duplicated alignments were found at: 1117791 different position(s) Total count of deduplicated leftover sequences: 11613745 (85.18% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam: 12312882 Total number duplicated alignments removed: 1846060 (14.99%) Duplicated alignments were found at: 941145 different position(s) Total count of deduplicated leftover sequences: 10466822 (85.01% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam: 11581685 Total number duplicated alignments removed: 1726942 (14.91%) Duplicated alignments were found at: 879906 different position(s) Total count of deduplicated leftover sequences: 9854743 (85.09% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam: 12331886 Total number duplicated alignments removed: 1918064 (15.55%) Duplicated alignments were found at: 946129 different position(s) Total count of deduplicated leftover sequences: 10413822 (84.45% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam: 11050080 Total number duplicated alignments removed: 1579974 (14.30%) Duplicated alignments were found at: 825606 different position(s) Total count of deduplicated leftover sequences: 9470106 (85.70% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam: 9986594 Total number duplicated alignments removed: 1536515 (15.39%) Duplicated alignments were found at: 782021 different position(s) Total count of deduplicated leftover sequences: 8450079 (84.61% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam: 11023910 Total number duplicated alignments removed: 1723786 (15.64%) Duplicated alignments were found at: 865786 different position(s) Total count of deduplicated leftover sequences: 9300124 (84.36% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam: 12720630 Total number duplicated alignments removed: 2161126 (16.99%) Duplicated alignments were found at: 1085821 different position(s) Total count of deduplicated leftover sequences: 10559504 (83.01% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam: 12229033 Total number duplicated alignments removed: 1939155 (15.86%) Duplicated alignments were found at: 929619 different position(s) Total count of deduplicated leftover sequences: 10289878 (84.14% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam: 9316818 Total number duplicated alignments removed: 1420739 (15.25%) Duplicated alignments were found at: 811691 different position(s) Total count of deduplicated leftover sequences: 7896079 (84.75% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam: 11191274 Total number duplicated alignments removed: 1835341 (16.40%) Duplicated alignments were found at: 997702 different position(s) Total count of deduplicated leftover sequences: 9355933 (83.60% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam: 9915441 Total number duplicated alignments removed: 2705164 (27.28%) Duplicated alignments were found at: 1698251 different position(s) Total count of deduplicated leftover sequences: 7210277 (72.72% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam: 11727816 Total number duplicated alignments removed: 3318046 (28.29%) Duplicated alignments were found at: 2042936 different position(s) Total count of deduplicated leftover sequences: 8409770 (71.71% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam: 10439071 Total number duplicated alignments removed: 3739516 (35.82%) Duplicated alignments were found at: 2094280 different position(s) Total count of deduplicated leftover sequences: 6699555 (64.18% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam: 9405544 Total number duplicated alignments removed: 2636021 (28.03%) Duplicated alignments were found at: 1665648 different position(s) Total count of deduplicated leftover sequences: 6769523 (71.97% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam: 6380873 Total number duplicated alignments removed: 1736608 (27.22%) Duplicated alignments were found at: 1097543 different position(s) Total count of deduplicated leftover sequences: 4644265 (72.78% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam: 12255648 Total number duplicated alignments removed: 3263582 (26.63%) Duplicated alignments were found at: 1915571 different position(s) Total count of deduplicated leftover sequences: 8992066 (73.37% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam: 8593705 Total number duplicated alignments removed: 2262879 (26.33%) Duplicated alignments were found at: 1443182 different position(s) Total count of deduplicated leftover sequences: 6330826 (73.67% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam: 8267039 Total number duplicated alignments removed: 1883875 (22.79%) Duplicated alignments were found at: 1160963 different position(s) Total count of deduplicated leftover sequences: 6383164 (77.21% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam: 10438000 Total number duplicated alignments removed: 2802912 (26.85%) Duplicated alignments were found at: 1823622 different position(s) Total count of deduplicated leftover sequences: 7635088 (73.15% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam: 8967128 Total number duplicated alignments removed: 2474742 (27.60%) Duplicated alignments were found at: 1499379 different position(s) Total count of deduplicated leftover sequences: 6492386 (72.40% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam: 8408055 Total number duplicated alignments removed: 1984624 (23.60%) Duplicated alignments were found at: 1201335 different position(s) Total count of deduplicated leftover sequences: 6423431 (76.40% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam: 10233760 Total number duplicated alignments removed: 2436682 (23.81%) Duplicated alignments were found at: 1417870 different position(s) Total count of deduplicated leftover sequences: 7797078 (76.19% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam: 10209529 Total number duplicated alignments removed: 2284909 (22.38%) Duplicated alignments were found at: 1428268 different position(s) Total count of deduplicated leftover sequences: 7924620 (77.62% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam: 13724717 Total number duplicated alignments removed: 3630031 (26.45%) Duplicated alignments were found at: 2189122 different position(s) Total count of deduplicated leftover sequences: 10094686 (73.55% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam: 10790980 Total number duplicated alignments removed: 2580715 (23.92%) Duplicated alignments were found at: 1499838 different position(s) Total count of deduplicated leftover sequences: 8210265 (76.08% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam: 13143700 Total number duplicated alignments removed: 2877178 (21.89%) Duplicated alignments were found at: 1635843 different position(s) Total count of deduplicated leftover sequences: 10266522 (78.11% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam: 8444728 Total number duplicated alignments removed: 2148266 (25.44%) Duplicated alignments were found at: 1332291 different position(s) Total count of deduplicated leftover sequences: 6296462 (74.56% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam: 4103253 Total number duplicated alignments removed: 1336980 (32.58%) Duplicated alignments were found at: 804018 different position(s) Total count of deduplicated leftover sequences: 2766273 (67.42% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam: 9655530 Total number duplicated alignments removed: 2556625 (26.48%) Duplicated alignments were found at: 1509525 different position(s) Total count of deduplicated leftover sequences: 7098905 (73.52% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam: 8423410 Total number duplicated alignments removed: 2230577 (26.48%) Duplicated alignments were found at: 1361870 different position(s) Total count of deduplicated leftover sequences: 6192833 (73.52% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam: 10697352 Total number duplicated alignments removed: 2526429 (23.62%) Duplicated alignments were found at: 1585629 different position(s) Total count of deduplicated leftover sequences: 8170923 (76.38% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam: 11624042 Total number duplicated alignments removed: 2623096 (22.57%) Duplicated alignments were found at: 1648237 different position(s) Total count of deduplicated leftover sequences: 9000946 (77.43% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam: 6267321 Total number duplicated alignments removed: 1900244 (30.32%) Duplicated alignments were found at: 1204077 different position(s) Total count of deduplicated leftover sequences: 4367077 (69.68% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam: 10396121 Total number duplicated alignments removed: 2895134 (27.85%) Duplicated alignments were found at: 1778247 different position(s) Total count of deduplicated leftover sequences: 7500987 (72.15% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam: 6323590 Total number duplicated alignments removed: 1603675 (25.36%) Duplicated alignments were found at: 963679 different position(s) Total count of deduplicated leftover sequences: 4719915 (74.64% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam: 8694087 Total number duplicated alignments removed: 1956411 (22.50%) Duplicated alignments were found at: 1112526 different position(s) Total count of deduplicated leftover sequences: 6737676 (77.50% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam: 11240945 Total number duplicated alignments removed: 2599604 (23.13%) Duplicated alignments were found at: 1452536 different position(s) Total count of deduplicated leftover sequences: 8641341 (76.87% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam: 12390014 Total number duplicated alignments removed: 3444505 (27.80%) Duplicated alignments were found at: 2000861 different position(s) Total count of deduplicated leftover sequences: 8945509 (72.20% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam: 11468068 Total number duplicated alignments removed: 2764190 (24.10%) Duplicated alignments were found at: 1689980 different position(s) Total count of deduplicated leftover sequences: 8703878 (75.90% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam: 8898557 Total number duplicated alignments removed: 2505655 (28.16%) Duplicated alignments were found at: 1529678 different position(s) Total count of deduplicated leftover sequences: 6392902 (71.84% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam: 6443740 Total number duplicated alignments removed: 2081383 (32.30%) Duplicated alignments were found at: 1265421 different position(s) Total count of deduplicated leftover sequences: 4362357 (67.70% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam: 6871475 Total number duplicated alignments removed: 1959853 (28.52%) Duplicated alignments were found at: 1245701 different position(s) Total count of deduplicated leftover sequences: 4911622 (71.48% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam: 4644692 Total number duplicated alignments removed: 1206577 (25.98%) Duplicated alignments were found at: 766007 different position(s) Total count of deduplicated leftover sequences: 3438115 (74.02% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam: 5777318 Total number duplicated alignments removed: 1567966 (27.14%) Duplicated alignments were found at: 1031120 different position(s) Total count of deduplicated leftover sequences: 4209352 (72.86% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam: 8020237 Total number duplicated alignments removed: 1983971 (24.74%) Duplicated alignments were found at: 1179618 different position(s) Total count of deduplicated leftover sequences: 6036266 (75.26% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam: 11206077 Total number duplicated alignments removed: 3923633 (35.01%) Duplicated alignments were found at: 2312024 different position(s) Total count of deduplicated leftover sequences: 7282444 (64.99% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam: 10110532 Total number duplicated alignments removed: 3711212 (36.71%) Duplicated alignments were found at: 2206337 different position(s) Total count of deduplicated leftover sequences: 6399320 (63.29% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam: 13173399 Total number duplicated alignments removed: 4597382 (34.90%) Duplicated alignments were found at: 2730000 different position(s) Total count of deduplicated leftover sequences: 8576017 (65.10% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam: 10112774 Total number duplicated alignments removed: 3692163 (36.51%) Duplicated alignments were found at: 2223544 different position(s) Total count of deduplicated leftover sequences: 6420611 (63.49% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam: 6084804 Total number duplicated alignments removed: 2053760 (33.75%) Duplicated alignments were found at: 1305099 different position(s) Total count of deduplicated leftover sequences: 4031044 (66.25% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz" *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 14 Output will be written to the current directory ('/gscratch/scrubbed/sr320/1217') Summarising bedGraph parameters: =============================================================== Generating additional output in bedGraph and coverage format bedGraph format: coverage format: Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting cytosine methylation information in CpG context only (default) The bedGraph UNIX sort command will use the following memory setting: '75%'. Temporary directory used for sorting is the output directory Checking file >>EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 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Processed lines: 5500000 Processed lines: 6500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 7000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7835836 lines in total Total number of methylation call strings processed: 15671672 Final Cytosine Methylation Report ================================= Total number of C's analysed: 183501406 Total methylated C's in CpG context: 6658001 Total methylated C's in CHG context: 852229 Total methylated C's in CHH context: 1574350 Total C to T conversions in CpG context: 18809270 Total C to T conversions in CHG context: 36884209 Total C to T conversions in CHH context: 118723347 C methylated in CpG context: 26.1% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 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lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Finished processing child process. Exiting.. Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 11613745 lines in total Total number of methylation call strings processed: 23227490 Final Cytosine Methylation Report ================================= Total number of C's analysed: 256681996 Total methylated C's in CpG context: 10137100 Total methylated C's in CHG context: 1260299 Total methylated C's in CHH context: 2323535 Total C to T conversions in CpG context: 24263858 Total C to T conversions in CHG context: 51430750 Total C to T conversions in CHH context: 167266454 C methylated in CpG context: 29.5% C methylated in CHG context: 2.4% C methylated in CHH context: 1.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10466822 lines in total Total number of methylation call strings processed: 20933644 Final Cytosine Methylation Report ================================= Total number of C's analysed: 231214858 Total methylated C's in CpG context: 8681437 Total methylated C's in CHG context: 1156157 Total methylated C's in CHH context: 1936920 Total C to T conversions in CpG context: 22978618 Total C to T conversions in CHG context: 46067897 Total C to T conversions in CHH context: 150393829 C methylated in CpG context: 27.4% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9854743 lines in total Total number of methylation call strings processed: 19709486 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224084049 Total methylated C's in CpG context: 8423482 Total methylated C's in CHG context: 1104529 Total methylated C's in CHH context: 1867274 Total C to T conversions in CpG context: 22028913 Total C to T conversions in CHG context: 44713152 Total C to T conversions in CHH context: 145946699 C methylated in CpG context: 27.7% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10413822 lines in total Total number of methylation call strings processed: 20827644 Final Cytosine Methylation Report ================================= Total number of C's analysed: 243953258 Total methylated C's in CpG context: 8558544 Total methylated C's in CHG context: 1135855 Total methylated C's in CHH context: 2017566 Total C to T conversions in CpG context: 25838202 Total C to T conversions in CHG context: 48531203 Total C to T conversions in CHH context: 157871888 C methylated in CpG context: 24.9% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9470106 lines in total Total number of methylation call strings processed: 18940212 Final Cytosine Methylation Report ================================= Total number of C's analysed: 217946429 Total methylated C's in CpG context: 8187042 Total methylated C's in CHG context: 1062536 Total methylated C's in CHH context: 1832611 Total C to T conversions in CpG context: 21761145 Total C to T conversions in CHG context: 43433409 Total C to T conversions in CHH context: 141669686 C methylated in CpG context: 27.3% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 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6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8450079 lines in total Total number of methylation call strings processed: 16900158 Final Cytosine Methylation Report ================================= Total number of C's analysed: 196938082 Total methylated C's in CpG context: 7564205 Total methylated C's in CHG context: 967557 Total methylated C's in CHH context: 1694338 Total C to T conversions in CpG context: 19544907 Total C to T conversions in CHG context: 39233900 Total C to T conversions in CHH context: 127933175 C methylated in CpG context: 27.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9300124 lines in total Total number of methylation call strings processed: 18600248 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215109906 Total methylated C's in CpG context: 8244675 Total methylated C's in CHG context: 1071477 Total methylated C's in CHH context: 1772832 Total C to T conversions in CpG context: 21307910 Total C to T conversions in CHG context: 42824701 Total C to T conversions in CHH context: 139888311 C methylated in CpG context: 27.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10500000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10500000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10559504 lines in total Total number of methylation call strings processed: 21119008 Final Cytosine Methylation Report ================================= Total number of C's analysed: 225992948 Total methylated C's in CpG context: 9046557 Total methylated C's in CHG context: 1202237 Total methylated C's in CHH context: 2001278 Total C to T conversions in CpG context: 21842118 Total C to T conversions in CHG context: 45361388 Total C to T conversions in CHH context: 146539370 C methylated in CpG context: 29.3% C methylated in CHG context: 2.6% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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Exiting.. Finished processing child process. Exiting.. Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10289878 lines in total Total number of methylation call strings processed: 20579756 Final Cytosine Methylation Report ================================= Total number of C's analysed: 222520026 Total methylated C's in CpG context: 8205504 Total methylated C's in CHG context: 1105916 Total methylated C's in CHH context: 1849444 Total C to T conversions in CpG context: 22514794 Total C to T conversions in CHG context: 44690621 Total C to T conversions in CHH context: 144153747 C methylated in CpG context: 26.7% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 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Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7896079 lines in total Total number of methylation call strings processed: 15792158 Final Cytosine Methylation Report ================================= Total number of C's analysed: 180013500 Total methylated C's in CpG context: 6934397 Total methylated C's in CHG context: 872844 Total methylated C's in CHH context: 1579087 Total C to T conversions in CpG context: 17647358 Total C to T conversions in CHG context: 35893215 Total C to T conversions in CHH context: 117086599 C methylated in CpG context: 28.2% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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Exiting.. Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9355933 lines in total Total number of methylation call strings processed: 18711866 Final Cytosine Methylation Report ================================= Total number of C's analysed: 214985786 Total methylated C's in CpG context: 8245428 Total methylated C's in CHG context: 1047240 Total methylated C's in CHH context: 1811240 Total C to T conversions in CpG context: 21238566 Total C to T conversions in CHG context: 42806098 Total C to T conversions in CHH context: 139837214 C methylated in CpG context: 28.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 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Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7210277 lines in total Total number of methylation call strings processed: 14420554 Final Cytosine Methylation Report ================================= Total number of C's analysed: 154371720 Total methylated C's in CpG context: 6619617 Total methylated C's in CHG context: 739999 Total methylated C's in CHH context: 1943298 Total C to T conversions in CpG context: 14863708 Total C to T conversions in CHG context: 32156644 Total C to T conversions in CHH context: 98048454 C methylated in CpG context: 30.8% C methylated in CHG context: 2.2% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 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8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8409770 lines in total Total number of methylation call strings processed: 16819540 Final Cytosine Methylation Report ================================= Total number of C's analysed: 181742375 Total methylated C's in CpG context: 7874020 Total methylated C's in CHG context: 929405 Total methylated C's in CHH context: 2251146 Total C to T conversions in CpG context: 16740253 Total C to T conversions in CHG context: 36920601 Total C to T conversions in CHH context: 117026950 C methylated in CpG context: 32.0% C methylated in CHG context: 2.5% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6699555 lines in total Total number of methylation call strings processed: 13399110 Final Cytosine Methylation Report ================================= Total number of C's analysed: 136016129 Total methylated C's in CpG context: 5750945 Total methylated C's in CHG context: 699624 Total methylated C's in CHH context: 1733351 Total C to T conversions in CpG context: 13021245 Total C to T conversions in CHG context: 28351144 Total C to T conversions in CHH context: 86459820 C methylated in CpG context: 30.6% C methylated in CHG context: 2.4% C methylated in CHH context: 2.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6769523 lines in total Total number of methylation call strings processed: 13539046 Final Cytosine Methylation Report ================================= Total number of C's analysed: 142831749 Total methylated C's in CpG context: 5958725 Total methylated C's in CHG context: 672814 Total methylated C's in CHH context: 1876297 Total C to T conversions in CpG context: 13541358 Total C to T conversions in CHG context: 29209282 Total C to T conversions in CHH context: 91573273 C methylated in CpG context: 30.6% C methylated in CHG context: 2.3% C methylated in CHH context: 2.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4644265 lines in total Total number of methylation call strings processed: 9288530 Final Cytosine Methylation Report ================================= Total number of C's analysed: 99137282 Total methylated C's in CpG context: 4217985 Total methylated C's in CHG context: 535634 Total methylated C's in CHH context: 1932988 Total C to T conversions in CpG context: 9196803 Total C to T conversions in CHG context: 20037165 Total C to T conversions in CHH context: 63216707 C methylated in CpG context: 31.4% C methylated in CHG context: 2.6% C methylated in CHH context: 3.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 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8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8992066 lines in total Total number of methylation call strings processed: 17984132 Final Cytosine Methylation Report ================================= Total number of C's analysed: 176538868 Total methylated C's in CpG context: 7344361 Total methylated C's in CHG context: 912079 Total methylated C's in CHH context: 2297548 Total C to T conversions in CpG context: 16933790 Total C to T conversions in CHG context: 36262599 Total C to T conversions in CHH context: 112788491 C methylated in CpG context: 30.3% C methylated in CHG context: 2.5% C methylated in CHH context: 2.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6330826 lines in total Total number of methylation call strings processed: 12661652 Final Cytosine Methylation Report ================================= Total number of C's analysed: 124508835 Total methylated C's in CpG context: 4903316 Total methylated C's in CHG context: 619102 Total methylated C's in CHH context: 1795108 Total C to T conversions in CpG context: 12097133 Total C to T conversions in CHG context: 25334277 Total C to T conversions in CHH context: 79759899 C methylated in CpG context: 28.8% C methylated in CHG context: 2.4% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6383164 lines in total Total number of methylation call strings processed: 12766328 Final Cytosine Methylation Report ================================= Total number of C's analysed: 122908719 Total methylated C's in CpG context: 4824979 Total methylated C's in CHG context: 612515 Total methylated C's in CHH context: 1827593 Total C to T conversions in CpG context: 12090566 Total C to T conversions in CHG context: 25238601 Total C to T conversions in CHH context: 78314465 C methylated in CpG context: 28.5% C methylated in CHG context: 2.4% C methylated in CHH context: 2.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 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5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7635088 lines in total Total number of methylation call strings processed: 15270176 Final Cytosine Methylation Report ================================= Total number of C's analysed: 169475057 Total methylated C's in CpG context: 6721143 Total methylated C's in CHG context: 1081552 Total methylated C's in CHH context: 3482873 Total C to T conversions in CpG context: 15986854 Total C to T conversions in CHG context: 34252524 Total C to T conversions in CHH context: 107950111 C methylated in CpG context: 29.6% C methylated in CHG context: 3.1% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6492386 lines in total Total number of methylation call strings processed: 12984772 Final Cytosine Methylation Report ================================= Total number of C's analysed: 139836026 Total methylated C's in CpG context: 5749134 Total methylated C's in CHG context: 652679 Total methylated C's in CHH context: 1958750 Total C to T conversions in CpG context: 13380784 Total C to T conversions in CHG context: 28960958 Total C to T conversions in CHH context: 89133721 C methylated in CpG context: 30.1% C methylated in CHG context: 2.2% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6423431 lines in total Total number of methylation call strings processed: 12846862 Final Cytosine Methylation Report ================================= Total number of C's analysed: 127237948 Total methylated C's in CpG context: 5351229 Total methylated C's in CHG context: 663359 Total methylated C's in CHH context: 2095978 Total C to T conversions in CpG context: 12254820 Total C to T conversions in CHG context: 26439097 Total C to T conversions in CHH context: 80433465 C methylated in CpG context: 30.4% C methylated in CHG context: 2.4% C methylated in CHH context: 2.5% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 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5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7797078 lines in total Total number of methylation call strings processed: 15594156 Final Cytosine Methylation Report ================================= Total number of C's analysed: 151781122 Total methylated C's in CpG context: 5915753 Total methylated C's in CHG context: 746213 Total methylated C's in CHH context: 1797219 Total C to T conversions in CpG context: 15089108 Total C to T conversions in CHG context: 31172597 Total C to T conversions in CHH context: 97060232 C methylated in CpG context: 28.2% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 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5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7924620 lines in total Total number of methylation call strings processed: 15849240 Final Cytosine Methylation Report ================================= Total number of C's analysed: 169230320 Total methylated C's in CpG context: 6854838 Total methylated C's in CHG context: 805593 Total methylated C's in CHH context: 2153742 Total C to T conversions in CpG context: 16729782 Total C to T conversions in CHG context: 34594121 Total C to T conversions in CHH context: 108092244 C methylated in CpG context: 29.1% C methylated in CHG context: 2.3% C methylated in CHH context: 2.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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Exiting.. Finished processing child process. Exiting.. Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10000000 Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10094686 lines in total Total number of methylation call strings processed: 20189372 Final Cytosine Methylation Report ================================= Total number of C's analysed: 212732771 Total methylated C's in CpG context: 8409431 Total methylated C's in CHG context: 937010 Total methylated C's in CHH context: 2366691 Total C to T conversions in CpG context: 21389527 Total C to T conversions in CHG context: 42655847 Total C to T conversions in CHH context: 136974265 C methylated in CpG context: 28.2% C methylated in CHG context: 2.1% C methylated in CHH context: 1.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8210265 lines in total Total number of methylation call strings processed: 16420530 Final Cytosine Methylation Report ================================= Total number of C's analysed: 182131746 Total methylated C's in CpG context: 7773669 Total methylated C's in CHG context: 910797 Total methylated C's in CHH context: 2287864 Total C to T conversions in CpG context: 17313389 Total C to T conversions in CHG context: 37265101 Total C to T conversions in CHH context: 116580926 C methylated in CpG context: 31.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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Exiting.. Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10266522 lines in total Total number of methylation call strings processed: 20533044 Final Cytosine Methylation Report ================================= Total number of C's analysed: 222524486 Total methylated C's in CpG context: 8754862 Total methylated C's in CHG context: 1102130 Total methylated C's in CHH context: 2694418 Total C to T conversions in CpG context: 21458168 Total C to T conversions in CHG context: 44943458 Total C to T conversions in CHH context: 143571450 C methylated in CpG context: 29.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6296462 lines in total Total number of methylation call strings processed: 12592924 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128398540 Total methylated C's in CpG context: 5213255 Total methylated C's in CHG context: 627120 Total methylated C's in CHH context: 2204316 Total C to T conversions in CpG context: 12567730 Total C to T conversions in CHG context: 26364706 Total C to T conversions in CHH context: 81421413 C methylated in CpG context: 29.3% C methylated in CHG context: 2.3% C methylated in CHH context: 2.6% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 2766273 lines in total Total number of methylation call strings processed: 5532546 Final Cytosine Methylation Report ================================= Total number of C's analysed: 57532394 Total methylated C's in CpG context: 2287343 Total methylated C's in CHG context: 323890 Total methylated C's in CHH context: 1768982 Total C to T conversions in CpG context: 5639671 Total C to T conversions in CHG context: 11658279 Total C to T conversions in CHH context: 35854229 C methylated in CpG context: 28.9% C methylated in CHG context: 2.7% C methylated in CHH context: 4.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7098905 lines in total Total number of methylation call strings processed: 14197810 Final Cytosine Methylation Report ================================= Total number of C's analysed: 150742463 Total methylated C's in CpG context: 6936899 Total methylated C's in CHG context: 814250 Total methylated C's in CHH context: 2156222 Total C to T conversions in CpG context: 13822954 Total C to T conversions in CHG context: 31050905 Total C to T conversions in CHH context: 95961233 C methylated in CpG context: 33.4% C methylated in CHG context: 2.6% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6192833 lines in total Total number of methylation call strings processed: 12385666 Final Cytosine Methylation Report ================================= Total number of C's analysed: 115906900 Total methylated C's in CpG context: 4644294 Total methylated C's in CHG context: 619856 Total methylated C's in CHH context: 1638581 Total C to T conversions in CpG context: 11620008 Total C to T conversions in CHG context: 23551619 Total C to T conversions in CHH context: 73832542 C methylated in CpG context: 28.6% C methylated in CHG context: 2.6% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 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8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8170923 lines in total Total number of methylation call strings processed: 16341846 Final Cytosine Methylation Report ================================= Total number of C's analysed: 156322050 Total methylated C's in CpG context: 6612365 Total methylated C's in CHG context: 770831 Total methylated C's in CHH context: 2168983 Total C to T conversions in CpG context: 15198462 Total C to T conversions in CHG context: 31981857 Total C to T conversions in CHH context: 99589552 C methylated in CpG context: 30.3% C methylated in CHG context: 2.4% C methylated in CHH context: 2.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9000946 lines in total Total number of methylation call strings processed: 18001892 Final Cytosine Methylation Report ================================= Total number of C's analysed: 203726589 Total methylated C's in CpG context: 8959141 Total methylated C's in CHG context: 996952 Total methylated C's in CHH context: 2787951 Total C to T conversions in CpG context: 18995825 Total C to T conversions in CHG context: 41660215 Total C to T conversions in CHH context: 130326505 C methylated in CpG context: 32.0% C methylated in CHG context: 2.3% C methylated in CHH context: 2.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4367077 lines in total Total number of methylation call strings processed: 8734154 Final Cytosine Methylation Report ================================= Total number of C's analysed: 88024093 Total methylated C's in CpG context: 4047323 Total methylated C's in CHG context: 479419 Total methylated C's in CHH context: 1871691 Total C to T conversions in CpG context: 8070663 Total C to T conversions in CHG context: 17975035 Total C to T conversions in CHH context: 55579962 C methylated in CpG context: 33.4% C methylated in CHG context: 2.6% C methylated in CHH context: 3.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 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5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Now waiting for all child processes to complete Processed lines: 7500000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7500987 lines in total Total number of methylation call strings processed: 15001974 Final Cytosine Methylation Report ================================= Total number of C's analysed: 143389134 Total methylated C's in CpG context: 6473128 Total methylated C's in CHG context: 794893 Total methylated C's in CHH context: 2249885 Total C to T conversions in CpG context: 13251440 Total C to T conversions in CHG context: 29375321 Total C to T conversions in CHH context: 91244467 C methylated in CpG context: 32.8% C methylated in CHG context: 2.6% C methylated in CHH context: 2.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4719915 lines in total Total number of methylation call strings processed: 9439830 Final Cytosine Methylation Report ================================= Total number of C's analysed: 85575964 Total methylated C's in CpG context: 3859626 Total methylated C's in CHG context: 469729 Total methylated C's in CHH context: 1198594 Total C to T conversions in CpG context: 8425101 Total C to T conversions in CHG context: 17659824 Total C to T conversions in CHH context: 53963090 C methylated in CpG context: 31.4% C methylated in CHG context: 2.6% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6737676 lines in total Total number of methylation call strings processed: 13475352 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128475689 Total methylated C's in CpG context: 5690111 Total methylated C's in CHG context: 686060 Total methylated C's in CHH context: 1836981 Total C to T conversions in CpG context: 12491913 Total C to T conversions in CHG context: 26714902 Total C to T conversions in CHH context: 81055722 C methylated in CpG context: 31.3% C methylated in CHG context: 2.5% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 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8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8641341 lines in total Total number of methylation call strings processed: 17282682 Final Cytosine Methylation Report ================================= Total number of C's analysed: 158634154 Total methylated C's in CpG context: 6281105 Total methylated C's in CHG context: 854946 Total methylated C's in CHH context: 1753269 Total C to T conversions in CpG context: 16254051 Total C to T conversions in CHG context: 33112776 Total C to T conversions in CHH context: 100378007 C methylated in CpG context: 27.9% C methylated in CHG context: 2.5% C methylated in CHH context: 1.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 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Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8945509 lines in total Total number of methylation call strings processed: 17891018 Final Cytosine Methylation Report ================================= Total number of C's analysed: 181303125 Total methylated C's in CpG context: 8133825 Total methylated C's in CHG context: 907176 Total methylated C's in CHH context: 2249034 Total C to T conversions in CpG context: 17357263 Total C to T conversions in CHG context: 37254559 Total C to T conversions in CHH context: 115401268 C methylated in CpG context: 31.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 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8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8703878 lines in total Total number of methylation call strings processed: 17407756 Final Cytosine Methylation Report ================================= Total number of C's analysed: 181129898 Total methylated C's in CpG context: 7299763 Total methylated C's in CHG context: 895027 Total methylated C's in CHH context: 2311106 Total C to T conversions in CpG context: 17951668 Total C to T conversions in CHG context: 36965157 Total C to T conversions in CHH context: 115707177 C methylated in CpG context: 28.9% C methylated in CHG context: 2.4% C methylated in CHH context: 2.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6392902 lines in total Total number of methylation call strings processed: 12785804 Final Cytosine Methylation Report ================================= Total number of C's analysed: 126318223 Total methylated C's in CpG context: 5908942 Total methylated C's in CHG context: 702435 Total methylated C's in CHH context: 1841804 Total C to T conversions in CpG context: 11618123 Total C to T conversions in CHG context: 25937403 Total C to T conversions in CHH context: 80309516 C methylated in CpG context: 33.7% C methylated in CHG context: 2.6% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4362357 lines in total Total number of methylation call strings processed: 8724714 Final Cytosine Methylation Report ================================= Total number of C's analysed: 89710026 Total methylated C's in CpG context: 3860035 Total methylated C's in CHG context: 483168 Total methylated C's in CHH context: 1807632 Total C to T conversions in CpG context: 8426280 Total C to T conversions in CHG context: 18264364 Total C to T conversions in CHH context: 56868547 C methylated in CpG context: 31.4% C methylated in CHG context: 2.6% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4911622 lines in total Total number of methylation call strings processed: 9823244 Final Cytosine Methylation Report ================================= Total number of C's analysed: 96701418 Total methylated C's in CpG context: 4236787 Total methylated C's in CHG context: 538030 Total methylated C's in CHH context: 1814920 Total C to T conversions in CpG context: 9099073 Total C to T conversions in CHG context: 19735564 Total C to T conversions in CHH context: 61277044 C methylated in CpG context: 31.8% C methylated in CHG context: 2.7% C methylated in CHH context: 2.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 3438115 lines in total Total number of methylation call strings processed: 6876230 Final Cytosine Methylation Report ================================= Total number of C's analysed: 74285747 Total methylated C's in CpG context: 3347989 Total methylated C's in CHG context: 403265 Total methylated C's in CHH context: 1509605 Total C to T conversions in CpG context: 6780487 Total C to T conversions in CHG context: 15120311 Total C to T conversions in CHH context: 47124090 C methylated in CpG context: 33.1% C methylated in CHG context: 2.6% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4209352 lines in total Total number of methylation call strings processed: 8418704 Final Cytosine Methylation Report ================================= Total number of C's analysed: 86316145 Total methylated C's in CpG context: 3751343 Total methylated C's in CHG context: 464615 Total methylated C's in CHH context: 1765502 Total C to T conversions in CpG context: 8102850 Total C to T conversions in CHG context: 17545411 Total C to T conversions in CHH context: 54686424 C methylated in CpG context: 31.6% C methylated in CHG context: 2.6% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 6000000 Finished processing child process. Exiting.. Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Processed lines: 6000000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Processed lines: 6000000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6036266 lines in total Total number of methylation call strings processed: 12072532 Final Cytosine Methylation Report ================================= Total number of C's analysed: 120448317 Total methylated C's in CpG context: 5162434 Total methylated C's in CHG context: 610621 Total methylated C's in CHH context: 1841547 Total C to T conversions in CpG context: 11661347 Total C to T conversions in CHG context: 24880747 Total C to T conversions in CHH context: 76291621 C methylated in CpG context: 30.7% C methylated in CHG context: 2.4% C methylated in CHH context: 2.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 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6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7282444 lines in total Total number of methylation call strings processed: 14564888 Final Cytosine Methylation Report ================================= Total number of C's analysed: 139950493 Total methylated C's in CpG context: 5977998 Total methylated C's in CHG context: 651184 Total methylated C's in CHH context: 1768421 Total C to T conversions in CpG context: 13704103 Total C to T conversions in CHG context: 28593233 Total C to T conversions in CHH context: 89255554 C methylated in CpG context: 30.4% C methylated in CHG context: 2.2% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6399320 lines in total Total number of methylation call strings processed: 12798640 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128539262 Total methylated C's in CpG context: 5867583 Total methylated C's in CHG context: 687621 Total methylated C's in CHH context: 2454676 Total C to T conversions in CpG context: 11862497 Total C to T conversions in CHG context: 26124666 Total C to T conversions in CHH context: 81542219 C methylated in CpG context: 33.1% C methylated in CHG context: 2.6% C methylated in CHH context: 2.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 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8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8576017 lines in total Total number of methylation call strings processed: 17152034 Final Cytosine Methylation Report ================================= Total number of C's analysed: 167743909 Total methylated C's in CpG context: 8085260 Total methylated C's in CHG context: 910439 Total methylated C's in CHH context: 2251034 Total C to T conversions in CpG context: 15228220 Total C to T conversions in CHG context: 34537608 Total C to T conversions in CHH context: 106731348 C methylated in CpG context: 34.7% C methylated in CHG context: 2.6% C methylated in CHH context: 2.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6420611 lines in total Total number of methylation call strings processed: 12841222 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128026299 Total methylated C's in CpG context: 5689722 Total methylated C's in CHG context: 671794 Total methylated C's in CHH context: 2537937 Total C to T conversions in CpG context: 11970270 Total C to T conversions in CHG context: 25906277 Total C to T conversions in CHH context: 81250299 C methylated in CpG context: 32.2% C methylated in CHG context: 2.5% C methylated in CHH context: 3.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 LN:27737463 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/geoduck/v01 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 4000000 Now waiting for all child processes to complete Processed lines: 3500000 Processed lines: 4000000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4031044 lines in total Total number of methylation call strings processed: 8062088 Final Cytosine Methylation Report ================================= Total number of C's analysed: 79983322 Total methylated C's in CpG context: 3855731 Total methylated C's in CHG context: 431899 Total methylated C's in CHH context: 1321843 Total C to T conversions in CpG context: 7250942 Total C to T conversions in CHG context: 16319796 Total C to T conversions in CHH context: 50803111 C methylated in CpG context: 34.7% C methylated in CHG context: 2.6% C methylated in CHH context: 2.5% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1217/CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1217/CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 52 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-200_S25_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-200_S25_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-208_S28_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-208_S28_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-208_S28_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-209_S29_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-209_S29_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-209_S29_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-229_S36_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-229_S36_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-229_S36_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-230_S37_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-230_S37_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-230_S37_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== No Bismark/Bowtie2 single-end BAM files detected Found Bismark/Bowtie2 paired-end files No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 52 Bismark BAM file(s)... >> Reading from Bismark report: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html << [bam_sort_core] merging from 0 files and 28 in-memory blocks... 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Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-103_S27_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1084861 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 838867 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 675348 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 771355 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 694256 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 676942 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 495336 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 695303 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 438486 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 575576 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 570579 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 606443 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 489725 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 626011 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 499547 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 395422 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 420528 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 304048 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-103_S27_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-103_S27_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-104_S28_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1245587 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 972582 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 779148 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 885398 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 806823 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 781504 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 574871 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 805014 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 508231 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 670718 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 654979 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 701313 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 568484 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 707519 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 574717 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 454207 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 481518 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 346412 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-104_S28_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-104_S28_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-111_S29_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1191107 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 919576 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 734661 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 845147 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 756515 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 738196 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 545035 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 758039 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 480139 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 634255 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 620582 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 664082 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 538729 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 676868 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 545617 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 432366 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 462079 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 328702 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-111_S29_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-111_S29_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-113_S30_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1144955 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 887443 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 713156 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 820426 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 742515 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 722827 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 533945 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 737135 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 466646 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 616450 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 600686 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 641027 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 521484 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 651840 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 530329 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 417711 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 446720 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 324079 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-113_S30_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-113_S30_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-119_S31_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1258095 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 981838 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 783744 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 903172 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 814296 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 793418 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 581495 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 816384 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 515848 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 677051 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 672248 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 707857 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 578501 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 726275 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 589938 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 466175 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 495298 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 357030 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-119_S31_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-119_S31_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-120_S32_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1149296 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 891788 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 709909 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 825490 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 734685 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 713899 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 529135 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 735663 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 466720 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 618795 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 604403 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 644350 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 526388 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 660854 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 532091 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 418026 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 452442 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 318699 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-120_S32_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-120_S32_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-127_S33_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1080767 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 835656 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 669892 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 769248 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 695838 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 674370 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 497398 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 693054 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 441134 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 576963 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 571834 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 603117 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 492545 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 624704 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 499341 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 393815 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 418916 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 298019 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-127_S33_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-127_S33_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-128_S34_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1118299 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 868235 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 697636 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 794861 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 718042 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 698463 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 516544 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 718157 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 454963 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 598576 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 587298 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 625777 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 511044 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 646813 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 519831 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 408189 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 436717 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 309215 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-128_S34_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-128_S34_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-135_S35_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1111554 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 861610 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 696231 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 791967 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 710008 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 693184 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 512744 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 717754 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 453428 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 598852 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 583083 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 623176 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 508375 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 640525 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 514190 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 405937 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 432890 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 307670 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-135_S35_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-135_S35_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-136_S36_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1138865 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 879482 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 710165 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 808271 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 725471 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 714051 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 521796 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 728520 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 460988 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 609333 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 598730 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 634410 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 519292 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 654163 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 521834 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 415638 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 443714 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 314317 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-136_S36_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-136_S36_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-143_S37_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1031704 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 802134 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 645547 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 733058 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 658967 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 644780 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 476265 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 665879 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 423164 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 553777 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 544486 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 579307 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 471307 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 598154 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 478612 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 375442 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 405105 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 287266 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-143_S37_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-143_S37_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-145_S38_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1123355 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 869315 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 694748 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 795166 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 718802 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 703924 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 517083 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 720656 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 456431 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 601856 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 595335 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 628128 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 514060 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 640967 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 519907 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 406366 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 438128 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 313701 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-145_S38_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-145_S38_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-151_S2_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 917488 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 710836 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 572506 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 651179 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 586577 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 571817 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 421052 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 589920 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 373543 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 493551 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 477687 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 512479 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 417542 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 534622 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 426534 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 331754 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 359835 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 260112 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-151_S2_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-151_S2_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-152_S3_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 985275 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 761753 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 612427 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 692270 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 628856 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 611275 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 456942 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 635587 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 399396 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 531151 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 510000 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 552500 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 451232 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 569697 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 455064 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 355309 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 384776 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 274441 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-152_S3_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-152_S3_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-153_S4_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 823252 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 634980 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 510329 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 585349 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 522095 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 513299 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 378483 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 528072 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 332036 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 441562 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 429418 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 459135 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 375203 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 472706 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 379642 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 297137 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 321938 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 232067 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-153_S4_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-153_S4_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-154_S5_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 888035 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 690016 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 550880 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 625712 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 567151 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 554398 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 410273 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 568429 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 361707 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 480747 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 464292 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 494758 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 404268 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 507274 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 409208 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 322155 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 346467 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 253569 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-154_S5_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-154_S5_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-159_S6_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 696991 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 538435 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 435628 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 493156 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 444835 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 437174 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 322082 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 447375 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 281339 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 376613 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 362371 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 387040 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 315456 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 407522 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 320771 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 249595 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 271640 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 197802 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-159_S6_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-159_S6_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-160_S7_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 983464 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 762039 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 612215 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 695096 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 633032 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 619295 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 452038 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 630025 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 399644 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 528350 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 514303 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 549748 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 448936 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 568370 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 453690 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 356275 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 386758 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 276622 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-160_S7_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-160_S7_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-161_S8_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 839695 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 653856 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 521097 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 600273 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 535499 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 527366 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 386794 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 539081 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 343247 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 448148 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 441994 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 469099 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 381538 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 484678 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 387699 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 303897 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 327884 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 234600 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-161_S8_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-161_S8_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-162_S9_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 824811 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 636674 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 511422 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 588916 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 523360 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 513804 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 381151 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 528499 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 333536 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 439322 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 433963 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 460897 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 373712 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 475525 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 380650 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 296799 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 322633 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 231606 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-162_S9_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-162_S9_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-167_S10_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1018116 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 785397 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 626447 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 711392 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 640091 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 628486 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 460858 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 643157 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 405664 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 546922 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 523529 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 568951 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 458151 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 575423 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 458729 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 365934 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 389376 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 281952 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-167_S10_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-167_S10_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-168_S11_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 851833 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 658637 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 532651 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 607722 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 541913 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 533405 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 395443 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 550033 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 348188 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 457276 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 445413 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 475085 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 388593 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 497461 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 395878 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 306998 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 335908 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 241347 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-168_S11_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-168_S11_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-169_S12_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 813911 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 625817 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 501452 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 563569 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 514149 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 500743 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 370520 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 515777 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 326970 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 436873 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 418853 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 449813 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 363957 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 466678 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 368345 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 291196 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 313484 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 227693 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-169_S12_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-169_S12_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-170_S13_L002.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 922019 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 718685 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 579664 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 667234 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 598437 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 575309 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 428688 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 595151 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 374691 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 496883 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 490605 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 517070 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 424042 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 539467 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 429896 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 335247 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 366582 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 267188 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-170_S13_L002.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-170_S13_L002.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-175_S14_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 988407 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 764177 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 611384 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 690495 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 630755 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 615274 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 451643 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 633856 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 399555 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 533542 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 512287 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 553228 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 449652 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 567070 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 454946 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 358216 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 381508 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 279672 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-175_S14_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-175_S14_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-176_S15_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1159032 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 900348 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 718766 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 828066 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 741726 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 717732 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 538566 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 744939 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 469032 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 621815 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 611769 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 651006 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 527137 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 661544 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 538992 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 423563 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 451365 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 322183 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-176_S15_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-176_S15_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-181_S16_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 998161 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 768701 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 619104 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 699129 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 637275 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 615659 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 457724 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 638718 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 402123 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 536706 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 513651 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 555522 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 454680 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 574243 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 456918 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 360109 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 387428 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 279820 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-181_S16_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-181_S16_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-182_S17_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1151279 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 888521 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 711485 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 820744 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 734933 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 718122 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 529592 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 737582 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 463641 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 616317 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 599860 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 642837 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 520472 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 652934 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 530515 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 414750 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 445036 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 319418 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-182_S17_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-182_S17_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-184_S18_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 848319 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 655019 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 517902 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 584845 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 533780 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 516401 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 381508 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 535872 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 337659 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 458185 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 432639 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 474384 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 381630 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 492486 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 379007 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 304134 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 322647 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 237367 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-184_S18_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-184_S18_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-185_S19_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 484179 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 373957 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 300673 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 342166 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 305901 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 302013 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 223663 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 310818 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 196060 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 260328 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 251300 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 268719 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 218854 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 287116 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 223166 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 170762 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 190139 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 137016 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-185_S19_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-185_S19_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-187_S20_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 881972 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 676395 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 537813 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 606694 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 553812 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 536520 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 398885 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 561750 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 348321 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 480620 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 446585 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 490597 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 397847 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 501399 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 393666 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 310045 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 333037 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 245945 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-187_S20_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-187_S20_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-188_S21_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 798150 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 615466 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 495784 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 567021 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 511133 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 497142 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 363280 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 511105 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 322414 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 427587 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 412612 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 442809 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 360304 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 459543 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 363610 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 288904 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 311855 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 224087 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-188_S21_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-188_S21_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-193_S22_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 940810 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 725522 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 581439 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 659857 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 597631 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 583141 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 431107 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 601439 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 379198 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 504234 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 488112 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 524874 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 426238 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 543391 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 430378 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 339210 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 365463 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 262264 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-193_S22_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-193_S22_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-194_S23_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1062314 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 821406 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 659527 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 749875 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 678861 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 660722 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 485774 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 682495 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 428876 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 576099 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 553837 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 593795 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 485470 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 609850 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 485152 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 384247 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 411437 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 297624 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-194_S23_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-194_S23_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-199_S24_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 638642 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 489136 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 397405 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 447812 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 402771 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 391983 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 293167 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 410189 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 258109 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 343796 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 328259 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 353616 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 290825 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 371946 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 290202 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 227350 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 246994 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 179607 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-199_S24_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-199_S24_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-200_S25_L003.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 844120 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 649218 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 524205 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 593654 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 537636 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 521971 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 388534 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 540152 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 337515 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 456011 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 433925 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 470310 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 383574 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 486062 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 384431 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 301035 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 324842 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 234051 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-200_S25_L003.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-200_S25_L003.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-205_S26_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 633868 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 489365 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 392582 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 447283 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 405765 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 389583 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 288420 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 405302 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 255438 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 343287 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 326515 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 353084 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 287684 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 367743 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 289319 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 227685 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 246330 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 178113 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-205_S26_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-205_S26_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-206_S27_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 819271 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 633748 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 508285 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 573892 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 523880 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 502290 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 369655 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 524936 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 329216 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 446368 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 418828 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 460621 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 370383 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 477303 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 369033 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 292288 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 315950 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 228844 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-206_S27_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-206_S27_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-208_S28_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 959798 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 739451 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 593722 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 682325 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 613105 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 592973 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 438640 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 613937 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 386665 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 513649 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 501028 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 535057 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 434593 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 553280 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 438881 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 348769 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 372849 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 275459 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-208_S28_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-208_S28_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-209_S29_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 991820 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 765645 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 617532 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 698975 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 636316 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 613630 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 453739 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 635411 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 402034 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 535118 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 517565 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 552793 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 454112 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 568648 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 453748 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 356583 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 384548 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 278130 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-209_S29_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-209_S29_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-214_S30_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1040752 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 804070 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 644840 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 732741 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 667086 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 647371 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 471837 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 665764 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 417522 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 557644 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 541195 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 582086 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 470372 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 592504 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 475296 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 375326 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 402364 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 290665 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-214_S30_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-214_S30_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-215_S31_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 787457 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 605843 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 488162 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 548026 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 498521 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 483934 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 360961 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 504654 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 317439 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 425813 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 405567 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 433779 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 356256 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 452628 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 360234 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 278919 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 303620 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 219955 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-215_S31_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-215_S31_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-220_S32_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 651275 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 502417 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 404651 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 455894 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 410467 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 403915 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 296192 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 413495 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 262974 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 351401 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 335396 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 363128 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 295032 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 377557 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 294735 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 233828 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 252190 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 181839 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-220_S32_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-220_S32_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-221_S33_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 694072 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 530785 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 427521 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 488137 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 439980 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 428529 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 317419 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 443343 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 276962 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 372833 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 358735 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 386741 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 313721 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 404708 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 315587 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 247440 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 268934 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 193081 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-221_S33_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-221_S33_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-226_S34_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 557259 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 430644 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 345154 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 389519 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 353048 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 342963 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 254345 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 355825 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 225260 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 299356 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 287375 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 309429 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 253934 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 321961 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 251222 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 197802 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 217183 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 154555 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-226_S34_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-226_S34_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-227_S35_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 639892 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 494526 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 398276 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 450713 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 404972 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 401346 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 292955 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 411968 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 258569 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 345000 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 334987 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 356896 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 291728 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 376146 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 290620 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 228970 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 250136 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 179827 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-227_S35_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-227_S35_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-229_S36_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 793018 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 612412 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 491510 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 554188 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 503590 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 489180 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 359190 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 507185 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 316121 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 428924 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 408830 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 441795 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 358005 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 459699 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 360378 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 284460 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 306547 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 223890 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-229_S36_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-229_S36_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-230_S37_L004.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 884635 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 682411 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 552029 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 629842 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 565750 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 551130 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 407491 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 570448 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 357899 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 475053 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 466137 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 495323 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 402587 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 514149 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 409282 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 321136 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 346471 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 247340 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-230_S37_L004.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-230_S37_L004.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-41_S38_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 818143 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 632253 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 509202 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 578985 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 522764 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 511518 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 377164 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 528289 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 330752 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 442308 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 427749 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 456164 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 370653 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 476452 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 374465 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 293334 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 320271 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 232542 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-41_S38_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-41_S38_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-42_S39_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 884520 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 681912 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 549373 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 624791 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 570838 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 550131 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 405945 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 571687 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 359550 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 478814 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 461898 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 493727 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 402130 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 507384 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 405569 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 316393 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 342993 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 248931 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-42_S39_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-42_S39_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-43_S40_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 814989 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 627668 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 507139 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 575366 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 518695 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 503899 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 372483 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 523135 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 328660 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 435901 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 424382 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 452889 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 370802 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 470545 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 368403 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 292391 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 318579 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 226235 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-43_S40_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-43_S40_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1217/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-44_S41_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 588975 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 453991 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 365994 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 416373 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 373321 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 363497 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 273122 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 377813 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 236744 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 316503 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 305652 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 327312 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 268339 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 341289 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 267283 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 210410 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 229577 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 164350 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-44_S41_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-44_S41_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq!