Path to genome folder specified as: /gscratch/srlab/sr320/data/olurida-bs/v98/ 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/olurida-bs/v98/Bisulfite_Genome/ Created Bisulfite Genome folder /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/ Created Bisulfite Genome folder /gscratch/srlab/sr320/data/olurida-bs/v98/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 Contig1 22764285 22795910 Contig2 27090156 27104728 Contig3 26869028 26873076 Contig4 22244904 22305039 Contig5 17972940 17947785 Contig6 13471922 13483087 Contig7 11381119 11338009 Contig8 8660806 8675448 Contig9 8116832 8092680 Contig10 6492241 6508998 Contig11 6407337 6384712 Contig12 6109012 6117685 Contig13 6238644 6202821 Contig14 6125854 6124268 Total number of conversions performed: C->T: 189945080 G->A: 189954246 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/olurida-bs/v98/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/olurida-bs/v98/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: 00:00:09 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time reading reference sizes: 00:00:09 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:06 bmax according to bmaxDivN setting: 9276486 Using parameters --bmax 6957365 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 6957365 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Time to join reference sequences: 00:00:07 bmax according to bmaxDivN setting: 9276486 Using parameters --bmax 6957365 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 6957365 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:09 Allocating rank array Ranking v-sort output V-Sorting samples time: 00:00:09 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:05 Invoking Larsson-Sadakane on ranks Ranking v-sort output time: 00:00:06 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:09 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 36, merged 130; iterating... Invoking Larsson-Sadakane on ranks time: 00:00:10 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 23; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 44, merged 134; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 14, merged 10; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 19, merged 25; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 12, merged 9; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.06813e+06 (target: 6957364) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 205 Reserving size (6957365) for bucket 1 Getting block 2 of 205 Getting block 3 of 205 Getting block 4 of 205 Getting block 5 of 205 Reserving size (6957365) for bucket 2 Reserving size (6957365) for bucket 3 Reserving size (6957365) for bucket 4 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 Reserving size (6957365) for bucket 5 Getting block 12 of 205 Getting block 13 of 205 Getting block 14 of 205 Getting block 15 of 205 Getting block 16 of 205 Getting block 17 of 205 Getting block 18 of 205 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 Getting block 26 of 205 Getting block 27 of 205 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 2 Calculating Z arrays for bucket 4 Reserving size (6957365) for bucket 6 Reserving size (6957365) for bucket 7 Reserving size (6957365) for bucket 8 Reserving size (6957365) for bucket 9 Reserving size (6957365) for bucket 10 Reserving size (6957365) for bucket 11 Calculating Z arrays for bucket 5 Reserving size (6957365) for bucket 12 Reserving size (6957365) for bucket 13 Reserving size (6957365) for bucket 14 Reserving size (6957365) for bucket 15 Reserving size (6957365) for bucket 16 Reserving size (6957365) for bucket 17 Reserving size (6957365) for bucket 18 Reserving size (6957365) for bucket 19 Reserving size (6957365) for bucket 20 Reserving size (6957365) for bucket 21 Reserving size (6957365) for bucket 22 Reserving size (6957365) for bucket 23 Reserving size (6957365) for bucket 24 Reserving size (6957365) for bucket 25 Reserving size (6957365) for bucket 26 Reserving size (6957365) for bucket 27 Calculating Z arrays for bucket 1 Calculating Z arrays for bucket 16 Calculating Z arrays for bucket 14 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 15 Calculating Z arrays for bucket 18 Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 17 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 27 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 25 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 9 Calculating Z arrays for bucket 11 Calculating Z arrays for bucket 26 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 12 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 13 Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 2: Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 10: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 27: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 18: Splitting and merging Splitting and merging time: 00:00:00 Split 6, merged 7; iterating... bucket 4: 10% bucket 2: 10% bucket 12: 10% bucket 16: 10% bucket 9: 10% bucket 15: 10% bucket 1: 10% bucket 11: 10% bucket 3: 10% bucket 22: 10% bucket 13: 10% bucket 23: 10% bucket 6: 10% bucket 8: 10% bucket 5: 10% bucket 7: 10% bucket 21: 10% bucket 26: 10% bucket 14: 10% bucket 10: 10% bucket 17: 10% bucket 18: 10% bucket 19: 10% bucket 20: 10% bucket 25: 10% bucket 24: 10% bucket 27: 10% bucket 12: 20% bucket 1: 20% bucket 2: 20% bucket 16: 20% bucket 9: 20% bucket 23: 20% bucket 4: 20% bucket 15: 20% bucket 13: 20% bucket 16: 30% bucket 3: 20% bucket 6: 20% bucket 7: 20% bucket 8: 20% bucket 12: 30% bucket 17: 20% bucket 20: 20% bucket 11: 20% bucket 22: 20% bucket 5: 20% bucket 26: 20% bucket 1: 30% bucket 18: 20% bucket 21: 20% bucket 14: 20% bucket 25: 20% bucket 19: 20% bucket 10: 20% bucket 2: 30% bucket 27: 20% bucket 24: 20% bucket 9: 30% bucket 16: 40% bucket 23: 30% bucket 15: 30% bucket 3: 30% bucket 22: 30% bucket 13: 30% bucket 4: 30% bucket 21: 30% bucket 6: 30% bucket 14: 30% bucket 7: 30% bucket 8: 30% bucket 1: 40% bucket 12: 40% bucket 17: 30% bucket 27: 30% bucket 11: 30% bucket 18: 30% bucket 5: 30% bucket 26: 30% bucket 2: 40% bucket 25: 30% bucket 20: 30% bucket 3: 40% bucket 19: 30% bucket 24: 30% bucket 22: 40% bucket 10: 30% bucket 9: 40% bucket 16: 50% bucket 15: 40% bucket 13: 40% bucket 7: 40% bucket 23: 40% bucket 1: 50% bucket 6: 40% bucket 21: 40% bucket 4: 40% bucket 12: 50% bucket 27: 40% bucket 14: 40% bucket 8: 40% bucket 18: 40% bucket 9: 50% bucket 3: 50% bucket 26: 40% bucket 16: 60% bucket 17: 40% bucket 25: 40% bucket 7: 50% bucket 1: 60% bucket 5: 40% bucket 15: 50% bucket 13: 50% bucket 2: 50% bucket 22: 50% bucket 6: 50% bucket 10: 40% bucket 11: 40% bucket 12: 60% bucket 20: 40% bucket 19: 40% bucket 24: 40% bucket 9: 60% bucket 3: 60% bucket 4: 50% bucket 18: 50% bucket 27: 50% bucket 1: 70% bucket 23: 50% bucket 26: 50% bucket 8: 50% bucket 7: 60% bucket 16: 70% bucket 25: 50% Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 3; iterating... Avg bucket size: 5.01916e+06 (target: 6957364) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 2 of 207 Getting block 1 of 207 Reserving size (6957365) for bucket 2 Reserving size (6957365) for bucket 1 Getting block 3 of 207 Getting block 4 of 207 Getting block 5 of 207 Getting block 6 of 207 Getting block 7 of 207 Getting block 8 of 207 Getting block 9 of 207 Getting block 10 of 207 Getting block 11 of 207 Getting block 12 of 207 Getting block 13 of 207 Getting block 14 of 207 Getting block 15 of 207 Getting block 16 of 207 Getting block 17 of 207 Getting block 18 of 207 Getting block 19 of 207 Getting block 20 of 207 Getting block 21 of 207 Getting block 22 of 207 Getting block 23 of 207 Calculating Z arrays for bucket 2 Calculating Z arrays for bucket 1 Reserving size (6957365) for bucket 3 Reserving size (6957365) for bucket 4 Reserving size (6957365) for bucket 5 Getting block 24 of 207 Reserving size (6957365) for bucket 6 Reserving size (6957365) for bucket 7 Reserving size (6957365) for bucket 8 Reserving size (6957365) for bucket 9 Reserving size (6957365) for bucket 10 Reserving size (6957365) for bucket 11 Reserving size (6957365) for bucket 12 Reserving size (6957365) for bucket 13 Reserving size (6957365) for bucket 14 Reserving size (6957365) for bucket 15 Reserving size (6957365) for bucket 16 Reserving size (6957365) for bucket 17 Getting block 25 of 207 Reserving size (6957365) for bucket 18 Getting block 26 of 207 Getting block 27 of 207 Reserving size (6957365) for bucket 19 Reserving size (6957365) for bucket 20 Reserving size (6957365) for bucket 21 Reserving size (6957365) for bucket 22 Reserving size (6957365) for bucket 23 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Reserving size (6957365) for bucket 24 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 10 Calculating Z arrays for bucket 11 Calculating Z arrays for bucket 12 Calculating Z arrays for bucket 14 Calculating Z arrays for bucket 15 Reserving size (6957365) for bucket 25 Calculating Z arrays for bucket 17 Calculating Z arrays for bucket 13 Calculating Z arrays for bucket 16 Calculating Z arrays for bucket 18 Reserving size (6957365) for bucket 26 Reserving size (6957365) for bucket 27 Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 23 Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 4: Calculating Z arrays for bucket 24 Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 10: Calculating Z arrays for bucket 25 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 11: Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 27: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 26: bucket 15: 60% bucket 14: 50% bucket 5: 50% bucket 21: 50% bucket 2: 60% bucket 22: 60% bucket 17: 50% bucket 6: 60% bucket 12: 70% bucket 13: 60% bucket 16: 80% bucket 10: 50% bucket 11: 50% bucket 9: 70% bucket 3: 70% bucket 18: 60% bucket 4: 60% bucket 20: 50% bucket 7: 70% bucket 6: 10% bucket 24: 50% bucket 1: 80% bucket 19: 50% bucket 8: 60% bucket 27: 60% bucket 5: 60% bucket 12: 80% bucket 26: 60% bucket 2: 70% bucket 15: 70% bucket 23: 60% bucket 12: 10% bucket 22: 10% bucket 25: 60% bucket 1: 10% bucket 3: 10% bucket 5: 10% bucket 14: 60% bucket 6: 70% bucket 11: 10% bucket 20: 10% bucket 14: 10% bucket 23: 10% bucket 18: 10% bucket 15: 10% bucket 19: 10% bucket 13: 10% bucket 22: 70% bucket 17: 10% bucket 2: 10% bucket 16: 10% bucket 21: 60% bucket 4: 10% bucket 21: 10% bucket 9: 10% bucket 27: 10% bucket 7: 10% bucket 8: 10% bucket 10: 10% bucket 17: 60% bucket 26: 10% bucket 25: 10% bucket 9: 80% bucket 24: 10% bucket 11: 60% bucket 13: 70% bucket 18: 70% bucket 3: 80% bucket 16: 90% bucket 26: 70% bucket 7: 80% bucket 4: 70% bucket 1: 90% bucket 6: 20% bucket 10: 60% bucket 12: 90% bucket 8: 70% bucket 20: 60% bucket 2: 80% bucket 5: 70% bucket 19: 60% bucket 24: 60% bucket 15: 80% bucket 14: 20% bucket 27: 70% bucket 12: 20% bucket 15: 20% bucket 11: 20% bucket 6: 80% bucket 4: 20% bucket 20: 20% bucket 23: 70% bucket 22: 80% bucket 25: 70% bucket 23: 20% bucket 21: 20% bucket 1: 20% bucket 14: 70% bucket 3: 20% bucket 5: 20% bucket 9: 90% bucket 7: 90% bucket 17: 70% bucket 13: 20% bucket 19: 20% bucket 11: 70% bucket 18: 20% bucket 17: 20% bucket 22: 20% bucket 2: 20% bucket 3: 90% bucket 21: 70% bucket 9: 20% bucket 13: 80% bucket 26: 80% bucket 18: 80% bucket 7: 20% bucket 27: 20% bucket 1: 100% Sorting block of length 4330862 for bucket 1 (Using difference cover) bucket 4: 80% bucket 16: 100% Sorting block of length 5869001 for bucket 16 (Using difference cover) bucket 10: 20% bucket 16: 20% bucket 8: 20% bucket 6: 30% bucket 12: 100% Sorting block of length 3423447 for bucket 12 (Using difference cover) bucket 26: 20% bucket 25: 20% bucket 2: 90% bucket 8: 80% bucket 15: 90% bucket 27: 80% bucket 10: 70% bucket 24: 20% bucket 20: 70% bucket 5: 80% bucket 14: 30% bucket 19: 70% bucket 6: 90% bucket 11: 30% bucket 22: 90% bucket 24: 70% bucket 12: 30% bucket 15: 30% bucket 21: 30% bucket 5: 30% bucket 4: 30% bucket 23: 30% bucket 18: 90% bucket 15: 100% Sorting block of length 5872196 for bucket 15 (Using difference cover) bucket 25: 80% bucket 23: 80% bucket 26: 90% bucket 9: 100% Sorting block of length 6769045 for bucket 9 (Using difference cover) bucket 7: 100% Sorting block of length 6137912 for bucket 7 (Using difference cover) bucket 11: 80% bucket 3: 100% Sorting block of length 3292019 for bucket 3 (Using difference cover) bucket 20: 30% bucket 3: 30% bucket 19: 30% bucket 14: 80% bucket 1: 30% bucket 4: 90% bucket 17: 80% bucket 22: 30% bucket 25: 30% bucket 13: 90% bucket 13: 30% bucket 2: 30% bucket 17: 30% bucket 18: 30% bucket 21: 80% bucket 2: 100% Sorting block of length 5028840 for bucket 2 (Using difference cover) bucket 7: 30% Sorting block time: 00:00:02 Returning block of 3423448 for bucket 12 bucket 27: 30% bucket 22: 100% Sorting block of length 6540423 for bucket 22 (Using difference cover) bucket 8: 90% bucket 6: 40% bucket 8: 30% bucket 9: 30% Getting block 28 of 205 Reserving size (6957365) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 6: 100% Sorting block of length 4312979 for bucket 6 (Using difference cover) bucket 16: 30% bucket 10: 30% bucket 10: 80% bucket 5: 90% bucket 27: 90% bucket 19: 80% Sorting block time: 00:00:03 Returning block of 4330863 for bucket 1 bucket 21: 40% bucket 20: 80% Getting block 29 of 205 Reserving size (6957365) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 26: 30% bucket 14: 40% bucket 20: 40% bucket 12: 40% bucket 24: 30% bucket 15: 40% Sorting block time: 00:00:01 Returning block of 3292020 for bucket 3 Getting block 30 of 205 Reserving size (6957365) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 11: 40% bucket 5: 40% bucket 4: 40% bucket 18: 100% Sorting block of length 6380513 for bucket 18 (Using difference cover) bucket 1: 40% bucket 3: 40% bucket 25: 90% bucket 11: 90% bucket 4: 100% Sorting block of length 5987197 for bucket 4 (Using difference cover) bucket 23: 40% bucket 17: 90% bucket 24: 80% bucket 19: 40% bucket 14: 90% bucket 23: 90% bucket 26: 100% Sorting block of length 6748912 for bucket 26 (Using difference cover) bucket 18: 40% bucket 13: 40% Sorting block time: 00:00:04 Returning block of 5869002 for bucket 16 bucket 25: 40% bucket 2: 40% bucket 22: 40% bucket 17: 40% bucket 6: 50% bucket 13: 100% Sorting block of length 6538129 for bucket 13 (Using difference cover) Getting block 31 of 205 Reserving size (6957365) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: bucket 9: 40% bucket 7: 40% bucket 8: 40% bucket 16: 40% bucket 27: 40% bucket 10: 40% bucket 15: 50% bucket 21: 50% bucket 8: 100% Sorting block of length 1133622 for bucket 8 (Using difference cover) bucket 12: 50% bucket 14: 50% bucket 21: 90% Sorting block time: 00:00:03 Returning block of 5872197 for bucket 15 bucket 20: 50% bucket 5: 100% Sorting block of length 6235317 for bucket 5 (Using difference cover) Sorting block time: 00:00:04 Returning block of 6137913 for bucket 7 Getting block 32 of 205 Reserving size (6957365) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: bucket 4: 50% bucket 10: 90% bucket 26: 40% bucket 5: 50% Sorting block time: 00:00:03 Returning block of 4312980 for bucket 6 bucket 27: 100% Sorting block of length 5925426 for bucket 27 (Using difference cover) Getting block 33 of 205 Reserving size (6957365) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: bucket 24: 40% bucket 1: 50% bucket 3: 50% bucket 19: 90% Sorting block time: 00:00:01 Returning block of 1133623 for bucket 8 bucket 28: 10% Getting block 34 of 205 Reserving size (6957365) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: Sorting block time: 00:00:04 Returning block of 5028841 for bucket 2 Getting block 35 of 205 Reserving size (6957365) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: bucket 11: 50% bucket 20: 90% bucket 29: 10% Getting block 36 of 205 Reserving size (6957365) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: bucket 25: 50% bucket 23: 50% bucket 11: 100% Sorting block of length 5724390 for bucket 11 (Using difference cover) bucket 19: 50% bucket 25: 100% Sorting block of length 3750601 for bucket 25 (Using difference cover) Sorting block time: 00:00:04 Returning block of 6769046 for bucket 9 bucket 13: 50% bucket 18: 50% bucket 2: 50% bucket 17: 100% Sorting block of length 6402428 for bucket 17 (Using difference cover) Getting block 37 of 205 Reserving size (6957365) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: bucket 17: 50% bucket 6: 60% bucket 21: 60% Sorting block time: 00:00:04 Returning block of 6540424 for bucket 22 bucket 9: 50% bucket 7: 50% bucket 14: 100% Sorting block of length 5035918 for bucket 14 (Using difference cover) bucket 8: 50% bucket 23: 100% Sorting block of length 2612152 for bucket 23 (Using difference cover) bucket 30: 10% Getting block 38 of 205 Reserving size (6957365) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: bucket 22: 50% bucket 31: 10% bucket 20: 60% bucket 27: 50% bucket 15: 60% bucket 24: 90% bucket 10: 100% Sorting block of length 5248294 for bucket 10 (Using difference cover) bucket 12: 60% bucket 16: 50% Sorting block time: 00:00:04 Returning block of 6380514 for bucket 18 bucket 10: 50% bucket 14: 60% bucket 4: 60% bucket 5: 60% Getting block 39 of 205 Reserving size (6957365) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: bucket 3: 60% bucket 21: 100% Sorting block of length 6094181 for bucket 21 (Using difference cover) Sorting block time: 00:00:04 Returning block of 6748913 for bucket 26 bucket 26: 50% bucket 1: 60% bucket 24: 50% bucket 32: 10% bucket 13: 60% Getting block 40 of 205 Reserving size (6957365) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: bucket 11: 60% Sorting block time: 00:00:05 Returning block of 5987198 for bucket 4 Sorting block time: 00:00:02 Returning block of 2612153 for bucket 23 bucket 18: 60% Getting block 41 of 205 Reserving size (6957365) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: bucket 22: 60% bucket 20: 70% bucket 19: 60% Getting block 42 of 205 Reserving size (6957365) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: bucket 23: 60% bucket 6: 70% bucket 35: 10% Sorting block time: 00:00:03 Returning block of 3750602 for bucket 25 bucket 2: 60% bucket 17: 60% Getting block 43 of 205 Reserving size (6957365) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: bucket 36: 10% bucket 19: 100% Sorting block of length 6475901 for bucket 19 (Using difference cover) bucket 15: 70% bucket 25: 60% bucket 8: 60% bucket 21: 70% bucket 7: 60% bucket 33: 10% bucket 9: 60% Sorting block time: 00:00:03 Returning block of 5925427 for bucket 27 bucket 28: 20% Getting block 44 of 205 Reserving size (6957365) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: bucket 27: 60% bucket 34: 10% bucket 20: 100% Sorting block of length 1219866 for bucket 20 (Using difference cover) bucket 16: 60% bucket 29: 20% bucket 12: 70% bucket 4: 70% bucket 14: 70% bucket 5: 70% Sorting block time: 00:00:05 Returning block of 6235318 for bucket 5 bucket 10: 60% Sorting block time: 00:00:04 Returning block of 5724391 for bucket 11 Sorting block time: 00:00:05 Returning block of 6538130 for bucket 13 bucket 39: 10% bucket 37: 10% bucket 3: 70% Getting block 45 of 205 Reserving size (6957365) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: bucket 24: 100% Sorting block of length 6232937 for bucket 24 (Using difference cover) bucket 13: 70% Getting block 46 of 205 Reserving size (6957365) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: bucket 1: 70% Getting block 47 of 205 Reserving size (6957365) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: Sorting block time: 00:00:04 Returning block of 5035919 for bucket 14 bucket 30: 20% bucket 26: 60% bucket 17: 70% Sorting block time: 00:00:01 Returning block of 1219867 for bucket 20 bucket 6: 80% bucket 18: 70% bucket 11: 70% bucket 24: 60% Getting block 48 of 205 Reserving size (6957365) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Getting block 49 of 205 Reserving size (6957365) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: bucket 38: 10% bucket 31: 20% bucket 15: 80% bucket 22: 70% bucket 19: 70% bucket 20: 80% bucket 2: 70% Sorting block time: 00:00:03 Returning block of 5248295 for bucket 10 Sorting block time: 00:00:04 Returning block of 6402429 for bucket 17 bucket 8: 70% bucket 21: 80% bucket 23: 70% Getting block 50 of 205 Reserving size (6957365) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 7: 70% Getting block 51 of 205 Reserving size (6957365) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 9: 70% bucket 25: 70% bucket 43: 10% bucket 36: 20% bucket 32: 20% bucket 4: 80% bucket 35: 20% bucket 27: 70% bucket 5: 80% Sorting block time: 00:00:04 Returning block of 6094182 for bucket 21 bucket 12: 80% bucket 28: 30% bucket 40: 10% bucket 42: 10% bucket 18: 80% bucket 16: 70% bucket 3: 80% bucket 14: 80% bucket 10: 70% Getting block 52 of 205 Reserving size (6957365) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 41: 10% bucket 29: 30% bucket 1: 80% bucket 20: 90% bucket 13: 80% bucket 6: 90% bucket 17: 80% bucket 34: 20% bucket 11: 80% bucket 39: 20% bucket 33: 20% bucket 26: 70% bucket 44: 10% bucket 45: 10% Sorting block time: 00:00:04 Returning block of 6475902 for bucket 19 bucket 15: 90% bucket 47: 10% bucket 19: 80% bucket 24: 70% Getting block 53 of 205 Reserving size (6957365) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 8: 80% bucket 2: 80% bucket 46: 10% bucket 23: 80% bucket 21: 90% bucket 48: 10% bucket 7: 80% bucket 9: 80% bucket 22: 80% bucket 31: 30% bucket 37: 20% bucket 4: 90% bucket 18: 90% bucket 30: 30% bucket 5: 90% bucket 6: 100% Sorting block of length 6322012 for bucket 6 (Using difference cover) bucket 12: 90% bucket 25: 80% bucket 3: 90% Sorting block time: 00:00:04 Returning block of 6232938 for bucket 24 bucket 49: 10% bucket 27: 80% bucket 14: 90% bucket 10: 80% bucket 32: 30% bucket 16: 80% bucket 1: 90% Getting block 54 of 205 Reserving size (6957365) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 38: 20% bucket 20: 100% Sorting block of length 4300806 for bucket 20 (Using difference cover) bucket 50: 10% bucket 36: 30% bucket 13: 90% bucket 29: 40% bucket 17: 90% bucket 11: 90% bucket 52: 10% bucket 9: 90% bucket 15: 100% Sorting block of length 3327584 for bucket 15 (Using difference cover) bucket 33: 30% bucket 35: 30% bucket 40: 20% bucket 42: 20% bucket 51: 10% bucket 21: 100% Sorting block of length 6048602 for bucket 21 (Using difference cover) bucket 8: 90% bucket 19: 90% bucket 28: 40% bucket 41: 20% bucket 26: 80% bucket 24: 80% bucket 2: 90% bucket 23: 90% bucket 39: 30% bucket 7: 90% bucket 43: 20% bucket 18: 100% Sorting block of length 6649202 for bucket 18 (Using difference cover) bucket 22: 90% bucket 4: 100% Sorting block of length 6568652 for bucket 4 (Using difference cover) bucket 5: 100% Sorting block of length 6416170 for bucket 5 (Using difference cover) bucket 27: 90% bucket 3: 100% Sorting block of length 5396004 for bucket 3 (Using difference cover) bucket 12: 100% Sorting block of length 3821596 for bucket 12 (Using difference cover) bucket 45: 20% bucket 14: 100% Sorting block of length 4085774 for bucket 14 (Using difference cover) bucket 1: 100% Sorting block of length 6592924 for bucket 1 (Using difference cover) bucket 53: 10% bucket 44: 20% bucket 10: 90% bucket 16: 90% Sorting block time: 00:00:01 Returning block of 3327585 for bucket 15 bucket 17: 100% Sorting block of length 6609158 for bucket 17 (Using difference cover) bucket 34: 30% bucket 13: 100% Sorting block of length 6582169 for bucket 13 (Using difference cover) Getting block 28 of 207 Reserving size (6957365) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 25: 90% bucket 47: 20% bucket 31: 40% bucket 48: 20% bucket 11: 100% Sorting block of length 5892703 for bucket 11 (Using difference cover) bucket 38: 30% Sorting block time: 00:00:03 Returning block of 4300807 for bucket 20 bucket 33: 40% bucket 46: 20% bucket 9: 100% Sorting block of length 2685280 for bucket 9 (Using difference cover) bucket 30: 40% bucket 54: 10% bucket 37: 30% Getting block 29 of 207 Reserving size (6957365) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 8: 100% Sorting block of length 6018058 for bucket 8 (Using difference cover) bucket 32: 40% bucket 36: 40% bucket 19: 100% Sorting block of length 2888241 for bucket 19 (Using difference cover) bucket 2: 100% Sorting block of length 6754400 for bucket 2 (Using difference cover) bucket 24: 90% bucket 7: 100% Sorting block of length 2845837 for bucket 7 (Using difference cover) bucket 23: 100% Sorting block of length 5764732 for bucket 23 (Using difference cover) bucket 50: 20% bucket 26: 90% bucket 28: 50% bucket 29: 50% bucket 40: 30% bucket 49: 20% bucket 35: 40% Sorting block time: 00:00:05 Returning block of 6322013 for bucket 6 bucket 27: 100% Sorting block of length 1923192 for bucket 27 (Using difference cover) bucket 22: 100% Sorting block of length 2719902 for bucket 22 (Using difference cover) Getting block 30 of 207 Reserving size (6957365) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 52: 20% bucket 42: 30% bucket 16: 100% Sorting block of length 4986719 for bucket 16 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6048603 for bucket 21 bucket 39: 40% Sorting block time: 00:00:02 Returning block of 3821597 for bucket 12 Sorting block time: 00:00:02 Returning block of 4085775 for bucket 14 bucket 10: 100% Sorting block of length 5605773 for bucket 10 (Using difference cover) Getting block 31 of 207 Reserving size (6957365) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: Getting block 32 of 207 Reserving size (6957365) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: Getting block 33 of 207 Reserving size (6957365) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: bucket 41: 30% bucket 43: 30% bucket 51: 20% bucket 33: 50% Sorting block time: 00:00:02 Returning block of 2888242 for bucket 19 Sorting block time: 00:00:02 Returning block of 2685281 for bucket 9 bucket 25: 100% Sorting block of length 3760550 for bucket 25 (Using difference cover) Getting block 34 of 207 Reserving size (6957365) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: bucket 29: 10% Getting block 35 of 207 Reserving size (6957365) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: bucket 28: 10% Sorting block time: 00:00:01 Returning block of 1923193 for bucket 27 Getting block 36 of 207 Reserving size (6957365) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: bucket 30: 50% bucket 45: 30% bucket 44: 30% bucket 32: 50% bucket 53: 20% Sorting block time: 00:00:04 Returning block of 5396005 for bucket 3 Sorting block time: 00:00:03 Returning block of 2845838 for bucket 7 Sorting block time: 00:00:05 Returning block of 6649203 for bucket 18 bucket 40: 40% bucket 24: 100% Sorting block of length 3774327 for bucket 24 (Using difference cover) bucket 31: 50% Getting block 37 of 207 Reserving size (6957365) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: Sorting block time: 00:00:02 Returning block of 2719903 for bucket 22 Getting block 38 of 207 Reserving size (6957365) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: bucket 37: 40% Getting block 39 of 207 Reserving size (6957365) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Getting block 40 of 207 Reserving size (6957365) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: bucket 47: 30% bucket 26: 100% Sorting block of length 5269275 for bucket 26 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6568653 for bucket 4 Sorting block time: 00:00:04 Returning block of 6609159 for bucket 17 Sorting block time: 00:00:05 Returning block of 6416171 for bucket 5 bucket 36: 50% bucket 48: 30% bucket 38: 40% bucket 34: 40% Getting block 41 of 207 Reserving size (6957365) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: bucket 30: 10% Getting block 42 of 207 Reserving size (6957365) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: Getting block 43 of 207 Reserving size (6957365) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: bucket 54: 20% bucket 31: 10% Sorting block time: 00:00:05 Returning block of 6582170 for bucket 13 bucket 32: 10% bucket 46: 30% bucket 33: 60% Getting block 44 of 207 Reserving size (6957365) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: bucket 52: 30% bucket 33: 10% bucket 29: 60% bucket 42: 40% bucket 35: 50% Sorting block time: 00:00:04 Returning block of 5764733 for bucket 23 Sorting block time: 00:00:05 Returning block of 6592925 for bucket 1 bucket 50: 30% bucket 34: 10% bucket 28: 60% Getting block 45 of 207 Reserving size (6957365) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: bucket 29: 20% Sorting block time: 00:00:05 Returning block of 5892704 for bucket 11 bucket 49: 30% Getting block 46 of 207 Reserving size (6957365) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: bucket 35: 10% bucket 28: 20% bucket 40: 50% bucket 36: 10% Sorting block time: 00:00:05 Returning block of 6018059 for bucket 8 Getting block 47 of 207 Reserving size (6957365) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 39: 50% Sorting block time: 00:00:03 Returning block of 3760551 for bucket 25 Getting block 48 of 207 Reserving size (6957365) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: bucket 39: 10% Getting block 49 of 207 Reserving size (6957365) 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 4986720 for bucket 16 bucket 41: 40% Sorting block time: 00:00:05 Returning block of 6754401 for bucket 2 bucket 43: 10% bucket 40: 10% Getting block 50 of 207 Reserving size (6957365) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: Sorting block time: 00:00:04 Returning block of 5605774 for bucket 10 bucket 43: 40% Getting block 51 of 207 Reserving size (6957365) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 51: 30% Getting block 52 of 207 Reserving size (6957365) 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 3774328 for bucket 24 bucket 38: 10% Getting block 53 of 207 Reserving size (6957365) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 37: 10% bucket 41: 10% bucket 42: 10% bucket 44: 10% bucket 31: 60% bucket 32: 60% bucket 30: 20% bucket 31: 20% bucket 32: 20% bucket 30: 60% bucket 45: 40% bucket 33: 20% bucket 34: 20% bucket 36: 60% bucket 38: 50% bucket 44: 40% bucket 53: 30% bucket 46: 10% bucket 29: 30% bucket 48: 40% bucket 54: 30% bucket 47: 40% bucket 45: 10% Sorting block time: 00:00:04 Returning block of 5269276 for bucket 26 bucket 40: 20% bucket 36: 20% bucket 28: 30% bucket 33: 70% bucket 34: 50% bucket 37: 50% bucket 35: 20% bucket 52: 40% bucket 39: 20% Getting block 54 of 207 Reserving size (6957365) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 50: 40% bucket 47: 10% bucket 42: 50% bucket 49: 40% bucket 43: 50% bucket 50: 10% bucket 49: 10% bucket 35: 60% bucket 48: 10% bucket 46: 40% bucket 43: 20% bucket 51: 10% bucket 39: 60% bucket 38: 20% bucket 32: 30% bucket 53: 10% bucket 28: 70% bucket 51: 40% bucket 41: 20% bucket 42: 20% bucket 52: 10% bucket 30: 30% bucket 44: 20% bucket 37: 20% bucket 31: 30% bucket 29: 70% bucket 41: 50% bucket 40: 60% bucket 31: 70% bucket 33: 30% bucket 32: 70% bucket 34: 30% bucket 38: 60% bucket 29: 40% bucket 45: 50% bucket 46: 20% bucket 36: 30% bucket 45: 20% bucket 39: 30% bucket 40: 30% bucket 35: 30% bucket 48: 50% bucket 30: 70% bucket 28: 40% bucket 36: 70% bucket 44: 30% bucket 53: 40% bucket 47: 20% bucket 49: 20% bucket 50: 50% bucket 49: 50% bucket 50: 20% bucket 54: 10% bucket 44: 50% bucket 43: 30% bucket 32: 40% bucket 34: 60% bucket 54: 40% bucket 48: 20% bucket 31: 40% bucket 43: 60% bucket 42: 30% bucket 47: 50% bucket 41: 30% bucket 51: 20% bucket 35: 70% bucket 33: 80% bucket 52: 20% bucket 38: 30% bucket 37: 30% bucket 53: 20% bucket 30: 40% bucket 42: 60% bucket 33: 40% bucket 52: 50% bucket 37: 60% bucket 34: 40% bucket 29: 50% bucket 41: 60% bucket 28: 80% bucket 39: 40% bucket 39: 70% bucket 46: 50% bucket 36: 40% bucket 29: 80% bucket 51: 50% bucket 46: 30% bucket 44: 40% bucket 31: 50% bucket 28: 50% bucket 45: 30% bucket 35: 40% bucket 40: 40% bucket 40: 70% bucket 31: 80% bucket 38: 70% bucket 50: 60% bucket 49: 30% bucket 45: 60% bucket 47: 30% bucket 32: 80% bucket 32: 50% bucket 48: 60% bucket 36: 80% bucket 50: 30% bucket 42: 40% bucket 41: 40% bucket 38: 40% bucket 54: 20% bucket 30: 50% bucket 43: 40% bucket 51: 30% bucket 37: 40% bucket 48: 30% bucket 47: 60% bucket 35: 80% bucket 53: 30% bucket 33: 50% bucket 30: 80% bucket 52: 30% bucket 53: 50% bucket 34: 50% bucket 29: 60% bucket 44: 60% bucket 39: 50% bucket 33: 90% bucket 49: 60% bucket 52: 60% bucket 54: 50% bucket 43: 70% bucket 44: 50% bucket 42: 70% bucket 31: 60% bucket 36: 50% bucket 28: 60% bucket 41: 70% bucket 34: 70% bucket 45: 40% bucket 40: 50% bucket 37: 70% bucket 39: 80% bucket 35: 50% bucket 46: 40% bucket 38: 50% bucket 50: 70% bucket 28: 90% bucket 32: 60% bucket 49: 40% bucket 29: 90% bucket 47: 40% bucket 42: 50% bucket 41: 50% bucket 50: 40% bucket 51: 60% bucket 46: 60% bucket 30: 60% bucket 37: 50% bucket 36: 90% bucket 43: 50% bucket 53: 40% bucket 51: 40% bucket 33: 60% bucket 40: 80% bucket 38: 80% bucket 31: 70% bucket 54: 30% bucket 29: 70% bucket 48: 40% bucket 34: 60% bucket 31: 90% bucket 48: 70% bucket 52: 40% bucket 39: 60% bucket 45: 70% bucket 44: 60% bucket 36: 60% bucket 28: 70% bucket 38: 60% bucket 32: 90% bucket 45: 50% bucket 35: 90% bucket 46: 50% bucket 40: 60% bucket 35: 60% bucket 32: 70% bucket 53: 60% bucket 47: 70% bucket 42: 60% bucket 47: 50% bucket 52: 70% bucket 41: 80% bucket 54: 60% bucket 41: 60% bucket 42: 80% bucket 30: 90% bucket 30: 70% bucket 28: 100% Sorting block of length 5639365 for bucket 28 (Using difference cover) bucket 49: 50% bucket 33: 70% bucket 50: 50% bucket 31: 80% bucket 49: 70% bucket 33: 100% Sorting block of length 2974894 for bucket 33 (Using difference cover) bucket 43: 60% bucket 43: 80% bucket 29: 80% bucket 53: 50% bucket 34: 70% bucket 37: 60% bucket 50: 80% bucket 48: 50% bucket 39: 70% bucket 54: 40% bucket 44: 70% bucket 51: 50% bucket 45: 60% bucket 39: 90% bucket 34: 80% bucket 52: 50% bucket 36: 100% Sorting block of length 4647227 for bucket 36 (Using difference cover) bucket 44: 70% bucket 36: 70% bucket 46: 70% bucket 38: 70% bucket 32: 80% bucket 37: 80% bucket 28: 80% bucket 51: 70% bucket 29: 100% Sorting block of length 4118817 for bucket 29 (Using difference cover) bucket 46: 60% bucket 40: 70% bucket 35: 70% bucket 32: 100% Sorting block of length 6519138 for bucket 32 (Using difference cover) bucket 48: 80% bucket 45: 80% Sorting block time: 00:00:02 Returning block of 2974895 for bucket 33 bucket 38: 90% bucket 42: 70% bucket 40: 90% bucket 47: 60% Getting block 55 of 205 Reserving size (6957365) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 41: 70% bucket 31: 100% Sorting block of length 3101151 for bucket 31 (Using difference cover) bucket 35: 100% Sorting block of length 6522238 for bucket 35 (Using difference cover) bucket 30: 80% bucket 33: 80% bucket 50: 60% bucket 31: 90% bucket 29: 90% bucket 52: 80% bucket 42: 90% bucket 43: 70% bucket 53: 70% bucket 34: 80% bucket 49: 60% bucket 30: 100% Sorting block of length 6420776 for bucket 30 (Using difference cover) bucket 41: 90% bucket 54: 70% bucket 39: 80% bucket 51: 60% bucket 53: 60% bucket 32: 90% bucket 47: 80% bucket 45: 70% bucket 48: 60% bucket 37: 70% bucket 44: 80% bucket 36: 80% Sorting block time: 00:00:04 Returning block of 5639366 for bucket 28 bucket 54: 50% bucket 38: 80% bucket 49: 80% Getting block 56 of 205 Reserving size (6957365) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 28: 90% bucket 43: 90% bucket 52: 60% Sorting block time: 00:00:03 Returning block of 4118818 for bucket 29 Sorting block time: 00:00:03 Returning block of 4647228 for bucket 36 bucket 40: 80% Getting block 57 of 205 Reserving size (6957365) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: Getting block 58 of 205 Reserving size (6957365) 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 3101152 for bucket 31 bucket 35: 80% bucket 42: 80% bucket 46: 70% bucket 46: 80% bucket 34: 90% bucket 39: 100% Sorting block of length 4374591 for bucket 39 (Using difference cover) Getting block 59 of 205 Reserving size (6957365) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 44: 80% bucket 50: 90% bucket 41: 80% bucket 32: 100% Sorting block of length 3632227 for bucket 32 (Using difference cover) bucket 51: 80% bucket 33: 90% bucket 30: 90% bucket 31: 100% Sorting block of length 5183721 for bucket 31 (Using difference cover) bucket 45: 90% bucket 48: 90% bucket 29: 100% Sorting block of length 2492397 for bucket 29 (Using difference cover) bucket 40: 100% Sorting block of length 4429685 for bucket 40 (Using difference cover) bucket 47: 70% bucket 38: 100% Sorting block of length 4975728 for bucket 38 (Using difference cover) bucket 37: 90% bucket 55: 10% bucket 50: 70% bucket 34: 90% bucket 43: 80% bucket 42: 100% Sorting block of length 4327748 for bucket 42 (Using difference cover) bucket 39: 90% bucket 52: 90% bucket 51: 70% bucket 37: 80% bucket 45: 80% bucket 44: 90% bucket 41: 100% Sorting block of length 6647969 for bucket 41 (Using difference cover) bucket 49: 70% bucket 36: 90% bucket 38: 90% bucket 48: 70% bucket 53: 70% Sorting block time: 00:00:04 Returning block of 6519139 for bucket 32 bucket 54: 80% bucket 28: 100% Sorting block of length 6584886 for bucket 28 (Using difference cover) bucket 56: 10% Getting block 60 of 205 Reserving size (6957365) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 54: 60% bucket 53: 80% bucket 40: 90% bucket 52: 70% bucket 43: 100% Sorting block of length 4026972 for bucket 43 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2492398 for bucket 29 bucket 35: 90% bucket 42: 90% Getting block 55 of 207 Reserving size (6957365) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: Sorting block time: 00:00:05 Returning block of 6522239 for bucket 35 bucket 49: 90% bucket 41: 90% bucket 46: 80% bucket 47: 90% Sorting block time: 00:00:02 Returning block of 3632228 for bucket 32 bucket 33: 100% Sorting block of length 5658859 for bucket 33 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6420777 for bucket 30 Getting block 61 of 205 Reserving size (6957365) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: bucket 30: 100% Sorting block of length 6730897 for bucket 30 (Using difference cover) Getting block 56 of 207 Reserving size (6957365) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: Sorting block time: 00:00:03 Returning block of 4374592 for bucket 39 Sorting block time: 00:00:03 Returning block of 4429686 for bucket 40 Getting block 62 of 205 Reserving size (6957365) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: Getting block 63 of 205 Reserving size (6957365) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: Getting block 64 of 205 Reserving size (6957365) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 47: 80% bucket 46: 90% bucket 34: 100% Sorting block of length 5816346 for bucket 34 (Using difference cover) bucket 39: 100% Sorting block of length 1189841 for bucket 39 (Using difference cover) bucket 44: 90% bucket 43: 90% bucket 36: 100% Sorting block of length 1357539 for bucket 36 (Using difference cover) bucket 51: 90% bucket 45: 100% Sorting block of length 1464416 for bucket 45 (Using difference cover) bucket 58: 10% bucket 37: 90% bucket 50: 80% bucket 53: 80% Sorting block time: 00:00:04 Returning block of 4975729 for bucket 38 bucket 51: 80% bucket 57: 10% bucket 48: 100% Sorting block of length 5889137 for bucket 48 (Using difference cover) bucket 44: 100% Sorting block of length 3463143 for bucket 44 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5183722 for bucket 31 bucket 45: 90% bucket 38: 100% Sorting block of length 5840502 for bucket 38 (Using difference cover) bucket 34: 100% Sorting block of length 6924629 for bucket 34 (Using difference cover) bucket 42: 100% Sorting block of length 602216 for bucket 42 (Using difference cover) bucket 37: 100% Sorting block of length 3235245 for bucket 37 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1189842 for bucket 39 bucket 48: 80% bucket 59: 10% Getting block 65 of 205 Reserving size (6957365) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: Getting block 57 of 207 Reserving size (6957365) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: Getting block 58 of 207 Reserving size (6957365) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: bucket 50: 100% Sorting block of length 6601073 for bucket 50 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4327749 for bucket 42 bucket 49: 80% bucket 56: 20% Sorting block time: 00:00:00 Returning block of 602217 for bucket 42 Getting block 59 of 207 Reserving size (6957365) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: Getting block 66 of 205 Reserving size (6957365) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: bucket 40: 100% Sorting block of length 6955993 for bucket 40 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1357540 for bucket 36 bucket 52: 100% Sorting block of length 2370009 for bucket 52 (Using difference cover) Getting block 60 of 207 Reserving size (6957365) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 55: 20% bucket 54: 70% bucket 35: 100% Sorting block of length 6516008 for bucket 35 (Using difference cover) bucket 52: 80% Sorting block time: 00:00:02 Returning block of 1464417 for bucket 45 bucket 41: 100% Sorting block of length 7856732 for bucket 41 (Using difference cover) bucket 55: 10% Getting block 67 of 205 Reserving size (6957365) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: Sorting block time: 00:00:03 Returning block of 4026973 for bucket 43 bucket 46: 90% bucket 54: 90% Getting block 68 of 205 Reserving size (6957365) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 56: 10% bucket 53: 90% bucket 61: 10% bucket 47: 90% bucket 49: 100% Sorting block of length 2564947 for bucket 49 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6647970 for bucket 41 bucket 60: 10% Sorting block time: 00:00:02 Returning block of 3235246 for bucket 37 bucket 44: 100% Sorting block of length 6381948 for bucket 44 (Using difference cover) bucket 43: 100% Sorting block of length 5868296 for bucket 43 (Using difference cover) Getting block 69 of 205 Reserving size (6957365) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: Sorting block time: 00:00:02 Returning block of 3463144 for bucket 44 Getting block 70 of 205 Reserving size (6957365) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: Getting block 61 of 207 Reserving size (6957365) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: bucket 57: 10% bucket 45: 100% Sorting block of length 5351930 for bucket 45 (Using difference cover) bucket 37: 100% Sorting block of length 4020496 for bucket 37 (Using difference cover) bucket 46: 100% Sorting block of length 6676383 for bucket 46 (Using difference cover) bucket 48: 90% bucket 51: 90% bucket 47: 100% Sorting block of length 1736109 for bucket 47 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5658860 for bucket 33 Sorting block time: 00:00:03 Returning block of 2370010 for bucket 52 bucket 58: 10% bucket 50: 90% Getting block 71 of 205 Reserving size (6957365) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: bucket 53: 90% bucket 49: 90% Sorting block time: 00:00:05 Returning block of 6584887 for bucket 28 Getting block 62 of 207 Reserving size (6957365) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 51: 100% Sorting block of length 5116473 for bucket 51 (Using difference cover) bucket 56: 30% Getting block 63 of 207 Reserving size (6957365) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 59: 10% bucket 60: 10% Sorting block time: 00:00:04 Returning block of 5816347 for bucket 34 bucket 57: 20% Sorting block time: 00:00:04 Returning block of 6730898 for bucket 30 bucket 52: 90% Getting block 64 of 207 Reserving size (6957365) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 65: 10% bucket 54: 80% bucket 46: 100% Sorting block of length 3929443 for bucket 46 (Using difference cover) bucket 55: 20% bucket 62: 10% Getting block 65 of 207 Reserving size (6957365) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: Sorting block time: 00:00:02 Returning block of 1736110 for bucket 47 bucket 68: 10% Sorting block time: 00:00:02 Returning block of 2564948 for bucket 49 Getting block 72 of 205 Reserving size (6957365) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 63: 10% bucket 55: 30% Getting block 73 of 205 Reserving size (6957365) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: bucket 56: 20% Sorting block time: 00:00:04 Returning block of 5840503 for bucket 38 bucket 58: 20% bucket 64: 10% Sorting block time: 00:00:04 Returning block of 5889138 for bucket 48 Getting block 66 of 207 bucket 67: 10% Reserving size (6957365) for bucket 66 Calculating Z arrays for bucket 66 Sorting block time: 00:00:04 bucket 66: 10% Entering block accumulator loop for bucket 66: bucket 59: 20% bucket 54: 100% bucket 53: 100% Returning block of 6924630 for bucket 34 Sorting block of length 3805840 for bucket 54 (Using difference cover) Getting block 74 of 205 Sorting block of length 6414992 for bucket 53 (Using difference cover) Reserving size (6957365) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: Sorting block time: 00:00:05 Returning block of 6601074 for bucket 50 bucket 49: 100% Sorting block of length 1815497 for bucket 49 (Using difference cover) bucket 47: 100% Sorting block of length 6574602 for bucket 47 (Using difference cover) bucket 57: 20% bucket 61: 20% bucket 50: 100% Sorting block of length 6548595 for bucket 50 (Using difference cover) bucket 70: 10% bucket 48: 100% Sorting block of length 6782278 for bucket 48 (Using difference cover) Getting block 75 of 205 Reserving size (6957365) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 69: 10% bucket 61: 10% Getting block 76 of 205 Reserving size (6957365) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 71: 10% bucket 58: 20% Sorting block time: 00:00:03 Returning block of 4020497 for bucket 37 bucket 56: 40% bucket 51: 100% Sorting block of length 6758003 for bucket 51 (Using difference cover) bucket 55: 30% Sorting block time: 00:00:04 Returning block of 6516009 for bucket 35 Getting block 67 of 207 Reserving size (6957365) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: bucket 64: 10% Sorting block time: 00:00:04 Returning block of 6381949 for bucket 44 bucket 60: 20% bucket 53: 100% Sorting block of length 5645165 for bucket 53 (Using difference cover) bucket 59: 20% Getting block 68 of 207 Reserving size (6957365) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 60: 20% bucket 55: 40% bucket 62: 10% Getting block 77 of 205 Reserving size (6957365) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 63: 10% bucket 57: 30% Sorting block time: 00:00:01 Returning block of 1815498 for bucket 49 bucket 65: 20% Sorting block time: 00:00:04 bucket 65: 10% Sorting block time: 00:00:06 bucket 52: 100% bucket 54: 90% Returning block of 5351931 for bucket 45 Returning block of 6955994 for bucket 40 Sorting block of length 6779499 for bucket 52 (Using difference cover) bucket 72: 10% Sorting block time: 00:00:03 Returning block of 3929444 for bucket 46 Getting block 69 of 207 Reserving size (6957365) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: bucket 56: 30% bucket 68: 20% bucket 64: 20% Getting block 70 of 207 Reserving size (6957365) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: Getting block 71 of 207 Reserving size (6957365) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: Sorting block time: 00:00:05 Returning block of 5868297 for bucket 43 bucket 73: 10% Getting block 72 of 207 Reserving size (6957365) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: Getting block 73 of 207 Reserving size (6957365) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: Sorting block time: 00:00:06 Returning block of 7856733 for bucket 41 bucket 58: 30% bucket 62: 20% bucket 69: 20% bucket 58: 30% Sorting block time: 00:00:04 Returning block of 5116474 for bucket 51 Getting block 74 of 207 Reserving size (6957365) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: bucket 57: 30% bucket 61: 20% Getting block 78 of 205 Reserving size (6957365) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 66: 10% Sorting block time: 00:00:03 Returning block of 3805841 for bucket 54 bucket 63: 20% bucket 71: 20% Sorting block time: 00:00:06 Returning block of 6676384 for bucket 46 bucket 74: 10% Getting block 79 of 205 Reserving size (6957365) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 76: 10% bucket 67: 20% Getting block 80 of 205 Reserving size (6957365) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 70: 20% bucket 60: 30% bucket 75: 10% bucket 66: 20% bucket 55: 40% bucket 67: 10% bucket 64: 20% bucket 55: 50% bucket 59: 30% bucket 61: 30% bucket 68: 10% bucket 63: 20% bucket 62: 20% bucket 65: 20% bucket 59: 30% bucket 77: 10% bucket 56: 50% Sorting block time: 00:00:04 Returning block of 6548596 for bucket 50 bucket 56: 40% bucket 54: 100% Sorting block of length 5285456 for bucket 54 (Using difference cover) Getting block 75 of 207 Reserving size (6957365) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: Sorting block time: 00:00:05 Returning block of 6414993 for bucket 53 bucket 57: 40% bucket 60: 30% bucket 70: 10% bucket 58: 40% bucket 71: 10% bucket 72: 20% Sorting block time: 00:00:04 Returning block of 5645166 for bucket 53 bucket 72: 10% bucket 69: 10% Getting block 81 of 205 Reserving size (6957365) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: Sorting block time: 00:00:05 Returning block of 6574603 for bucket 47 bucket 73: 10% Sorting block time: 00:00:05 Returning block of 6782279 for bucket 48 Getting block 76 of 207 Reserving size (6957365) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 57: 40% bucket 61: 30% Getting block 77 of 207 Reserving size (6957365) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: Sorting block time: 00:00:05 Returning block of 6758004 for bucket 51 Getting block 78 of 207 Reserving size (6957365) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 68: 30% bucket 66: 20% bucket 74: 10% bucket 73: 20% Getting block 79 of 207 Reserving size (6957365) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 71: 30% bucket 62: 30% bucket 60: 40% bucket 55: 50% bucket 67: 20% bucket 65: 30% bucket 58: 40% bucket 78: 10% bucket 74: 20% bucket 79: 10% bucket 80: 10% bucket 64: 30% bucket 59: 40% bucket 69: 30% bucket 67: 30% Sorting block time: 00:00:06 Returning block of 6779500 for bucket 52 bucket 63: 30% bucket 65: 30% bucket 70: 30% bucket 68: 20% bucket 62: 30% Getting block 80 of 207 Reserving size (6957365) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 56: 50% bucket 61: 40% bucket 58: 50% bucket 55: 60% bucket 75: 20% bucket 61: 40% bucket 76: 20% bucket 71: 20% bucket 70: 20% bucket 75: 10% bucket 66: 30% bucket 69: 20% bucket 76: 10% bucket 72: 20% bucket 57: 50% bucket 77: 20% bucket 73: 20% bucket 64: 30% bucket 66: 30% Sorting block time: 00:00:04 Returning block of 5285457 for bucket 54 bucket 77: 10% bucket 74: 20% bucket 60: 50% bucket 79: 10% bucket 78: 10% bucket 63: 30% bucket 57: 50% bucket 81: 10% Getting block 81 of 207 Reserving size (6957365) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 55: 60% bucket 64: 40% bucket 60: 40% bucket 71: 40% bucket 59: 50% bucket 67: 30% bucket 56: 60% bucket 72: 30% bucket 59: 40% bucket 80: 20% bucket 73: 30% bucket 65: 40% bucket 63: 40% bucket 70: 40% bucket 58: 60% bucket 80: 10% bucket 62: 40% bucket 74: 30% bucket 68: 30% bucket 56: 60% bucket 61: 50% bucket 79: 20% bucket 58: 50% bucket 78: 20% bucket 68: 40% bucket 62: 40% bucket 71: 30% bucket 70: 30% bucket 57: 60% bucket 75: 20% bucket 76: 20% bucket 69: 30% bucket 72: 30% bucket 73: 30% bucket 79: 20% bucket 60: 60% bucket 66: 40% bucket 65: 40% bucket 69: 40% bucket 67: 40% bucket 74: 30% bucket 77: 20% bucket 78: 20% bucket 55: 70% bucket 66: 40% bucket 61: 50% bucket 55: 70% bucket 81: 10% bucket 64: 50% bucket 77: 30% bucket 59: 60% bucket 75: 30% bucket 81: 20% bucket 71: 50% bucket 67: 40% bucket 63: 50% bucket 58: 70% bucket 65: 50% bucket 80: 30% bucket 70: 50% bucket 76: 30% bucket 62: 50% bucket 61: 60% bucket 56: 70% bucket 80: 20% bucket 68: 40% bucket 72: 40% bucket 73: 40% bucket 74: 40% bucket 71: 40% bucket 57: 60% bucket 63: 40% bucket 79: 30% bucket 57: 70% bucket 64: 40% bucket 70: 40% bucket 75: 30% bucket 69: 40% bucket 76: 30% bucket 60: 50% bucket 73: 40% bucket 60: 70% bucket 72: 40% bucket 56: 70% bucket 58: 60% bucket 66: 50% bucket 79: 30% bucket 68: 50% bucket 74: 40% bucket 78: 30% bucket 78: 30% bucket 77: 30% bucket 55: 80% bucket 64: 60% bucket 81: 20% bucket 59: 70% bucket 59: 50% bucket 67: 50% bucket 67: 50% bucket 69: 50% bucket 72: 50% bucket 71: 60% bucket 58: 80% bucket 61: 60% bucket 63: 60% bucket 81: 30% bucket 65: 50% bucket 62: 60% bucket 56: 80% bucket 61: 70% bucket 65: 60% bucket 62: 50% bucket 80: 30% bucket 68: 50% bucket 55: 80% bucket 70: 60% bucket 66: 50% bucket 80: 40% bucket 75: 40% bucket 57: 80% bucket 71: 50% bucket 77: 40% bucket 73: 50% bucket 75: 40% bucket 60: 80% bucket 70: 50% bucket 69: 50% bucket 79: 40% bucket 74: 50% bucket 73: 50% bucket 76: 40% bucket 66: 60% bucket 72: 50% bucket 79: 40% bucket 74: 50% bucket 78: 40% bucket 76: 40% bucket 77: 40% bucket 55: 90% bucket 72: 60% bucket 64: 70% bucket 59: 80% bucket 78: 40% bucket 81: 30% bucket 60: 60% bucket 57: 70% bucket 63: 50% bucket 67: 60% bucket 58: 70% bucket 68: 60% bucket 56: 80% bucket 58: 90% bucket 63: 70% bucket 56: 90% bucket 61: 80% bucket 62: 70% bucket 81: 40% bucket 65: 70% bucket 71: 70% bucket 67: 60% bucket 68: 60% bucket 80: 40% bucket 61: 70% bucket 64: 50% bucket 57: 90% bucket 80: 50% bucket 60: 90% bucket 71: 60% bucket 69: 60% bucket 75: 50% bucket 69: 60% bucket 72: 70% bucket 70: 70% bucket 73: 60% bucket 55: 90% bucket 70: 60% bucket 66: 70% bucket 76: 50% bucket 79: 50% bucket 72: 60% bucket 59: 60% bucket 66: 60% bucket 74: 60% bucket 79: 50% bucket 78: 50% bucket 73: 60% bucket 55: 100% Sorting block of length 4475196 for bucket 55 (Using difference cover) bucket 74: 60% bucket 77: 50% bucket 64: 80% bucket 59: 90% bucket 65: 60% bucket 75: 50% bucket 81: 40% bucket 67: 70% bucket 77: 50% bucket 78: 50% bucket 58: 100% Sorting block of length 6153834 for bucket 58 (Using difference cover) bucket 56: 100% Sorting block of length 6045758 for bucket 56 (Using difference cover) bucket 61: 90% bucket 63: 80% bucket 62: 80% bucket 65: 80% bucket 62: 60% bucket 71: 80% bucket 68: 70% bucket 58: 80% bucket 81: 50% bucket 76: 50% bucket 80: 50% bucket 57: 100% Sorting block of length 1271602 for bucket 57 (Using difference cover) bucket 68: 70% bucket 57: 80% bucket 72: 80% bucket 60: 100% Sorting block of length 1582629 for bucket 60 (Using difference cover) bucket 67: 70% bucket 63: 60% bucket 71: 70% bucket 60: 70% bucket 75: 60% bucket 69: 70% bucket 69: 70% bucket 73: 70% bucket 66: 80% bucket 61: 80% bucket 70: 70% bucket 76: 60% bucket 79: 60% Sorting block time: 00:00:01 Returning block of 1271603 for bucket 57 bucket 72: 70% Getting block 82 of 207 Reserving size (6957365) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 80: 60% bucket 74: 70% bucket 78: 60% bucket 70: 80% bucket 59: 100% Sorting block of length 5881497 for bucket 59 (Using difference cover) bucket 64: 90% Sorting block time: 00:00:01 Returning block of 1582630 for bucket 60 bucket 56: 90% bucket 77: 60% Getting block 83 of 207 Reserving size (6957365) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 73: 70% Sorting block time: 00:00:03 Returning block of 4475197 for bucket 55 bucket 79: 60% bucket 81: 50% bucket 67: 80% bucket 74: 70% Getting block 84 of 207 Reserving size (6957365) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 64: 60% bucket 66: 70% bucket 75: 60% bucket 59: 70% bucket 61: 100% Sorting block of length 6772691 for bucket 61 (Using difference cover) bucket 62: 90% bucket 63: 90% bucket 55: 100% Sorting block of length 3259402 for bucket 55 (Using difference cover) bucket 65: 90% bucket 65: 70% bucket 62: 70% bucket 78: 60% bucket 68: 80% bucket 80: 60% bucket 71: 90% bucket 71: 80% Sorting block time: 00:00:04 Returning block of 6153835 for bucket 58 bucket 75: 70% bucket 72: 90% Sorting block time: 00:00:04 Returning block of 6045759 for bucket 56 bucket 69: 80% Getting block 85 of 207 Reserving size (6957365) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 66: 90% bucket 73: 80% bucket 81: 60% bucket 68: 80% Getting block 86 of 207 Reserving size (6957365) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 77: 60% bucket 79: 70% bucket 76: 70% bucket 70: 80% bucket 72: 80% bucket 82: 10% bucket 74: 80% bucket 80: 70% bucket 78: 70% bucket 64: 100% Sorting block of length 5697342 for bucket 64 (Using difference cover) bucket 77: 70% bucket 58: 90% bucket 83: 10% bucket 76: 60% bucket 57: 90% bucket 60: 80% bucket 67: 90% bucket 81: 60% Sorting block time: 00:00:03 Returning block of 3259403 for bucket 55 bucket 79: 70% bucket 84: 10% Getting block 82 of 205 Reserving size (6957365) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 73: 80% bucket 65: 100% Sorting block of length 5473195 for bucket 65 (Using difference cover) bucket 67: 80% bucket 62: 100% Sorting block of length 6009374 for bucket 62 (Using difference cover) bucket 63: 100% Sorting block of length 6583176 for bucket 63 (Using difference cover) bucket 74: 80% bucket 66: 80% bucket 70: 90% Sorting block time: 00:00:04 Returning block of 5881498 for bucket 59 bucket 63: 70% bucket 62: 80% bucket 78: 70% bucket 68: 90% Getting block 87 of 207 Reserving size (6957365) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 75: 70% bucket 64: 70% bucket 61: 90% bucket 69: 80% bucket 56: 100% Sorting block of length 5455639 for bucket 56 (Using difference cover) bucket 80: 70% bucket 75: 80% bucket 71: 90% bucket 71: 100% Sorting block of length 6911063 for bucket 71 (Using difference cover) bucket 66: 100% Sorting block of length 5432898 for bucket 66 (Using difference cover) bucket 69: 90% bucket 73: 90% bucket 85: 10% Sorting block time: 00:00:05 Returning block of 6772692 for bucket 61 bucket 86: 10% bucket 79: 80% Getting block 88 of 207 Reserving size (6957365) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 76: 80% bucket 80: 80% bucket 74: 90% bucket 82: 20% bucket 70: 90% bucket 78: 80% bucket 72: 90% bucket 68: 90% bucket 77: 80% bucket 83: 20% bucket 67: 100% Sorting block of length 5201412 for bucket 67 (Using difference cover) bucket 72: 100% Sorting block of length 3799280 for bucket 72 (Using difference cover) bucket 81: 70% bucket 84: 20% bucket 79: 80% bucket 65: 80% bucket 82: 10% bucket 77: 70% bucket 81: 70% Sorting block time: 00:00:04 Returning block of 5697343 for bucket 64 bucket 59: 80% Getting block 89 of 207 Reserving size (6957365) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 62: 90% bucket 74: 90% bucket 70: 100% Sorting block of length 5807893 for bucket 70 (Using difference cover) bucket 68: 100% Sorting block of length 6507323 for bucket 68 (Using difference cover) bucket 87: 10% bucket 76: 70% bucket 73: 90% Sorting block time: 00:00:04 Returning block of 5473196 for bucket 65 bucket 58: 100% Sorting block of length 6439595 for bucket 58 (Using difference cover) Getting block 90 of 207 Reserving size (6957365) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 60: 90% bucket 67: 90% bucket 80: 80% bucket 75: 90% bucket 71: 100% Sorting block of length 3795132 for bucket 71 (Using difference cover) bucket 78: 80% bucket 75: 80% bucket 69: 100% Sorting block of length 5149105 for bucket 69 (Using difference cover) bucket 66: 90% bucket 73: 100% Sorting block of length 6403578 for bucket 73 (Using difference cover) bucket 69: 90% bucket 85: 20% bucket 79: 90% Sorting block time: 00:00:05 Returning block of 6009375 for bucket 62 bucket 86: 20% bucket 76: 90% bucket 74: 100% Sorting block of length 5093157 for bucket 74 (Using difference cover) bucket 78: 90% bucket 88: 10% Sorting block time: 00:00:04 Returning block of 5455640 for bucket 56 bucket 70: 100% Sorting block of length 3882822 for bucket 70 (Using difference cover) bucket 72: 100% Sorting block of length 4227155 for bucket 72 (Using difference cover) Getting block 91 of 207 Reserving size (6957365) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 61: 100% Sorting block of length 3676172 for bucket 61 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6583177 for bucket 63 Getting block 83 of 205 Reserving size (6957365) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 77: 90% bucket 82: 30% bucket 83: 30% Sorting block time: 00:00:03 Returning block of 3799281 for bucket 72 bucket 80: 90% Getting block 92 of 207 Reserving size (6957365) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: bucket 63: 80% Getting block 84 of 205 Reserving size (6957365) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 84: 30% Sorting block time: 00:00:04 Returning block of 5432899 for bucket 66 bucket 79: 90% bucket 57: 100% Sorting block of length 3350869 for bucket 57 (Using difference cover) Getting block 93 of 207 Reserving size (6957365) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 68: 100% Sorting block of length 6519768 for bucket 68 (Using difference cover) bucket 81: 80% bucket 81: 80% bucket 64: 80% bucket 82: 20% bucket 62: 100% Sorting block of length 5867057 for bucket 62 (Using difference cover) bucket 89: 10% Sorting block time: 00:00:04 Returning block of 5201413 for bucket 67 bucket 74: 100% Sorting block of length 4433424 for bucket 74 (Using difference cover) Getting block 94 of 207 Reserving size (6957365) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: bucket 87: 20% Sorting block time: 00:00:05 Returning block of 6911064 for bucket 71 bucket 73: 100% Sorting block of length 6169532 for bucket 73 (Using difference cover) bucket 90: 10% bucket 75: 100% Sorting block of length 3419486 for bucket 75 (Using difference cover) Getting block 85 of 205 Reserving size (6957365) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 69: 100% Sorting block of length 2189656 for bucket 69 (Using difference cover) bucket 80: 90% Sorting block time: 00:00:03 Returning block of 3795133 for bucket 71 bucket 77: 80% Getting block 95 of 207 Reserving size (6957365) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 85: 30% Sorting block time: 00:00:02 Returning block of 3882823 for bucket 70 bucket 78: 90% bucket 79: 100% Sorting block of length 3183742 for bucket 79 (Using difference cover) bucket 86: 30% bucket 91: 10% bucket 65: 90% Getting block 96 of 207 Reserving size (6957365) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 67: 100% Sorting block of length 5009759 for bucket 67 (Using difference cover) bucket 76: 100% Sorting block of length 5149705 for bucket 76 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3350870 for bucket 57 bucket 66: 100% Sorting block of length 5168566 for bucket 66 (Using difference cover) bucket 88: 20% Getting block 86 of 205 Reserving size (6957365) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 76: 80% bucket 83: 40% bucket 60: 100% Sorting block of length 4324866 for bucket 60 (Using difference cover) bucket 82: 40% bucket 78: 100% Sorting block of length 5932938 for bucket 78 (Using difference cover) bucket 75: 90% bucket 59: 90% bucket 77: 100% Sorting block of length 6848092 for bucket 77 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5807894 for bucket 70 bucket 84: 40% Sorting block time: 00:00:03 Returning block of 3676173 for bucket 61 Sorting block time: 00:00:05 Returning block of 6507324 for bucket 68 Sorting block time: 00:00:03 Returning block of 4227156 for bucket 72 Getting block 87 of 205 Reserving size (6957365) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 81: 90% Sorting block time: 00:00:04 Returning block of 5149106 for bucket 69 bucket 79: 100% Sorting block of length 4805353 for bucket 79 (Using difference cover) Getting block 88 of 205 Reserving size (6957365) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 92: 10% Getting block 97 of 207 Reserving size (6957365) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: Getting block 98 of 207 Reserving size (6957365) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 80: 100% Sorting block of length 5257029 for bucket 80 (Using difference cover) Getting block 99 of 207 Reserving size (6957365) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: Sorting block time: 00:00:02 Returning block of 2189657 for bucket 69 Getting block 89 of 205 Reserving size (6957365) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 89: 20% bucket 83: 10% bucket 93: 10% Sorting block time: 00:00:03 Returning block of 6519769 for bucket 68 bucket 81: 90% bucket 84: 10% Sorting block time: 00:00:04 Returning block of 5093158 for bucket 74 Getting block 90 of 205 Reserving size (6957365) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 87: 30% Sorting block time: 00:00:05 Returning block of 6439596 for bucket 58 Getting block 100 of 207 Reserving size (6957365) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: Sorting block time: 00:00:03 Returning block of 3419487 for bucket 75 Getting block 91 of 205 Reserving size (6957365) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 82: 30% bucket 90: 20% Getting block 101 of 207 Reserving size (6957365) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 63: 90% Sorting block time: 00:00:04 Returning block of 5867058 for bucket 62 Sorting block time: 00:00:04 Returning block of 4433425 for bucket 74 bucket 94: 10% bucket 85: 40% Sorting block time: 00:00:03 Returning block of 3183743 for bucket 79 Getting block 92 of 205 Reserving size (6957365) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: Getting block 93 of 205 Reserving size (6957365) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 80: 100% Sorting block of length 4289993 for bucket 80 (Using difference cover) Sorting block time: 00:00:06 Returning block of 6403579 for bucket 73 bucket 78: 100% Sorting block of length 2856252 for bucket 78 (Using difference cover) Getting block 102 of 207 Reserving size (6957365) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 86: 40% bucket 64: 90% bucket 85: 10% Getting block 103 of 207 Reserving size (6957365) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: bucket 96: 10% bucket 95: 10% bucket 91: 20% bucket 88: 30% bucket 82: 50% Sorting block time: 00:00:03 Returning block of 4324867 for bucket 60 bucket 83: 50% bucket 81: 100% Sorting block of length 6515533 for bucket 81 (Using difference cover) Getting block 94 of 205 Reserving size (6957365) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: bucket 84: 50% bucket 89: 30% bucket 77: 90% Sorting block time: 00:00:04 Returning block of 6169533 for bucket 73 Sorting block time: 00:00:03 Returning block of 5149706 for bucket 76 bucket 97: 10% bucket 87: 10% bucket 92: 20% bucket 86: 10% bucket 65: 100% Sorting block of length 6906744 for bucket 65 (Using difference cover) Getting block 104 of 207 Reserving size (6957365) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: Getting block 95 of 205 Reserving size (6957365) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 99: 10% bucket 98: 10% bucket 59: 100% Sorting block of length 5555793 for bucket 59 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5009760 for bucket 67 bucket 93: 20% bucket 75: 100% Sorting block of length 4883549 for bucket 75 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5168567 for bucket 66 Getting block 96 of 205 Reserving size (6957365) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 90: 30% bucket 81: 100% Sorting block of length 4342142 for bucket 81 (Using difference cover) Getting block 97 of 205 Reserving size (6957365) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: Sorting block time: 00:00:03 Returning block of 5257030 for bucket 80 bucket 87: 40% bucket 88: 10% Sorting block time: 00:00:02 Returning block of 2856253 for bucket 78 bucket 93: 10% Sorting block time: 00:00:04 Returning block of 4805354 for bucket 79 Getting block 98 of 205 Reserving size (6957365) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: Getting block 99 of 205 Reserving size (6957365) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: bucket 100: 10% bucket 83: 20% Getting block 100 of 205 Reserving size (6957365) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: bucket 76: 90% bucket 84: 20% Sorting block time: 00:00:05 Returning block of 5932939 for bucket 78 bucket 85: 50% bucket 91: 10% Getting block 105 of 207 Reserving size (6957365) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 94: 20% bucket 86: 50% bucket 90: 10% bucket 101: 10% Sorting block time: 00:00:05 Returning block of 6848093 for bucket 77 bucket 82: 40% Sorting block time: 00:00:03 Returning block of 4289994 for bucket 80 bucket 103: 10% bucket 89: 10% bucket 92: 10% bucket 102: 10% Getting block 106 of 207 Reserving size (6957365) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 82: 60% bucket 96: 20% Getting block 107 of 207 Reserving size (6957365) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 95: 20% bucket 88: 40% bucket 83: 60% bucket 91: 30% bucket 85: 20% bucket 84: 60% bucket 64: 100% Sorting block of length 3926164 for bucket 64 (Using difference cover) bucket 63: 100% Sorting block of length 5731540 for bucket 63 (Using difference cover) bucket 89: 40% bucket 104: 10% bucket 97: 20% bucket 92: 30% bucket 95: 10% bucket 98: 20% bucket 99: 20% bucket 93: 30% bucket 93: 20% bucket 90: 40% Sorting block time: 00:00:03 Returning block of 4342143 for bucket 81 Sorting block time: 00:00:04 Returning block of 6515534 for bucket 81 Sorting block time: 00:00:03 Returning block of 4883550 for bucket 75 bucket 87: 50% bucket 87: 20% Getting block 101 of 205 Reserving size (6957365) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: Getting block 102 of 205 Reserving size (6957365) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: Getting block 108 of 207 Reserving size (6957365) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 96: 10% Sorting block time: 00:00:04 Returning block of 5555794 for bucket 59 bucket 100: 20% bucket 85: 60% Getting block 103 of 205 Reserving size (6957365) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: bucket 105: 10% bucket 77: 100% Sorting block of length 5029223 for bucket 77 (Using difference cover) bucket 86: 60% bucket 84: 30% bucket 86: 20% bucket 94: 30% bucket 97: 10% Sorting block time: 00:00:04 Returning block of 6906745 for bucket 65 bucket 103: 20% bucket 95: 30% bucket 107: 10% bucket 106: 10% bucket 82: 70% bucket 100: 10% bucket 99: 10% bucket 83: 30% bucket 91: 20% Getting block 104 of 205 Reserving size (6957365) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: bucket 83: 70% bucket 76: 100% Sorting block of length 5258142 for bucket 76 (Using difference cover) bucket 101: 20% bucket 88: 20% bucket 98: 10% bucket 96: 30% bucket 88: 50% bucket 102: 20% bucket 84: 70% Sorting block time: 00:00:03 Returning block of 3926165 for bucket 64 bucket 91: 40% bucket 104: 20% bucket 94: 10% Getting block 105 of 205 Reserving size (6957365) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 92: 20% bucket 90: 20% bucket 89: 50% bucket 82: 50% bucket 89: 20% bucket 97: 30% bucket 85: 30% bucket 93: 30% bucket 92: 40% bucket 98: 30% bucket 99: 30% bucket 95: 20% bucket 93: 40% bucket 87: 60% bucket 90: 50% bucket 108: 10% Sorting block time: 00:00:04 Returning block of 5731541 for bucket 63 bucket 105: 20% bucket 87: 30% bucket 85: 70% Getting block 106 of 205 Reserving size (6957365) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 100: 30% bucket 101: 10% bucket 86: 70% bucket 107: 20% bucket 96: 20% bucket 106: 20% bucket 103: 30% Sorting block time: 00:00:03 Returning block of 5029224 for bucket 77 bucket 94: 40% bucket 95: 40% bucket 86: 30% bucket 83: 80% bucket 84: 40% bucket 82: 80% Getting block 107 of 205 Reserving size (6957365) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 84: 80% bucket 104: 30% bucket 88: 60% bucket 89: 60% bucket 96: 40% bucket 102: 10% bucket 101: 30% bucket 97: 20% Sorting block time: 00:00:03 Returning block of 5258143 for bucket 76 bucket 102: 30% bucket 91: 30% bucket 99: 20% bucket 91: 50% Getting block 108 of 205 Reserving size (6957365) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 100: 20% bucket 93: 40% bucket 88: 30% bucket 92: 30% bucket 97: 40% bucket 98: 20% bucket 92: 50% bucket 83: 40% bucket 108: 20% bucket 87: 70% bucket 90: 30% bucket 99: 40% bucket 98: 40% bucket 85: 40% bucket 93: 50% bucket 105: 30% bucket 90: 60% bucket 89: 30% bucket 103: 10% bucket 85: 80% bucket 87: 40% bucket 95: 30% bucket 82: 60% bucket 107: 30% bucket 86: 80% bucket 106: 30% bucket 94: 20% bucket 105: 10% bucket 103: 40% bucket 100: 40% bucket 82: 90% bucket 83: 90% bucket 104: 40% bucket 94: 50% bucket 95: 50% bucket 84: 90% bucket 101: 20% bucket 99: 30% bucket 93: 50% bucket 88: 70% bucket 84: 50% bucket 89: 70% bucket 96: 50% bucket 96: 30% bucket 106: 10% bucket 101: 40% bucket 102: 40% bucket 91: 60% bucket 86: 40% bucket 91: 40% bucket 104: 10% bucket 107: 10% bucket 108: 30% bucket 97: 50% bucket 105: 40% bucket 97: 30% bucket 85: 50% bucket 88: 40% bucket 92: 60% bucket 87: 80% bucket 98: 30% bucket 102: 20% bucket 90: 70% bucket 93: 60% bucket 98: 50% bucket 99: 50% bucket 87: 50% bucket 92: 40% bucket 100: 30% bucket 85: 90% bucket 107: 40% bucket 106: 40% bucket 86: 90% bucket 108: 10% bucket 95: 40% bucket 104: 50% bucket 83: 50% bucket 103: 50% bucket 82: 100% Sorting block of length 3230220 for bucket 82 (Using difference cover) bucket 83: 100% Sorting block of length 4397352 for bucket 83 (Using difference cover) bucket 100: 50% bucket 93: 60% bucket 84: 100% Sorting block of length 6626066 for bucket 84 (Using difference cover) bucket 95: 60% bucket 90: 40% bucket 94: 60% bucket 88: 80% bucket 89: 80% bucket 99: 40% bucket 96: 60% bucket 89: 40% bucket 94: 30% bucket 91: 70% bucket 105: 20% bucket 102: 50% bucket 108: 40% bucket 101: 50% bucket 82: 70% bucket 87: 90% bucket 85: 60% bucket 105: 50% bucket 84: 60% bucket 86: 50% bucket 103: 20% bucket 97: 60% bucket 101: 30% bucket 96: 40% bucket 92: 70% bucket 106: 20% bucket 91: 50% bucket 90: 80% bucket 93: 70% bucket 85: 100% Sorting block of length 5471886 for bucket 85 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3230221 for bucket 82 bucket 88: 50% bucket 102: 30% bucket 98: 60% bucket 99: 60% bucket 107: 50% Getting block 109 of 207 Reserving size (6957365) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 106: 50% bucket 97: 40% bucket 92: 50% bucket 100: 40% bucket 87: 60% bucket 86: 100% Sorting block of length 5370067 for bucket 86 (Using difference cover) bucket 104: 60% bucket 98: 40% bucket 93: 70% bucket 103: 60% Sorting block time: 00:00:03 Returning block of 4397353 for bucket 83 Getting block 110 of 207 Reserving size (6957365) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 95: 50% bucket 95: 70% bucket 100: 60% bucket 94: 70% bucket 89: 90% bucket 90: 50% bucket 107: 20% bucket 88: 90% bucket 108: 50% bucket 83: 60% bucket 96: 70% bucket 99: 50% bucket 105: 60% bucket 87: 100% Sorting block of length 2938909 for bucket 87 (Using difference cover) bucket 91: 80% bucket 82: 80% bucket 108: 20% bucket 102: 60% bucket 101: 60% Sorting block time: 00:00:05 Returning block of 6626067 for bucket 84 bucket 97: 70% bucket 96: 50% Getting block 111 of 207 Reserving size (6957365) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: bucket 91: 60% bucket 109: 10% bucket 84: 70% bucket 107: 60% bucket 92: 80% bucket 90: 90% bucket 106: 60% bucket 93: 80% bucket 85: 70% bucket 89: 50% bucket 101: 40% bucket 104: 70% bucket 103: 30% bucket 98: 70% bucket 99: 70% Sorting block time: 00:00:01 Returning block of 2938910 for bucket 87 bucket 105: 30% bucket 93: 80% Getting block 112 of 207 Reserving size (6957365) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 94: 40% bucket 104: 20% bucket 110: 10% Sorting block time: 00:00:03 Returning block of 5370068 for bucket 86 Sorting block time: 00:00:04 Returning block of 5471887 for bucket 85 bucket 103: 70% Getting block 113 of 207 Reserving size (6957365) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 97: 50% Getting block 114 of 207 Reserving size (6957365) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 92: 60% bucket 95: 60% bucket 87: 70% bucket 95: 80% bucket 86: 60% bucket 94: 80% bucket 100: 70% bucket 89: 100% Sorting block of length 4417171 for bucket 89 (Using difference cover) bucket 108: 60% bucket 88: 100% Sorting block of length 6895133 for bucket 88 (Using difference cover) bucket 105: 70% bucket 98: 50% bucket 88: 60% bucket 100: 50% bucket 106: 30% bucket 96: 80% bucket 102: 40% bucket 91: 90% bucket 111: 10% bucket 90: 60% bucket 99: 60% bucket 109: 20% bucket 102: 70% bucket 97: 80% bucket 107: 70% bucket 101: 70% bucket 93: 90% bucket 104: 80% bucket 90: 100% Sorting block of length 4105449 for bucket 90 (Using difference cover) bucket 108: 30% bucket 106: 70% bucket 92: 90% bucket 112: 10% bucket 85: 80% bucket 82: 90% bucket 113: 10% bucket 99: 80% bucket 110: 20% bucket 98: 80% bucket 91: 70% bucket 96: 60% bucket 89: 60% bucket 93: 90% bucket 84: 80% bucket 83: 70% bucket 114: 10% bucket 103: 80% bucket 108: 70% bucket 101: 50% bucket 100: 80% bucket 107: 30% bucket 105: 40% bucket 94: 50% Sorting block time: 00:00:03 Returning block of 4417172 for bucket 89 bucket 95: 90% bucket 94: 90% Getting block 115 of 207 Reserving size (6957365) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 103: 40% bucket 87: 80% bucket 105: 80% bucket 92: 70% bucket 95: 70% bucket 109: 30% bucket 96: 90% bucket 111: 20% bucket 97: 60% bucket 113: 20% bucket 86: 70% bucket 91: 100% Sorting block of length 4639661 for bucket 91 (Using difference cover) bucket 98: 60% bucket 88: 70% Sorting block time: 00:00:04 Returning block of 6895134 for bucket 88 bucket 93: 100% Sorting block of length 3316413 for bucket 93 (Using difference cover) bucket 104: 90% bucket 107: 80% Sorting block time: 00:00:03 Returning block of 4105450 for bucket 90 bucket 110: 30% Getting block 116 of 207 Reserving size (6957365) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: Getting block 117 of 207 Reserving size (6957365) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: bucket 112: 20% bucket 106: 80% bucket 97: 90% bucket 102: 80% bucket 100: 60% bucket 89: 70% bucket 102: 50% bucket 90: 70% bucket 92: 100% Sorting block of length 6594679 for bucket 92 (Using difference cover) bucket 101: 80% bucket 114: 20% bucket 104: 30% bucket 108: 80% bucket 98: 90% bucket 99: 90% bucket 85: 90% bucket 99: 70% bucket 106: 40% bucket 103: 90% bucket 108: 40% bucket 84: 90% bucket 115: 10% bucket 82: 100% Sorting block of length 3834492 for bucket 82 (Using difference cover) bucket 96: 70% bucket 100: 90% bucket 91: 80% bucket 105: 90% bucket 110: 40% bucket 83: 80% bucket 94: 100% Sorting block of length 6938579 for bucket 94 (Using difference cover) bucket 93: 100% Sorting block of length 6910254 for bucket 93 (Using difference cover) bucket 95: 100% Sorting block of length 4791816 for bucket 95 (Using difference cover) bucket 109: 40% bucket 111: 30% bucket 101: 60% bucket 113: 30% bucket 87: 90% Sorting block time: 00:00:02 Returning block of 3316414 for bucket 93 bucket 107: 40% bucket 95: 80% bucket 96: 100% Sorting block of length 6184689 for bucket 96 (Using difference cover) Getting block 118 of 207 Reserving size (6957365) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: bucket 104: 100% Sorting block of length 4772282 for bucket 104 (Using difference cover) bucket 107: 90% bucket 97: 70% bucket 116: 10% bucket 89: 80% bucket 112: 30% bucket 117: 10% bucket 94: 60% bucket 105: 50% bucket 106: 90% Sorting block time: 00:00:03 Returning block of 4639662 for bucket 91 bucket 108: 90% bucket 114: 30% bucket 97: 100% Sorting block of length 6465503 for bucket 97 (Using difference cover) bucket 88: 80% bucket 102: 90% Getting block 119 of 207 Reserving size (6957365) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: bucket 98: 70% bucket 110: 50% bucket 92: 80% bucket 86: 80% bucket 103: 100% Sorting block of length 2987069 for bucket 103 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3834493 for bucket 82 bucket 100: 70% bucket 115: 20% bucket 99: 100% Sorting block of length 6129481 for bucket 99 (Using difference cover) Getting block 109 of 205 Reserving size (6957365) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 105: 100% Sorting block of length 5383171 for bucket 105 (Using difference cover) bucket 101: 90% bucket 98: 100% Sorting block of length 6422487 for bucket 98 (Using difference cover) bucket 106: 50% bucket 109: 50% bucket 85: 100% Sorting block of length 3263592 for bucket 85 (Using difference cover) bucket 90: 80% bucket 102: 60% bucket 100: 100% Sorting block of length 6085651 for bucket 100 (Using difference cover) bucket 103: 50% bucket 111: 40% bucket 84: 100% Sorting block of length 4855835 for bucket 84 (Using difference cover) bucket 113: 40% bucket 83: 90% bucket 108: 50% bucket 107: 100% Sorting block of length 4356647 for bucket 107 (Using difference cover) bucket 99: 80% bucket 116: 20% bucket 112: 40% bucket 118: 10% bucket 117: 20% Sorting block time: 00:00:05 Returning block of 6594680 for bucket 92 bucket 96: 80% bucket 87: 100% Sorting block of length 2145085 for bucket 87 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2987070 for bucket 103 bucket 105: 60% bucket 106: 100% Sorting block of length 4618268 for bucket 106 (Using difference cover) Getting block 120 of 207 Reserving size (6957365) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 91: 90% Getting block 121 of 207 Reserving size (6957365) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 108: 100% Sorting block of length 6027294 for bucket 108 (Using difference cover) bucket 114: 40% bucket 101: 70% bucket 104: 40% Sorting block time: 00:00:04 Returning block of 4791817 for bucket 95 bucket 89: 90% Getting block 122 of 207 Reserving size (6957365) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 110: 60% Sorting block time: 00:00:04 Returning block of 6184690 for bucket 96 bucket 107: 50% Sorting block time: 00:00:04 Returning block of 4772283 for bucket 104 bucket 97: 80% bucket 119: 10% bucket 95: 90% Sorting block time: 00:00:04 Returning block of 6910255 for bucket 93 Getting block 123 of 207 Reserving size (6957365) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: Getting block 124 of 207 Reserving size (6957365) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 102: 100% Sorting block of length 4134375 for bucket 102 (Using difference cover) bucket 115: 30% Getting block 110 of 205 Reserving size (6957365) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 94: 70% Sorting block time: 00:00:05 Returning block of 6938580 for bucket 94 bucket 98: 80% bucket 109: 60% bucket 88: 90% Sorting block time: 00:00:03 Returning block of 3263593 for bucket 85 bucket 92: 90% Getting block 111 of 205 Reserving size (6957365) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: Getting block 125 of 207 Reserving size (6957365) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: Sorting block time: 00:00:02 Returning block of 2145086 for bucket 87 bucket 111: 50% bucket 86: 90% Getting block 112 of 205 Reserving size (6957365) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 113: 50% bucket 120: 10% bucket 101: 100% Sorting block of length 6777981 for bucket 101 (Using difference cover) bucket 116: 30% bucket 100: 80% bucket 112: 50% bucket 103: 60% bucket 117: 30% bucket 118: 20% bucket 105: 70% bucket 83: 100% Sorting block of length 6068889 for bucket 83 (Using difference cover) bucket 90: 90% bucket 114: 50% bucket 121: 10% Sorting block time: 00:00:04 Returning block of 4855836 for bucket 84 bucket 110: 70% Sorting block time: 00:00:05 Returning block of 5383172 for bucket 105 Sorting block time: 00:00:04 Returning block of 4356648 for bucket 107 bucket 109: 10% Sorting block time: 00:00:05 Returning block of 6129482 for bucket 99 Getting block 113 of 205 Reserving size (6957365) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: Sorting block time: 00:00:06 Returning block of 6465504 for bucket 97 bucket 106: 60% bucket 122: 10% bucket 108: 60% bucket 101: 80% bucket 124: 10% bucket 102: 70% Getting block 126 of 207 Reserving size (6957365) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: Getting block 127 of 207 Reserving size (6957365) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: Getting block 128 of 207 Reserving size (6957365) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: bucket 123: 10% Getting block 129 of 207 Reserving size (6957365) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: bucket 96: 90% bucket 119: 20% bucket 91: 100% Sorting block of length 6641778 for bucket 91 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6085652 for bucket 100 Sorting block time: 00:00:03 Returning block of 4618269 for bucket 106 Sorting block time: 00:00:03 Returning block of 4134376 for bucket 102 bucket 115: 40% bucket 99: 90% Sorting block time: 00:00:03 Returning block of 6027295 for bucket 108 Getting block 130 of 207 Reserving size (6957365) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: Getting block 131 of 207 Reserving size (6957365) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: Sorting block time: 00:00:05 Returning block of 6422488 for bucket 98 Getting block 132 of 207 Reserving size (6957365) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 89: 100% Sorting block of length 3724916 for bucket 89 (Using difference cover) bucket 109: 70% Getting block 133 of 207 Reserving size (6957365) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: Getting block 134 of 207 Reserving size (6957365) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 95: 100% Sorting block of length 5996082 for bucket 95 (Using difference cover) bucket 97: 90% bucket 111: 60% bucket 113: 60% bucket 120: 20% bucket 125: 10% bucket 116: 40% bucket 112: 60% bucket 107: 60% bucket 94: 80% bucket 110: 80% bucket 104: 50% bucket 117: 40% bucket 88: 100% Sorting block of length 6509758 for bucket 88 (Using difference cover) bucket 114: 60% bucket 118: 30% bucket 105: 80% bucket 92: 100% Sorting block of length 4441417 for bucket 92 (Using difference cover) bucket 110: 10% bucket 115: 50% bucket 121: 20% bucket 98: 90% bucket 100: 90% bucket 111: 10% bucket 86: 100% Sorting block of length 6490007 for bucket 86 (Using difference cover) bucket 127: 10% bucket 124: 20% bucket 112: 10% bucket 128: 10% bucket 122: 20% bucket 103: 70% bucket 129: 10% bucket 126: 10% Sorting block time: 00:00:04 Returning block of 6068890 for bucket 83 bucket 123: 20% bucket 119: 30% bucket 130: 10% Getting block 114 of 205 Reserving size (6957365) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: Sorting block time: 00:00:02 Returning block of 3724917 for bucket 89 bucket 109: 80% bucket 131: 10% Getting block 115 of 205 Reserving size (6957365) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 132: 10% bucket 133: 10% bucket 90: 100% Sorting block of length 4459986 for bucket 90 (Using difference cover) bucket 113: 70% bucket 106: 70% bucket 134: 10% bucket 111: 70% Sorting block time: 00:00:05 Returning block of 6777982 for bucket 101 bucket 115: 60% bucket 113: 10% bucket 125: 20% bucket 120: 30% bucket 101: 90% bucket 108: 70% Getting block 135 of 207 Reserving size (6957365) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 96: 100% Sorting block of length 5854439 for bucket 96 (Using difference cover) bucket 110: 90% bucket 102: 80% bucket 99: 100% Sorting block of length 5447964 for bucket 99 (Using difference cover) bucket 116: 50% bucket 112: 70% bucket 97: 100% Sorting block of length 3486808 for bucket 97 (Using difference cover) bucket 117: 50% bucket 114: 70% bucket 109: 20% bucket 118: 40% bucket 105: 90% bucket 126: 20% bucket 121: 30% bucket 128: 20% bucket 127: 20% bucket 124: 30% bucket 129: 20% Sorting block time: 00:00:03 Returning block of 4441418 for bucket 92 bucket 130: 20% Sorting block time: 00:00:04 Returning block of 5996083 for bucket 95 Getting block 116 of 205 Reserving size (6957365) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: Sorting block time: 00:00:05 Returning block of 6641779 for bucket 91 bucket 119: 40% bucket 94: 90% bucket 123: 30% bucket 122: 30% Getting block 117 of 205 Reserving size (6957365) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: bucket 109: 90% Sorting block time: 00:00:03 Returning block of 4459987 for bucket 90 bucket 131: 20% Getting block 118 of 205 Reserving size (6957365) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: Getting block 119 of 205 Reserving size (6957365) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: bucket 98: 100% Sorting block of length 4265560 for bucket 98 (Using difference cover) bucket 113: 80% bucket 100: 100% Sorting block of length 5142018 for bucket 100 (Using difference cover) bucket 132: 20% bucket 111: 20% bucket 107: 70% bucket 133: 20% bucket 125: 30% bucket 134: 20% bucket 115: 70% bucket 114: 10% bucket 111: 80% bucket 110: 20% bucket 112: 20% bucket 110: 100% Sorting block of length 3635109 for bucket 110 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6490008 for bucket 86 bucket 120: 40% bucket 104: 60% bucket 116: 60% Getting block 120 of 205 Reserving size (6957365) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 135: 10% bucket 103: 80% Sorting block time: 00:00:05 Returning block of 6509759 for bucket 88 bucket 112: 80% bucket 114: 80% bucket 105: 100% Sorting block of length 4550536 for bucket 105 (Using difference cover) bucket 117: 60% Getting block 121 of 205 Reserving size (6957365) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: Sorting block time: 00:00:02 Returning block of 3486809 for bucket 97 Getting block 122 of 205 Reserving size (6957365) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 115: 10% bucket 118: 50% bucket 126: 30% bucket 129: 30% bucket 124: 40% bucket 128: 30% bucket 101: 100% Sorting block of length 4927851 for bucket 101 (Using difference cover) bucket 121: 40% bucket 127: 30% bucket 113: 20% bucket 130: 30% bucket 108: 80% bucket 122: 40% bucket 115: 80% bucket 113: 90% bucket 123: 40% bucket 109: 100% Sorting block of length 3734263 for bucket 109 (Using difference cover) bucket 119: 50% Sorting block time: 00:00:04 Returning block of 5447965 for bucket 99 bucket 131: 30% bucket 106: 80% bucket 132: 30% Getting block 123 of 205 Reserving size (6957365) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 133: 30% Sorting block time: 00:00:05 Returning block of 5854440 for bucket 96 bucket 102: 90% Sorting block time: 00:00:02 Returning block of 3635110 for bucket 110 bucket 125: 40% Getting block 124 of 205 Reserving size (6957365) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: Getting block 136 of 207 Reserving size (6957365) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 111: 90% bucket 94: 100% Sorting block of length 6265561 for bucket 94 (Using difference cover) bucket 134: 30% Sorting block time: 00:00:03 Returning block of 4265561 for bucket 98 bucket 126: 40% Getting block 125 of 205 Reserving size (6957365) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: bucket 116: 70% Sorting block time: 00:00:04 Returning block of 5142019 for bucket 100 bucket 109: 30% bucket 120: 50% Getting block 126 of 205 Reserving size (6957365) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: bucket 112: 90% bucket 135: 20% bucket 114: 90% bucket 116: 10% bucket 117: 70% bucket 117: 10% bucket 118: 10% bucket 119: 10% Sorting block time: 00:00:03 Returning block of 4550537 for bucket 105 bucket 110: 30% bucket 129: 40% bucket 118: 60% bucket 107: 80% Getting block 127 of 205 Reserving size (6957365) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 124: 50% bucket 130: 40% bucket 111: 30% bucket 127: 40% bucket 128: 40% bucket 121: 50% Sorting block time: 00:00:03 Returning block of 3734264 for bucket 109 bucket 112: 30% bucket 115: 90% bucket 113: 100% Sorting block of length 2816792 for bucket 113 (Using difference cover) bucket 103: 90% Getting block 137 of 207 Reserving size (6957365) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 122: 50% bucket 123: 50% bucket 120: 10% bucket 114: 20% bucket 131: 40% bucket 119: 60% bucket 132: 40% bucket 121: 10% bucket 125: 50% bucket 122: 10% bucket 133: 40% bucket 126: 50% Sorting block time: 00:00:04 Returning block of 4927852 for bucket 101 bucket 136: 10% bucket 112: 100% Sorting block of length 5586424 for bucket 112 (Using difference cover) bucket 111: 100% Sorting block of length 4889384 for bucket 111 (Using difference cover) Getting block 128 of 205 Reserving size (6957365) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: bucket 114: 100% Sorting block of length 6886396 for bucket 114 (Using difference cover) bucket 108: 90% bucket 116: 80% bucket 134: 40% bucket 113: 30% bucket 123: 10% bucket 120: 60% bucket 104: 70% Sorting block time: 00:00:02 Returning block of 2816793 for bucket 113 bucket 115: 20% bucket 117: 80% Getting block 138 of 207 Reserving size (6957365) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 135: 30% bucket 102: 100% Sorting block of length 6203744 for bucket 102 (Using difference cover) bucket 127: 50% bucket 137: 10% bucket 130: 50% bucket 106: 90% bucket 129: 50% bucket 124: 10% Sorting block time: 00:00:04 Returning block of 6265562 for bucket 94 bucket 124: 60% bucket 127: 10% bucket 128: 50% bucket 118: 70% Getting block 129 of 205 Reserving size (6957365) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: bucket 125: 10% bucket 115: 100% Sorting block of length 6078807 for bucket 115 (Using difference cover) bucket 121: 60% bucket 122: 60% bucket 125: 60% bucket 117: 20% bucket 131: 50% bucket 123: 60% bucket 116: 20% bucket 126: 10% bucket 118: 20% bucket 112: 40% bucket 119: 70% bucket 132: 50% bucket 133: 50% bucket 109: 40% bucket 126: 60% bucket 136: 20% bucket 107: 90% bucket 111: 40% bucket 110: 40% bucket 127: 60% bucket 117: 90% bucket 137: 20% bucket 116: 90% Sorting block time: 00:00:03 Returning block of 4889385 for bucket 111 bucket 134: 50% bucket 122: 20% bucket 103: 100% Sorting block of length 6493858 for bucket 103 (Using difference cover) Getting block 139 of 207 Reserving size (6957365) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 119: 20% Sorting block time: 00:00:03 Returning block of 5586425 for bucket 112 bucket 120: 70% bucket 118: 80% bucket 120: 20% bucket 135: 40% Getting block 140 of 207 Reserving size (6957365) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: bucket 130: 60% bucket 138: 10% bucket 124: 70% bucket 114: 30% bucket 129: 60% bucket 127: 20% bucket 121: 20% bucket 108: 100% Sorting block of length 6834912 for bucket 108 (Using difference cover) bucket 128: 60% bucket 128: 10% bucket 125: 70% bucket 113: 40% Sorting block time: 00:00:04 Returning block of 6886397 for bucket 114 bucket 131: 60% bucket 117: 100% Sorting block of length 1790963 for bucket 117 (Using difference cover) Sorting block time: 00:00:04 Returning block of 6078808 for bucket 115 bucket 123: 70% bucket 121: 70% Getting block 141 of 207 Reserving size (6957365) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 123: 20% bucket 122: 70% Getting block 142 of 207 Reserving size (6957365) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: Sorting block time: 00:00:04 Returning block of 6203745 for bucket 102 bucket 126: 70% bucket 136: 30% bucket 124: 20% bucket 132: 60% bucket 133: 60% Getting block 130 of 205 Reserving size (6957365) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: bucket 106: 100% Sorting block of length 6730501 for bucket 106 (Using difference cover) bucket 104: 80% bucket 119: 80% bucket 137: 30% Sorting block time: 00:00:00 Returning block of 1790964 for bucket 117 Getting block 143 of 207 Reserving size (6957365) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 125: 20% bucket 116: 100% Sorting block of length 6869834 for bucket 116 (Using difference cover) bucket 115: 30% bucket 138: 20% bucket 127: 70% bucket 117: 30% bucket 116: 30% bucket 139: 10% bucket 134: 60% bucket 118: 90% bucket 118: 30% bucket 128: 70% bucket 130: 70% bucket 126: 20% bucket 135: 50% bucket 124: 80% bucket 120: 80% bucket 112: 50% bucket 129: 70% bucket 140: 10% bucket 111: 50% bucket 122: 30% bucket 109: 50% bucket 125: 80% bucket 127: 30% Sorting block time: 00:00:04 Returning block of 6493859 for bucket 103 bucket 129: 10% bucket 121: 80% bucket 131: 70% Getting block 131 of 205 Reserving size (6957365) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 126: 80% bucket 110: 50% bucket 119: 30% bucket 141: 10% bucket 123: 80% bucket 122: 80% bucket 107: 100% Sorting block of length 2518122 for bucket 107 (Using difference cover) bucket 113: 50% bucket 142: 10% bucket 136: 40% bucket 121: 30% bucket 132: 70% bucket 120: 30% bucket 133: 70% bucket 137: 40% bucket 119: 90% bucket 128: 20% bucket 127: 80% bucket 138: 30% bucket 114: 40% Sorting block time: 00:00:04 Returning block of 6730502 for bucket 106 bucket 143: 10% bucket 128: 80% bucket 130: 80% bucket 134: 70% bucket 139: 20% Getting block 132 of 205 Reserving size (6957365) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 118: 100% Sorting block of length 6151253 for bucket 118 (Using difference cover) bucket 124: 30% Sorting block time: 00:00:05 Returning block of 6834913 for bucket 108 bucket 123: 30% bucket 129: 80% bucket 135: 60% bucket 124: 90% bucket 125: 90% bucket 125: 30% bucket 120: 90% Getting block 133 of 205 Reserving size (6957365) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: Sorting block time: 00:00:01 Returning block of 2518123 for bucket 107 Getting block 134 of 205 Reserving size (6957365) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 130: 10% Sorting block time: 00:00:04 Returning block of 6869835 for bucket 116 bucket 121: 90% bucket 131: 80% bucket 126: 90% bucket 140: 20% bucket 127: 40% Getting block 144 of 207 Reserving size (6957365) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 142: 20% bucket 116: 40% bucket 117: 40% bucket 115: 40% bucket 123: 90% bucket 126: 30% bucket 122: 90% bucket 118: 40% bucket 104: 90% bucket 141: 20% bucket 111: 60% bucket 136: 50% bucket 132: 80% bucket 112: 60% bucket 137: 50% bucket 133: 80% bucket 127: 90% bucket 119: 100% Sorting block of length 3167135 for bucket 119 (Using difference cover) bucket 122: 40% bucket 138: 40% bucket 128: 90% bucket 129: 20% bucket 130: 90% bucket 143: 20% bucket 134: 80% bucket 139: 30% bucket 129: 90% bucket 125: 100% Sorting block of length 6027999 for bucket 125 (Using difference cover) bucket 121: 40% bucket 113: 60% bucket 124: 100% Sorting block of length 5142286 for bucket 124 (Using difference cover) bucket 135: 70% bucket 120: 100% Sorting block of length 6870970 for bucket 120 (Using difference cover) bucket 109: 60% bucket 131: 10% bucket 128: 30% bucket 126: 100% Sorting block of length 6655307 for bucket 126 (Using difference cover) bucket 120: 40% bucket 131: 90% bucket 110: 60% bucket 121: 100% Sorting block of length 2260415 for bucket 121 (Using difference cover) bucket 119: 40% bucket 127: 50% bucket 124: 40% bucket 144: 10% bucket 142: 30% bucket 140: 30% bucket 122: 100% Sorting block of length 4751381 for bucket 122 (Using difference cover) bucket 125: 40% bucket 123: 100% Sorting block of length 2682682 for bucket 123 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3167136 for bucket 119 bucket 136: 60% bucket 123: 40% bucket 132: 90% Getting block 145 of 207 Reserving size (6957365) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 141: 30% bucket 137: 60% bucket 127: 100% Sorting block of length 6909014 for bucket 127 (Using difference cover) Sorting block time: 00:00:04 Returning block of 6151254 for bucket 118 bucket 114: 50% bucket 133: 90% bucket 132: 10% Getting block 146 of 207 Reserving size (6957365) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: bucket 138: 50% bucket 133: 10% bucket 128: 100% Sorting block of length 6782162 for bucket 128 (Using difference cover) bucket 130: 100% Sorting block of length 6035670 for bucket 130 (Using difference cover) bucket 116: 50% bucket 129: 100% Sorting block of length 2778233 for bucket 129 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2260416 for bucket 121 bucket 139: 40% bucket 111: 70% bucket 134: 90% Getting block 147 of 207 Reserving size (6957365) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 126: 40% bucket 117: 50% bucket 143: 30% bucket 134: 10% bucket 118: 50% bucket 130: 20% bucket 135: 80% bucket 112: 70% Sorting block time: 00:00:02 Returning block of 2682683 for bucket 123 Getting block 148 of 207 Reserving size (6957365) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 122: 50% bucket 104: 100% Sorting block of length 6233186 for bucket 104 (Using difference cover) bucket 131: 100% Sorting block of length 6698396 for bucket 131 (Using difference cover) bucket 115: 50% bucket 127: 60% Sorting block time: 00:00:04 Returning block of 5142287 for bucket 124 Sorting block time: 00:00:04 Returning block of 6028000 for bucket 125 Getting block 149 of 207 Reserving size (6957365) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: bucket 113: 70% bucket 144: 20% bucket 121: 50% Getting block 150 of 207 Reserving size (6957365) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 142: 40% bucket 136: 70% bucket 132: 100% Sorting block of length 5165655 for bucket 132 (Using difference cover) bucket 137: 70% bucket 128: 40% bucket 133: 100% Sorting block of length 5005828 for bucket 133 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2778234 for bucket 129 bucket 141: 40% bucket 145: 10% bucket 140: 40% Getting block 151 of 207 Reserving size (6957365) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 131: 20% bucket 138: 60% bucket 146: 10% Sorting block time: 00:00:03 Returning block of 4751382 for bucket 122 bucket 109: 70% bucket 129: 30% Getting block 152 of 207 Reserving size (6957365) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: Sorting block time: 00:00:05 Returning block of 6870971 for bucket 120 bucket 120: 50% bucket 148: 10% bucket 110: 70% bucket 124: 50% bucket 123: 50% bucket 134: 100% Sorting block of length 3664821 for bucket 134 (Using difference cover) bucket 139: 50% bucket 119: 50% Getting block 153 of 207 Reserving size (6957365) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 147: 10% bucket 125: 50% bucket 132: 20% Sorting block time: 00:00:05 Returning block of 6655308 for bucket 126 bucket 135: 90% bucket 143: 40% Getting block 154 of 207 Reserving size (6957365) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: Sorting block time: 00:00:04 Returning block of 6035671 for bucket 130 Getting block 155 of 207 Reserving size (6957365) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: bucket 116: 60% bucket 133: 20% bucket 149: 10% Sorting block time: 00:00:04 Returning block of 6782163 for bucket 128 Sorting block time: 00:00:05 Returning block of 6909015 for bucket 127 bucket 114: 60% bucket 111: 80% bucket 117: 60% Getting block 156 of 207 Reserving size (6957365) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: Getting block 157 of 207 Reserving size (6957365) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 118: 60% bucket 112: 80% bucket 127: 70% bucket 136: 80% bucket 137: 80% bucket 126: 50% bucket 144: 30% bucket 150: 10% bucket 142: 50% bucket 122: 60% bucket 141: 50% bucket 138: 70% Sorting block time: 00:00:04 Returning block of 6233187 for bucket 104 bucket 151: 10% bucket 145: 20% bucket 130: 30% bucket 146: 20% Getting block 135 of 205 Reserving size (6957365) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 140: 50% bucket 134: 20% Sorting block time: 00:00:04 Returning block of 5165656 for bucket 132 Sorting block time: 00:00:03 Returning block of 3664822 for bucket 134 Sorting block time: 00:00:04 Returning block of 5005829 for bucket 133 bucket 152: 10% bucket 113: 80% bucket 139: 60% Getting block 158 of 207 Reserving size (6957365) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: Getting block 159 of 207 Reserving size (6957365) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 135: 100% Sorting block of length 5340744 for bucket 135 (Using difference cover) bucket 153: 10% bucket 147: 20% bucket 115: 60% bucket 148: 20% Getting block 160 of 207 Reserving size (6957365) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 121: 60% bucket 128: 50% bucket 143: 50% bucket 154: 10% bucket 120: 60% Sorting block time: 00:00:05 Returning block of 6698397 for bucket 131 bucket 155: 10% bucket 109: 80% bucket 132: 30% Getting block 161 of 207 Reserving size (6957365) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 149: 20% bucket 124: 60% bucket 123: 60% bucket 129: 40% bucket 125: 60% bucket 157: 10% bucket 137: 90% bucket 156: 10% bucket 136: 90% bucket 131: 30% bucket 150: 20% bucket 144: 40% bucket 142: 60% bucket 138: 80% bucket 119: 60% bucket 151: 20% bucket 145: 30% bucket 146: 30% bucket 141: 60% bucket 126: 60% bucket 127: 80% bucket 112: 90% bucket 152: 20% bucket 118: 70% bucket 116: 70% bucket 139: 70% bucket 111: 90% bucket 117: 70% bucket 159: 10% bucket 153: 20% bucket 158: 10% bucket 133: 30% bucket 140: 60% bucket 147: 30% bucket 110: 80% bucket 148: 30% bucket 160: 10% bucket 122: 70% Sorting block time: 00:00:03 Returning block of 5340745 for bucket 135 bucket 143: 60% bucket 114: 70% bucket 154: 20% Getting block 162 of 207 Reserving size (6957365) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 155: 20% bucket 132: 40% bucket 161: 10% bucket 149: 30% bucket 130: 40% bucket 121: 70% bucket 113: 90% bucket 120: 70% bucket 157: 20% bucket 137: 100% Sorting block of length 3876393 for bucket 137 (Using difference cover) bucket 136: 100% Sorting block of length 5578604 for bucket 136 (Using difference cover) bucket 156: 20% bucket 128: 60% bucket 150: 30% bucket 142: 70% bucket 115: 70% bucket 144: 50% bucket 138: 90% bucket 109: 90% bucket 123: 70% bucket 134: 30% bucket 151: 30% bucket 146: 40% bucket 124: 70% bucket 145: 40% bucket 141: 70% bucket 152: 30% bucket 139: 80% bucket 129: 50% bucket 135: 10% bucket 125: 70% bucket 159: 20% bucket 153: 30% bucket 158: 20% bucket 147: 40% bucket 148: 40% bucket 160: 20% bucket 140: 70% bucket 111: 100% Sorting block of length 3246345 for bucket 111 (Using difference cover) bucket 143: 70% bucket 162: 10% bucket 133: 40% bucket 119: 70% bucket 154: 30% bucket 126: 70% bucket 132: 50% bucket 155: 30% bucket 117: 80% bucket 161: 20% Sorting block time: 00:00:02 Returning block of 3876394 for bucket 137 bucket 118: 80% bucket 149: 40% Getting block 163 of 207 Reserving size (6957365) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: bucket 112: 100% Sorting block of length 5019802 for bucket 112 (Using difference cover) bucket 116: 80% bucket 127: 90% bucket 131: 40% bucket 151: 40% bucket 157: 30% bucket 146: 50% bucket 150: 40% bucket 122: 80% bucket 138: 100% Sorting block of length 6679345 for bucket 138 (Using difference cover) bucket 121: 80% bucket 142: 80% bucket 156: 30% bucket 144: 60% bucket 110: 90% bucket 158: 30% bucket 114: 80% bucket 160: 30% Sorting block time: 00:00:04 Returning block of 5578605 for bucket 136 bucket 152: 40% bucket 130: 50% bucket 145: 50% bucket 113: 100% Sorting block of length 4968964 for bucket 113 (Using difference cover) Getting block 164 of 207 Reserving size (6957365) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 159: 30% bucket 139: 90% bucket 153: 40% bucket 141: 80% bucket 147: 50% Sorting block time: 00:00:02 Returning block of 3246346 for bucket 111 bucket 128: 70% bucket 124: 80% bucket 161: 30% Getting block 136 of 205 Reserving size (6957365) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 125: 80% bucket 148: 50% bucket 123: 80% bucket 143: 80% bucket 162: 20% bucket 118: 90% bucket 120: 80% bucket 109: 100% Sorting block of length 4674074 for bucket 109 (Using difference cover) bucket 149: 50% bucket 140: 80% bucket 154: 40% bucket 155: 40% bucket 163: 10% bucket 133: 50% bucket 134: 40% bucket 151: 50% bucket 115: 80% bucket 150: 50% bucket 146: 60% bucket 157: 40% Sorting block time: 00:00:03 Returning block of 5019803 for bucket 112 bucket 126: 80% Getting block 137 of 205 Reserving size (6957365) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 135: 20% bucket 117: 90% bucket 142: 90% bucket 129: 60% bucket 156: 40% bucket 116: 90% bucket 159: 40% bucket 160: 40% bucket 158: 40% bucket 144: 70% bucket 152: 50% bucket 121: 90% bucket 119: 80% bucket 153: 50% bucket 145: 60% bucket 127: 100% Sorting block of length 3921451 for bucket 127 (Using difference cover) bucket 164: 10% bucket 147: 60% Sorting block time: 00:00:03 Returning block of 4968965 for bucket 113 bucket 122: 90% bucket 139: 100% Sorting block of length 6410120 for bucket 139 (Using difference cover) bucket 131: 50% bucket 141: 90% Getting block 138 of 205 bucket 161: 40% Reserving size (6957365) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 162: 30% bucket 132: 60% bucket 124: 90% bucket 148: 60% bucket 123: 90% Sorting block time: 00:00:05 Returning block of 6679346 for bucket 138 bucket 149: 60% bucket 143: 90% bucket 163: 20% bucket 154: 50% Getting block 165 of 207 Reserving size (6957365) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 128: 80% bucket 155: 50% Sorting block time: 00:00:03 Returning block of 4674075 for bucket 109 bucket 146: 70% bucket 151: 60% bucket 140: 90% Getting block 139 of 205 Reserving size (6957365) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 130: 60% bucket 136: 10% bucket 150: 60% bucket 110: 100% Sorting block of length 5061185 for bucket 110 (Using difference cover) bucket 159: 50% bucket 125: 90% bucket 118: 100% Sorting block of length 5975402 for bucket 118 (Using difference cover) bucket 114: 90% bucket 157: 50% bucket 160: 50% bucket 133: 60% bucket 137: 10% bucket 142: 100% Sorting block of length 4897179 for bucket 142 (Using difference cover) bucket 152: 60% bucket 126: 90% bucket 158: 50% bucket 153: 60% bucket 156: 50% bucket 120: 90% bucket 117: 100% Sorting block of length 6018445 for bucket 117 (Using difference cover) bucket 144: 80% Sorting block time: 00:00:03 Returning block of 3921452 for bucket 127 bucket 147: 70% bucket 145: 70% Getting block 140 of 205 Reserving size (6957365) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: bucket 164: 20% bucket 116: 100% Sorting block of length 6403024 for bucket 116 (Using difference cover) bucket 122: 100% Sorting block of length 5634365 for bucket 122 (Using difference cover) bucket 115: 90% bucket 161: 50% bucket 121: 100% Sorting block of length 6643871 for bucket 121 (Using difference cover) bucket 162: 40% bucket 129: 70% bucket 134: 50% bucket 154: 60% bucket 146: 80% bucket 149: 70% bucket 141: 100% Sorting block of length 4325789 for bucket 141 (Using difference cover) bucket 163: 30% bucket 138: 10% bucket 143: 100% Sorting block of length 6633845 for bucket 143 (Using difference cover) bucket 135: 30% bucket 155: 60% bucket 165: 10% bucket 148: 70% bucket 160: 60% bucket 151: 70% bucket 119: 90% bucket 159: 60% bucket 123: 100% Sorting block of length 3502754 for bucket 123 (Using difference cover) bucket 152: 70% bucket 150: 70% bucket 124: 100% Sorting block of length 4528790 for bucket 124 (Using difference cover) bucket 157: 60% Sorting block time: 00:00:05 Returning block of 6410121 for bucket 139 bucket 153: 70% bucket 128: 90% bucket 140: 100% Sorting block of length 6872821 for bucket 140 (Using difference cover) bucket 158: 60% Sorting block time: 00:00:03 Returning block of 5061186 for bucket 110 bucket 125: 100% Sorting block of length 5177176 for bucket 125 (Using difference cover) bucket 131: 60% bucket 132: 70% bucket 164: 30% bucket 162: 50% bucket 146: 90% bucket 144: 90% bucket 133: 70% bucket 156: 60% bucket 147: 80% bucket 161: 60% bucket 145: 80% Sorting block time: 00:00:04 Returning block of 4897180 for bucket 142 bucket 136: 20% Getting block 166 of 207 Reserving size (6957365) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: Getting block 141 of 205 Reserving size (6957365) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 126: 100% Sorting block of length 6837840 for bucket 126 (Using difference cover) Getting block 167 of 207 Reserving size (6957365) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: bucket 137: 20% bucket 130: 70% Sorting block time: 00:00:03 Returning block of 5634366 for bucket 122 Sorting block time: 00:00:04 Returning block of 5975403 for bucket 118 bucket 120: 100% Sorting block of length 6844874 for bucket 120 (Using difference cover) bucket 154: 70% bucket 149: 80% Getting block 142 of 205 Reserving size (6957365) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: Getting block 143 of 205 Reserving size (6957365) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 152: 80% bucket 159: 70% bucket 163: 40% bucket 129: 80% bucket 150: 80% bucket 165: 20% Sorting block time: 00:00:03 Returning block of 4325790 for bucket 141 bucket 160: 70% Sorting block time: 00:00:04 Returning block of 6018446 for bucket 117 bucket 153: 80% bucket 114: 100% Sorting block of length 2651230 for bucket 114 (Using difference cover) bucket 139: 10% bucket 151: 80% Getting block 168 of 207 Reserving size (6957365) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 155: 70% Getting block 144 of 205 Reserving size (6957365) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 148: 80% Sorting block time: 00:00:04 Returning block of 6643872 for bucket 121 Sorting block time: 00:00:03 Returning block of 3502755 for bucket 123 Sorting block time: 00:00:04 Returning block of 6403025 for bucket 116 bucket 158: 70% Getting block 145 of 205 Reserving size (6957365) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 161: 70% Getting block 146 of 205 Reserving size (6957365) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: Getting block 147 of 205 Reserving size (6957365) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 157: 70% bucket 147: 90% bucket 115: 100% Sorting block of length 6851763 for bucket 115 (Using difference cover) bucket 134: 60% bucket 140: 10% bucket 138: 20% bucket 164: 40% Sorting block time: 00:00:03 Returning block of 4528791 for bucket 124 bucket 162: 60% bucket 146: 100% Sorting block of length 6219429 for bucket 146 (Using difference cover) bucket 156: 70% Getting block 148 of 205 Reserving size (6957365) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 145: 90% bucket 135: 40% Sorting block time: 00:00:02 Returning block of 2651231 for bucket 114 bucket 166: 10% Sorting block time: 00:00:04 Returning block of 5177177 for bucket 125 bucket 144: 100% Sorting block of length 5291579 for bucket 144 (Using difference cover) Getting block 149 of 205 Reserving size (6957365) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: Sorting block time: 00:00:05 Returning block of 6633846 for bucket 143 bucket 128: 100% Sorting block of length 3165677 for bucket 128 (Using difference cover) bucket 142: 10% bucket 136: 30% bucket 149: 90% Getting block 150 of 205 Reserving size (6957365) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 133: 80% bucket 152: 90% bucket 119: 100% Sorting block of length 4358868 for bucket 119 (Using difference cover) bucket 167: 10% Sorting block time: 00:00:04 Returning block of 6872822 for bucket 140 Getting block 169 of 207 Reserving size (6957365) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 154: 80% bucket 159: 80% bucket 160: 80% Getting block 170 of 207 Reserving size (6957365) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 150: 90% bucket 163: 50% bucket 153: 90% bucket 137: 30% bucket 151: 90% bucket 132: 80% bucket 143: 10% bucket 131: 70% bucket 165: 30% bucket 168: 10% bucket 147: 100% Sorting block of length 1496557 for bucket 147 (Using difference cover) bucket 155: 80% bucket 130: 80% bucket 158: 80% bucket 148: 90% bucket 161: 80% bucket 157: 80% Sorting block time: 00:00:05 Returning block of 6837841 for bucket 126 Sorting block time: 00:00:05 Returning block of 6844875 for bucket 120 bucket 145: 100% Sorting block of length 6226580 for bucket 145 (Using difference cover) bucket 164: 50% Sorting block time: 00:00:02 Returning block of 3165678 for bucket 128 bucket 144: 10% Getting block 151 of 205 Reserving size (6957365) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 147: 10% bucket 162: 70% Sorting block time: 00:00:01 Returning block of 1496558 for bucket 147 Getting block 152 of 205 Reserving size (6957365) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: Getting block 153 of 205 Reserving size (6957365) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: Getting block 171 of 207 Reserving size (6957365) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 145: 10% bucket 156: 80% bucket 141: 10% bucket 139: 20% bucket 129: 90% bucket 146: 10% bucket 154: 90% bucket 166: 20% Sorting block time: 00:00:04 Returning block of 6219430 for bucket 146 bucket 149: 100% Sorting block of length 4115123 for bucket 149 (Using difference cover) bucket 152: 100% Sorting block of length 5578844 for bucket 152 (Using difference cover) bucket 153: 100% Sorting block of length 6193664 for bucket 153 (Using difference cover) bucket 159: 90% bucket 167: 20% bucket 138: 30% Getting block 172 of 207 Reserving size (6957365) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: bucket 169: 10% bucket 170: 10% Sorting block time: 00:00:03 Returning block of 4358869 for bucket 119 bucket 160: 90% Sorting block time: 00:00:04 Returning block of 6851764 for bucket 115 bucket 163: 60% bucket 158: 90% Getting block 154 of 205 Reserving size (6957365) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 151: 100% Sorting block of length 4946996 for bucket 151 (Using difference cover) bucket 161: 90% bucket 150: 100% Sorting block of length 3517247 for bucket 150 (Using difference cover) Getting block 155 of 205 Reserving size (6957365) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: Sorting block time: 00:00:04 Returning block of 5291580 for bucket 144 bucket 140: 20% bucket 134: 70% bucket 149: 10% bucket 165: 40% bucket 142: 20% bucket 148: 10% Getting block 173 of 207 Reserving size (6957365) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: bucket 168: 20% bucket 155: 90% bucket 133: 90% bucket 148: 100% Sorting block of length 5854800 for bucket 148 (Using difference cover) bucket 137: 40% bucket 157: 90% bucket 136: 40% bucket 150: 10% bucket 164: 60% bucket 143: 20% bucket 162: 80% bucket 135: 50% bucket 171: 10% Sorting block time: 00:00:02 Returning block of 4115124 for bucket 149 bucket 156: 90% Getting block 174 of 207 Reserving size (6957365) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 131: 80% bucket 154: 100% Sorting block of length 5861973 for bucket 154 (Using difference cover) bucket 166: 30% bucket 130: 90% bucket 172: 10% bucket 159: 100% Sorting block of length 3066333 for bucket 159 (Using difference cover) bucket 167: 30% bucket 170: 20% Sorting block time: 00:00:02 Returning block of 3517248 for bucket 150 bucket 169: 20% bucket 147: 20% bucket 160: 100% Sorting block of length 5907916 for bucket 160 (Using difference cover) bucket 163: 70% bucket 158: 100% Sorting block of length 6454127 for bucket 158 (Using difference cover) Getting block 175 of 207 Reserving size (6957365) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 132: 90% bucket 144: 20% bucket 151: 10% bucket 153: 10% bucket 161: 100% Sorting block of length 4346999 for bucket 161 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6226581 for bucket 145 bucket 152: 10% bucket 168: 30% bucket 165: 50% bucket 145: 20% Getting block 176 of 207 Reserving size (6957365) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: bucket 146: 20% bucket 173: 10% bucket 155: 100% Sorting block of length 1056591 for bucket 155 (Using difference cover) bucket 162: 90% Sorting block time: 00:00:04 Returning block of 5578845 for bucket 152 Getting block 177 of 207 Reserving size (6957365) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 164: 70% Sorting block time: 00:00:04 Returning block of 4946997 for bucket 151 Sorting block time: 00:00:05 Returning block of 6193665 for bucket 153 Getting block 178 of 207 Reserving size (6957365) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: Sorting block time: 00:00:01 Returning block of 1056592 for bucket 155 bucket 171: 20% bucket 157: 100% Sorting block of length 891546 for bucket 157 (Using difference cover) bucket 138: 40% Getting block 179 of 207 Reserving size (6957365) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 142: 30% Getting block 180 of 207 Reserving size (6957365) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 139: 30% bucket 174: 10% Sorting block time: 00:00:02 Returning block of 3066334 for bucket 159 bucket 129: 100% Sorting block of length 5682476 for bucket 129 (Using difference cover) bucket 156: 100% Sorting block of length 6134690 for bucket 156 (Using difference cover) bucket 168: 40% bucket 134: 80% bucket 141: 20% Sorting block time: 00:00:04 Returning block of 5854801 for bucket 148 Sorting block time: 00:00:00 Returning block of 891547 for bucket 157 Getting block 181 of 207 Reserving size (6957365) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: Getting block 182 of 207 Reserving size (6957365) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 137: 50% bucket 140: 30% Getting block 183 of 207 Reserving size (6957365) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: bucket 172: 20% bucket 166: 40% bucket 148: 20% Sorting block time: 00:00:02 Returning block of 4347000 for bucket 161 bucket 143: 30% bucket 154: 10% Getting block 184 of 207 Reserving size (6957365) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 133: 100% Sorting block of length 6000362 for bucket 133 (Using difference cover) bucket 167: 40% bucket 150: 20% bucket 175: 10% bucket 170: 30% bucket 136: 50% bucket 155: 10% bucket 163: 80% bucket 169: 30% bucket 149: 20% bucket 165: 60% bucket 176: 10% Sorting block time: 00:00:04 Returning block of 5861974 for bucket 154 bucket 173: 20% Getting block 185 of 207 Reserving size (6957365) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 162: 100% Sorting block of length 6454226 for bucket 162 (Using difference cover) bucket 147: 30% bucket 177: 10% bucket 164: 80% Sorting block time: 00:00:04 Returning block of 5907917 for bucket 160 bucket 174: 20% bucket 181: 10% bucket 178: 10% bucket 179: 10% bucket 171: 30% Getting block 186 of 207 Reserving size (6957365) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: bucket 180: 10% bucket 135: 60% bucket 151: 20% bucket 152: 20% bucket 144: 30% bucket 130: 100% Sorting block of length 2202643 for bucket 130 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6454128 for bucket 158 bucket 153: 20% bucket 146: 30% bucket 182: 10% bucket 168: 50% bucket 145: 30% Getting block 187 of 207 Reserving size (6957365) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: bucket 183: 10% bucket 172: 30% bucket 132: 100% Sorting block of length 4263091 for bucket 132 (Using difference cover) bucket 131: 90% bucket 138: 50% bucket 166: 50% bucket 142: 40% bucket 184: 10% bucket 175: 20% bucket 167: 50% bucket 170: 40% bucket 141: 30% bucket 148: 30% bucket 169: 40% bucket 163: 90% Sorting block time: 00:00:01 Returning block of 2202644 for bucket 130 bucket 176: 20% Sorting block time: 00:00:04 Returning block of 5682477 for bucket 129 bucket 165: 70% Getting block 156 of 205 Reserving size (6957365) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 185: 10% bucket 173: 30% Getting block 157 of 205 Reserving size (6957365) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 134: 90% bucket 136: 60% Sorting block time: 00:00:05 Returning block of 6134691 for bucket 156 bucket 181: 20% bucket 177: 20% bucket 155: 20% bucket 137: 60% bucket 139: 40% bucket 154: 20% bucket 164: 90% Getting block 188 of 207 Reserving size (6957365) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 150: 30% bucket 172: 40% bucket 143: 40% Sorting block time: 00:00:04 Returning block of 6000363 for bucket 133 bucket 174: 30% bucket 179: 20% bucket 178: 20% bucket 186: 10% bucket 171: 40% bucket 180: 20% Getting block 158 of 205 Reserving size (6957365) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: bucket 140: 40% bucket 187: 10% Sorting block time: 00:00:03 Returning block of 4263092 for bucket 132 bucket 182: 20% Getting block 159 of 205 Reserving size (6957365) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 168: 60% bucket 183: 20% Sorting block time: 00:00:04 Returning block of 6454227 for bucket 162 bucket 151: 30% bucket 166: 60% bucket 147: 40% bucket 144: 40% bucket 135: 70% bucket 175: 30% bucket 184: 20% Getting block 189 of 207 Reserving size (6957365) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 149: 30% bucket 167: 60% bucket 163: 100% Sorting block of length 5855880 for bucket 163 (Using difference cover) bucket 170: 50% bucket 169: 50% bucket 176: 30% bucket 146: 40% bucket 165: 80% bucket 185: 20% bucket 153: 30% bucket 173: 40% bucket 152: 30% bucket 142: 50% bucket 181: 30% bucket 177: 30% bucket 145: 40% bucket 138: 60% bucket 188: 10% bucket 164: 100% Sorting block of length 1945535 for bucket 164 (Using difference cover) bucket 172: 50% bucket 148: 40% bucket 179: 30% bucket 174: 40% bucket 186: 20% bucket 178: 30% bucket 180: 30% bucket 171: 50% bucket 131: 100% Sorting block of length 5505328 for bucket 131 (Using difference cover) bucket 155: 30% bucket 187: 20% bucket 182: 30% bucket 175: 40% bucket 137: 70% bucket 168: 70% bucket 183: 30% bucket 166: 70% bucket 150: 40% Sorting block time: 00:00:01 Returning block of 1945536 for bucket 164 bucket 156: 10% bucket 136: 70% Getting block 190 of 207 Reserving size (6957365) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 177: 40% bucket 189: 10% bucket 141: 40% bucket 154: 30% bucket 184: 30% bucket 139: 50% bucket 158: 10% bucket 143: 50% bucket 157: 10% bucket 167: 70% bucket 176: 40% bucket 134: 100% Sorting block of length 5274975 for bucket 134 (Using difference cover) bucket 169: 60% bucket 179: 40% bucket 165: 90% bucket 173: 50% bucket 144: 50% bucket 172: 60% bucket 181: 40% bucket 170: 60% bucket 135: 80% bucket 185: 30% bucket 188: 20% bucket 147: 50% bucket 151: 40% bucket 186: 30% bucket 174: 50% bucket 178: 40% bucket 145: 50% bucket 180: 40% bucket 187: 30% bucket 171: 60% Sorting block time: 00:00:04 Returning block of 5855881 for bucket 163 bucket 153: 40% bucket 159: 10% bucket 140: 50% Getting block 191 of 207 Reserving size (6957365) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: bucket 146: 50% bucket 182: 40% bucket 175: 50% bucket 149: 40% bucket 148: 50% bucket 183: 40% bucket 152: 40% bucket 166: 80% bucket 177: 50% bucket 189: 20% bucket 168: 80% bucket 190: 10% Sorting block time: 00:00:04 Returning block of 5505329 for bucket 131 bucket 138: 70% bucket 142: 60% bucket 184: 40% Getting block 160 of 205 Reserving size (6957365) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 176: 50% bucket 179: 50% bucket 169: 70% bucket 137: 80% bucket 167: 80% bucket 181: 50% bucket 172: 70% bucket 173: 60% bucket 165: 100% Sorting block of length 6249850 for bucket 165 (Using difference cover) bucket 185: 40% bucket 188: 30% bucket 170: 70% bucket 187: 40% bucket 186: 40% bucket 143: 60% bucket 158: 20% bucket 139: 60% bucket 174: 60% bucket 178: 50% bucket 180: 50% bucket 136: 80% Sorting block time: 00:00:03 Returning block of 5274976 for bucket 134 bucket 171: 70% Getting block 161 of 205 Reserving size (6957365) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 191: 10% bucket 150: 50% bucket 155: 40% bucket 154: 40% bucket 182: 50% bucket 157: 20% bucket 189: 30% bucket 141: 50% bucket 175: 60% bucket 151: 50% bucket 147: 60% bucket 145: 60% bucket 177: 60% bucket 183: 50% bucket 144: 60% bucket 146: 60% bucket 166: 90% bucket 168: 90% bucket 190: 20% bucket 156: 20% bucket 176: 60% bucket 184: 50% bucket 179: 60% bucket 181: 60% bucket 169: 80% bucket 172: 80% bucket 173: 70% bucket 167: 90% bucket 135: 90% bucket 188: 40% bucket 185: 50% bucket 152: 50% bucket 187: 50% bucket 153: 50% bucket 186: 50% bucket 148: 60% bucket 170: 80% bucket 140: 60% bucket 174: 70% bucket 180: 60% bucket 178: 60% bucket 138: 80% bucket 137: 90% bucket 191: 20% bucket 159: 20% bucket 171: 80% bucket 177: 70% bucket 143: 70% Sorting block time: 00:00:04 Returning block of 6249851 for bucket 165 bucket 182: 60% bucket 189: 40% bucket 149: 50% bucket 175: 70% bucket 161: 10% Getting block 192 of 207 Reserving size (6957365) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 142: 70% bucket 179: 70% bucket 166: 100% Sorting block of length 6919917 for bucket 166 (Using difference cover) bucket 183: 60% bucket 168: 100% Sorting block of length 6461609 for bucket 168 (Using difference cover) bucket 190: 30% bucket 176: 70% bucket 136: 90% bucket 184: 60% bucket 158: 30% bucket 160: 10% bucket 181: 70% bucket 146: 70% bucket 172: 90% bucket 173: 80% bucket 167: 100% Sorting block of length 5572385 for bucket 167 (Using difference cover) bucket 139: 70% bucket 147: 70% bucket 187: 60% bucket 188: 50% bucket 186: 60% bucket 169: 90% bucket 151: 60% bucket 185: 60% bucket 150: 60% bucket 180: 70% bucket 145: 70% bucket 174: 80% bucket 178: 70% bucket 170: 90% bucket 171: 90% bucket 144: 70% bucket 155: 50% bucket 191: 30% bucket 189: 50% bucket 177: 80% bucket 182: 70% bucket 154: 50% bucket 175: 80% bucket 157: 30% bucket 192: 10% bucket 135: 100% Sorting block of length 4404946 for bucket 135 (Using difference cover) bucket 179: 80% bucket 137: 100% Sorting block of length 6681383 for bucket 137 (Using difference cover) bucket 141: 60% bucket 176: 80% bucket 152: 60% bucket 138: 90% bucket 172: 100% Sorting block of length 1950824 for bucket 172 (Using difference cover) bucket 156: 30% bucket 148: 70% bucket 190: 40% bucket 143: 80% bucket 183: 70% bucket 181: 80% bucket 184: 70% bucket 153: 60% bucket 173: 90% bucket 187: 70% bucket 188: 60% bucket 186: 70% bucket 170: 100% Sorting block of length 5212965 for bucket 170 (Using difference cover) bucket 169: 100% Sorting block of length 6222330 for bucket 169 (Using difference cover) bucket 140: 70% bucket 142: 80% bucket 185: 70% bucket 161: 20% bucket 180: 80% Sorting block time: 00:00:04 Returning block of 6919918 for bucket 166 bucket 146: 80% bucket 174: 90% bucket 178: 80% bucket 151: 70% bucket 191: 40% Getting block 193 of 207 Reserving size (6957365) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: bucket 189: 60% bucket 171: 100% Sorting block of length 6069672 for bucket 171 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1950825 for bucket 172 Sorting block time: 00:00:05 Returning block of 6461610 for bucket 168 Getting block 194 of 207 Reserving size (6957365) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 179: 90% bucket 158: 40% Sorting block time: 00:00:04 Returning block of 5572386 for bucket 167 bucket 177: 90% bucket 149: 60% Getting block 195 of 207 Reserving size (6957365) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 182: 80% bucket 150: 70% Getting block 196 of 207 Reserving size (6957365) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 147: 80% bucket 175: 90% bucket 192: 20% bucket 136: 100% Sorting block of length 3874764 for bucket 136 (Using difference cover) bucket 190: 50% bucket 160: 20% bucket 159: 30% bucket 144: 80% bucket 176: 90% Sorting block time: 00:00:03 Returning block of 4404947 for bucket 135 bucket 139: 80% Getting block 162 of 205 Reserving size (6957365) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 181: 90% bucket 145: 80% bucket 183: 80% bucket 155: 60% bucket 186: 80% bucket 184: 80% bucket 187: 80% bucket 173: 100% Sorting block of length 5604880 for bucket 173 (Using difference cover) bucket 188: 70% bucket 154: 60% bucket 138: 100% Sorting block of length 6937277 for bucket 138 (Using difference cover) bucket 180: 90% bucket 185: 80% bucket 174: 100% Sorting block of length 5930014 for bucket 174 (Using difference cover) bucket 191: 50% bucket 178: 90% bucket 193: 10% bucket 189: 70% Sorting block time: 00:00:03 Returning block of 5212966 for bucket 170 bucket 141: 70% bucket 143: 90% bucket 152: 70% bucket 194: 10% bucket 179: 100% Sorting block of length 6294389 for bucket 179 (Using difference cover) Getting block 197 of 207 Reserving size (6957365) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: bucket 195: 10% bucket 157: 40% bucket 177: 100% Sorting block of length 6472584 for bucket 177 (Using difference cover) bucket 182: 90% bucket 148: 80% bucket 196: 10% bucket 190: 60% bucket 192: 30% bucket 153: 70% bucket 175: 100% Sorting block of length 4554146 for bucket 175 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6681384 for bucket 137 Sorting block time: 00:00:03 Returning block of 3874765 for bucket 136 bucket 159: 40% Sorting block time: 00:00:04 Returning block of 6222331 for bucket 169 Getting block 163 of 205 Reserving size (6957365) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: Getting block 164 of 205 Reserving size (6957365) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 142: 90% Getting block 198 of 207 Reserving size (6957365) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 176: 100% Sorting block of length 2441868 for bucket 176 (Using difference cover) bucket 140: 80% bucket 151: 80% bucket 158: 50% bucket 181: 100% Sorting block of length 5114606 for bucket 181 (Using difference cover) bucket 186: 90% bucket 183: 90% bucket 187: 90% bucket 188: 80% bucket 146: 90% Sorting block time: 00:00:04 Returning block of 6069673 for bucket 171 bucket 149: 70% bucket 184: 90% bucket 161: 30% Getting block 199 of 207 Reserving size (6957365) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: bucket 185: 90% bucket 144: 90% bucket 180: 100% Sorting block of length 1989856 for bucket 180 (Using difference cover) bucket 147: 90% bucket 191: 60% bucket 193: 20% bucket 160: 30% bucket 189: 80% bucket 156: 40% bucket 178: 100% Sorting block of length 6221840 for bucket 178 (Using difference cover) bucket 194: 20% bucket 197: 10% bucket 150: 80% bucket 190: 70% Sorting block time: 00:00:04 Returning block of 5604881 for bucket 173 Sorting block time: 00:00:02 Returning block of 2441869 for bucket 176 bucket 195: 20% bucket 145: 90% Getting block 200 of 207 Reserving size (6957365) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 192: 40% bucket 182: 100% Sorting block of length 4923131 for bucket 182 (Using difference cover) Getting block 201 of 207 Reserving size (6957365) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: bucket 196: 20% Sorting block time: 00:00:03 Returning block of 4554147 for bucket 175 bucket 159: 50% Getting block 202 of 207 Reserving size (6957365) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 139: 90% Sorting block time: 00:00:01 Returning block of 1989857 for bucket 180 bucket 198: 10% Getting block 203 of 207 Reserving size (6957365) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: bucket 143: 100% Sorting block of length 5639959 for bucket 143 (Using difference cover) bucket 162: 10% bucket 154: 70% Sorting block time: 00:00:04 Returning block of 5930015 for bucket 174 bucket 186: 100% Sorting block of length 6244565 for bucket 186 (Using difference cover) bucket 164: 10% bucket 187: 100% Sorting block of length 3474778 for bucket 187 (Using difference cover) bucket 188: 90% Getting block 204 of 207 Reserving size (6957365) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: bucket 183: 100% Sorting block of length 5246983 for bucket 183 (Using difference cover) bucket 142: 100% Sorting block of length 5442667 for bucket 142 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6294390 for bucket 179 bucket 185: 100% Sorting block of length 4561925 for bucket 185 (Using difference cover) bucket 155: 70% bucket 199: 10% bucket 163: 10% bucket 184: 100% Sorting block of length 4129639 for bucket 184 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6937278 for bucket 138 Getting block 205 of 207 Reserving size (6957365) for bucket 205 Calculating Z arrays for bucket 205 Entering block accumulator loop for bucket 205: Sorting block time: 00:00:03 Returning block of 5114607 for bucket 181 Getting block 165 of 205 Reserving size (6957365) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 191: 70% Sorting block time: 00:00:04 Returning block of 6472585 for bucket 177 bucket 153: 80% bucket 189: 90% bucket 190: 80% Getting block 206 of 207 Reserving size (6957365) for bucket 206 Calculating Z arrays for bucket 206 Entering block accumulator loop for bucket 206: bucket 194: 30% bucket 193: 30% bucket 200: 10% bucket 152: 80% Getting block 207 of 207 Reserving size (6957365) for bucket 207 Calculating Z arrays for bucket 207 Entering block accumulator loop for bucket 207: bucket 197: 20% bucket 157: 50% bucket 148: 90% bucket 195: 30% bucket 201: 10% bucket 192: 50% bucket 158: 60% bucket 196: 30% bucket 144: 100% Sorting block of length 6772394 for bucket 144 (Using difference cover) bucket 146: 100% Sorting block of length 6696253 for bucket 146 (Using difference cover) bucket 151: 90% bucket 202: 10% bucket 140: 90% Sorting block time: 00:00:03 Returning block of 4923132 for bucket 182 bucket 203: 10% bucket 198: 20% bucket 149: 80% bucket 147: 100% Sorting block of length 5520560 for bucket 147 (Using difference cover) bucket 161: 40% bucket 204: 10% bucket 159: 60% bucket 188: 100% Sorting block of length 4427863 for bucket 188 (Using difference cover) bucket 156: 50% bucket 207: 10% Sorting block time: 00:00:04 Returning block of 6221841 for bucket 178 bucket 145: 100% Sorting block of length 6240641 for bucket 145 (Using difference cover) bucket 141: 80% bucket 160: 40% bucket 199: 20% bucket 200: 20% bucket 150: 90% Sorting block time: 00:00:03 Returning block of 3474779 for bucket 187 bucket 205: 10% bucket 191: 80% bucket 206: 10% Sorting block time: 00:00:03 Returning block of 5246984 for bucket 183 Sorting block time: 00:00:03 Returning block of 4561926 for bucket 185 bucket 189: 100% Sorting block of length 6893385 for bucket 189 (Using difference cover) bucket 190: 90% bucket 194: 40% bucket 197: 30% Sorting block time: 00:00:03 Returning block of 4129640 for bucket 184 bucket 193: 40% bucket 195: 40% Sorting block time: 00:00:04 Returning block of 5639960 for bucket 143 bucket 201: 20% bucket 164: 20% bucket 192: 60% Getting block 166 of 205 Reserving size (6957365) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 196: 40% Sorting block time: 00:00:04 Returning block of 5442668 for bucket 142 bucket 139: 100% Sorting block of length 2796295 for bucket 139 (Using difference cover) bucket 202: 20% Getting block 167 of 205 Reserving size (6957365) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: bucket 203: 20% bucket 153: 90% bucket 198: 30% bucket 207: 20% bucket 162: 20% bucket 165: 10% Sorting block time: 00:00:05 Returning block of 6244566 for bucket 186 bucket 152: 90% bucket 155: 80% bucket 163: 20% bucket 206: 20% bucket 204: 20% bucket 157: 60% bucket 158: 70% bucket 191: 90% bucket 200: 30% bucket 154: 80% bucket 151: 100% Sorting block of length 6672477 for bucket 151 (Using difference cover) bucket 199: 30% Sorting block time: 00:00:03 Returning block of 4427864 for bucket 188 bucket 205: 20% bucket 194: 50% bucket 207: 30% bucket 148: 100% Sorting block of length 5254334 for bucket 148 (Using difference cover) bucket 159: 70% bucket 190: 100% Sorting block of length 6806845 for bucket 190 (Using difference cover) Sorting block time: 00:00:03 Returning block of 5520561 for bucket 147 bucket 197: 40% bucket 161: 50% Sorting block time: 00:00:02 Returning block of 2796296 for bucket 139 Getting block 168 of 205 Reserving size (6957365) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: Sorting block time: 00:00:05 Returning block of 6772395 for bucket 144 bucket 195: 50% Getting block 169 of 205 Reserving size (6957365) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 201: 30% bucket 193: 50% bucket 149: 90% bucket 202: 30% bucket 203: 30% bucket 192: 70% bucket 141: 90% bucket 196: 50% Getting block 170 of 205 Reserving size (6957365) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: Sorting block time: 00:00:05 Returning block of 6696254 for bucket 146 bucket 140: 100% Sorting block of length 5315338 for bucket 140 (Using difference cover) bucket 156: 60% bucket 206: 30% Sorting block time: 00:00:03 Returning block of 6893386 for bucket 189 bucket 204: 30% Getting block 171 of 205 Reserving size (6957365) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 160: 50% bucket 198: 40% bucket 166: 10% bucket 207: 40% bucket 150: 100% Sorting block of length 3840419 for bucket 150 (Using difference cover) bucket 199: 40% Sorting block time: 00:00:05 Returning block of 6240642 for bucket 145 bucket 194: 60% bucket 205: 30% bucket 191: 100% Sorting block of length 4322992 for bucket 191 (Using difference cover) bucket 164: 30% Getting block 172 of 205 Reserving size (6957365) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: bucket 158: 80% bucket 200: 40% bucket 162: 30% bucket 167: 10% bucket 165: 20% bucket 195: 60% bucket 202: 40% bucket 201: 40% bucket 197: 50% bucket 198: 50% bucket 152: 100% Sorting block of length 4976081 for bucket 152 (Using difference cover) bucket 193: 60% bucket 153: 100% Sorting block of length 6445165 for bucket 153 (Using difference cover) bucket 192: 80% bucket 207: 50% bucket 196: 60% bucket 206: 40% bucket 155: 90% bucket 157: 70% bucket 203: 40% bucket 199: 50% bucket 204: 40% bucket 170: 10% bucket 163: 30% Sorting block time: 00:00:04 Returning block of 5254335 for bucket 148 bucket 149: 100% Sorting block of length 5380081 for bucket 149 (Using difference cover) bucket 194: 70% Getting block 173 of 205 Reserving size (6957365) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: Sorting block time: 00:00:02 Returning block of 3840420 for bucket 150 Sorting block time: 00:00:03 Returning block of 5315339 for bucket 140 Sorting block time: 00:00:04 Returning block of 6806846 for bucket 190 Sorting block time: 00:00:04 Returning block of 6672478 for bucket 151 Getting block 174 of 205 Reserving size (6957365) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 207: 60% Getting block 175 of 205 Reserving size (6957365) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 200: 50% Getting block 176 of 205 Reserving size (6957365) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: bucket 201: 50% bucket 205: 40% bucket 193: 70% Sorting block time: 00:00:03 Returning block of 4322993 for bucket 191 bucket 168: 10% bucket 195: 70% bucket 198: 60% bucket 197: 60% bucket 154: 90% bucket 202: 50% bucket 166: 20% bucket 171: 10% bucket 206: 50% bucket 159: 80% bucket 196: 70% bucket 169: 10% bucket 192: 90% bucket 141: 100% Sorting block of length 5550259 for bucket 141 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4976082 for bucket 152 bucket 203: 50% bucket 161: 60% bucket 194: 80% Getting block 177 of 205 Reserving size (6957365) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 204: 50% bucket 172: 10% bucket 207: 70% bucket 156: 70% bucket 199: 60% bucket 201: 60% bucket 164: 40% bucket 167: 20% bucket 160: 60% bucket 158: 90% bucket 170: 20% Sorting block time: 00:00:03 Returning block of 5380082 for bucket 149 bucket 205: 50% Sorting block time: 00:00:04 Returning block of 6445166 for bucket 153 bucket 193: 80% bucket 197: 70% Getting block 178 of 205 Reserving size (6957365) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: Getting block 179 of 205 Reserving size (6957365) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 200: 60% bucket 206: 60% bucket 198: 70% bucket 202: 60% bucket 207: 80% bucket 195: 80% bucket 162: 40% bucket 165: 30% bucket 196: 80% bucket 204: 60% bucket 203: 60% bucket 192: 100% Sorting block of length 4481479 for bucket 192 (Using difference cover) bucket 157: 80% bucket 194: 90% bucket 155: 100% Sorting block of length 3324362 for bucket 155 (Using difference cover) bucket 163: 40% bucket 173: 10% bucket 201: 70% bucket 199: 70% bucket 206: 70% Sorting block time: 00:00:03 Returning block of 5550260 for bucket 141 bucket 166: 30% bucket 175: 10% bucket 198: 80% Getting block 180 of 205 Reserving size (6957365) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 205: 60% bucket 207: 90% bucket 176: 10% bucket 202: 70% bucket 197: 80% bucket 154: 100% Sorting block of length 5688136 for bucket 154 (Using difference cover) bucket 195: 90% bucket 168: 20% bucket 193: 90% bucket 164: 50% bucket 200: 70% bucket 172: 20% bucket 159: 90% bucket 174: 10% bucket 177: 10% bucket 204: 70% Sorting block time: 00:00:01 Returning block of 3324363 for bucket 155 bucket 167: 30% Getting block 181 of 205 Reserving size (6957365) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: bucket 203: 70% bucket 158: 100% Sorting block of length 6148672 for bucket 158 (Using difference cover) bucket 199: 80% bucket 201: 80% bucket 207: 100% Sorting block of length 2878083 for bucket 207 (Using difference cover) bucket 169: 20% Sorting block time: 00:00:02 Returning block of 4481480 for bucket 192 bucket 179: 10% bucket 196: 90% bucket 161: 70% bucket 171: 20% bucket 156: 80% bucket 194: 100% Sorting block of length 6870311 for bucket 194 (Using difference cover) bucket 198: 90% bucket 202: 80% bucket 206: 80% bucket 170: 30% bucket 205: 70% bucket 200: 80% bucket 204: 80% bucket 195: 100% Sorting block of length 3154346 for bucket 195 (Using difference cover) bucket 197: 90% bucket 199: 90% bucket 160: 70% bucket 203: 80% bucket 201: 90% bucket 162: 50% bucket 193: 100% Sorting block of length 4749141 for bucket 193 (Using difference cover) Sorting block time: 00:00:03 Returning block of 5688137 for bucket 154 bucket 157: 90% Sorting block time: 00:00:02 Returning block of 2878084 for bucket 207 bucket 196: 100% Sorting block of length 6956526 for bucket 196 (Using difference cover) Getting block 182 of 205 Reserving size (6957365) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 165: 40% bucket 173: 20% bucket 175: 20% bucket 176: 20% bucket 202: 90% bucket 178: 10% bucket 163: 50% bucket 206: 90% Sorting block time: 00:00:01 Returning block of 3154347 for bucket 195 bucket 164: 60% bucket 198: 100% Sorting block of length 6591020 for bucket 198 (Using difference cover) bucket 205: 80% bucket 168: 30% bucket 172: 30% bucket 197: 100% Sorting block of length 1537549 for bucket 197 (Using difference cover) bucket 204: 90% bucket 180: 10% bucket 159: 100% Sorting block of length 6071455 for bucket 159 (Using difference cover) bucket 166: 40% bucket 199: 100% Sorting block of length 2761095 for bucket 199 (Using difference cover) bucket 171: 30% bucket 200: 90% bucket 181: 10% bucket 169: 30% Sorting block time: 00:00:01 Returning block of 1537550 for bucket 197 Sorting block time: 00:00:04 Returning block of 6148673 for bucket 158 bucket 203: 90% bucket 179: 20% bucket 174: 20% bucket 161: 80% Getting block 183 of 205 bucket 202: 100% Reserving size (6957365) for bucket 183 Sorting block of length 1142595 for bucket 202 Calculating Z arrays for bucket 183 (Using difference cover) Entering block accumulator loop for bucket 183: bucket 170: 40% bucket 206: 100% Sorting block of length 5906101 for bucket 206 (Using difference cover) bucket 201: 100% Sorting block of length 6714275 for bucket 201 (Using difference cover) bucket 177: 20% bucket 167: 40% bucket 205: 90% Sorting block time: 00:00:01 Returning block of 1142596 for bucket 202 bucket 156: 90% Sorting block time: 00:00:05 Returning block of 6870312 for bucket 194 Sorting block time: 00:00:02 Returning block of 2761096 for bucket 199 bucket 162: 60% Sorting block time: 00:00:03 Returning block of 4749142 for bucket 193 bucket 204: 100% Sorting block of length 5471397 for bucket 204 (Using difference cover) bucket 165: 50% bucket 160: 80% bucket 164: 70% bucket 200: 100% Sorting block of length 5194604 for bucket 200 (Using difference cover) bucket 203: 100% Sorting block of length 6596930 for bucket 203 (Using difference cover) bucket 175: 30% Sorting block time: 00:00:04 Returning block of 6956527 for bucket 196 bucket 172: 40% bucket 176: 30% Sorting block time: 00:00:03 Returning block of 6071456 for bucket 159 Sorting block time: 00:00:03 Returning block of 6591021 for bucket 198 bucket 163: 60% Getting block 184 of 205 Reserving size (6957365) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 168: 40% bucket 205: 100% Sorting block of length 4669473 for bucket 205 (Using difference cover) bucket 182: 10% bucket 178: 20% bucket 173: 30% Sorting block time: 00:00:02 Returning block of 6714276 for bucket 201 Sorting block time: 00:00:02 Returning block of 5906102 for bucket 206 bucket 157: 100% Sorting block of length 6681752 for bucket 157 (Using difference cover) bucket 166: 50% bucket 179: 30% bucket 180: 20% bucket 183: 10% Sorting block time: 00:00:02 Returning block of 5471398 for bucket 204 bucket 170: 50% Sorting block time: 00:00:03 Returning block of 6596931 for bucket 203 Sorting block time: 00:00:02 Returning block of 4669474 for bucket 205 Sorting block time: 00:00:03 Returning block of 5194605 for bucket 200 bucket 177: 30% bucket 171: 40% bucket 181: 20% bucket 169: 40% bucket 174: 30% bucket 167: 50% bucket 165: 60% bucket 161: 90% bucket 164: 80% bucket 172: 50% bucket 168: 50% Sorting block time: 00:00:03 Returning block of 6681753 for bucket 157 bucket 163: 70% bucket 176: 40% Getting block 185 of 205 Reserving size (6957365) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 173: 40% bucket 162: 70% bucket 156: 100% Sorting block of length 4883778 for bucket 156 (Using difference cover) bucket 166: 60% bucket 160: 90% bucket 179: 40% bucket 183: 20% bucket 170: 60% bucket 175: 40% bucket 184: 10% bucket 177: 40% bucket 171: 50% bucket 182: 20% bucket 178: 30% bucket 165: 70% bucket 167: 60% bucket 180: 30% bucket 164: 90% Sorting block time: 00:00:02 Returning block of 4883779 for bucket 156 bucket 172: 60% Getting block 186 of 205 Reserving size (6957365) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: bucket 168: 60% bucket 163: 80% bucket 176: 50% bucket 181: 30% bucket 173: 50% bucket 174: 40% bucket 169: 50% bucket 166: 70% bucket 179: 50% bucket 183: 30% bucket 161: 100% Sorting block of length 3574245 for bucket 161 (Using difference cover) bucket 170: 70% Exited Ebwt loop fchr[A]: 0 fchr[C]: 519415916 fchr[G]: 709360996 fchr[T]: 709360996 fchr[$]: 1038966499 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 356457280 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 259741632 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 1038966499 bwtLen: 1038966500 sz: 259741625 bwtSz: 259741625 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 64935407 offsSz: 259741628 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 5411284 numLines: 5411284 ebwtTotLen: 346322176 ebwtTotSz: 346322176 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:05:25 Reading reference sizes bucket 177: 50% bucket 171: 60% bucket 162: 80% bucket 185: 10% bucket 165: 80% bucket 160: 100% Sorting block of length 4403652 for bucket 160 (Using difference cover) bucket 167: 70% bucket 164: 100% Sorting block of length 5830816 for bucket 164 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3574246 for bucket 161 Getting block 187 of 205 Reserving size (6957365) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: bucket 172: 70% bucket 168: 70% bucket 163: 90% bucket 176: 60% bucket 175: 50% Sorting block time: 00:00:02 Returning block of 4403653 for bucket 160 bucket 173: 60% bucket 184: 20% Getting block 188 of 205 Reserving size (6957365) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 182: 30% bucket 179: 60% bucket 166: 80% bucket 183: 40% Sorting block time: 00:00:02 Returning block of 5830817 for bucket 164 Getting block 189 of 205 Reserving size (6957365) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 178: 40% bucket 170: 80% bucket 180: 40% bucket 186: 10% bucket 177: 60% bucket 171: 70% bucket 181: 40% bucket 165: 90% bucket 174: 50% bucket 169: 60% bucket 167: 80% bucket 172: 80% bucket 163: 100% Sorting block of length 3033272 for bucket 163 (Using difference cover) bucket 168: 80% bucket 176: 70% bucket 173: 70% bucket 179: 70% Sorting block time: 00:00:01 Returning block of 3033273 for bucket 163 bucket 184: 30% bucket 162: 90% bucket 166: 90% Getting block 190 of 205 Reserving size (6957365) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 185: 20% bucket 183: 50% bucket 170: 90% bucket 189: 10% bucket 187: 10% bucket 177: 70% bucket 171: 80% bucket 165: 100% Sorting block of length 6463526 for bucket 165 (Using difference cover) bucket 175: 60% bucket 188: 10% bucket 182: 40% bucket 172: 90% bucket 168: 90% bucket 176: 80% Time reading reference sizes: 00:00:09 Calculating joined length Writing header Reserving space for joined string Joining reference sequences bucket 167: 90% bucket 180: 50% bucket 178: 50% bucket 179: 80% bucket 173: 80% bucket 181: 50% bucket 186: 20% bucket 190: 10% bucket 184: 40% bucket 166: 100% Sorting block of length 6355745 for bucket 166 (Using difference cover) bucket 170: 100% Sorting block of length 4299416 for bucket 170 (Using difference cover) bucket 183: 60% bucket 189: 20% bucket 174: 60% Sorting block time: 00:00:02 Returning block of 6463527 for bucket 165 Getting block 191 of 205 Reserving size (6957365) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: bucket 169: 70% bucket 177: 80% bucket 171: 90% Sorting block time: 00:00:01 Returning block of 4299417 for bucket 170 Getting block 192 of 205 Reserving size (6957365) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 172: 100% Sorting block of length 1178061 for bucket 172 (Using difference cover) bucket 168: 100% Sorting block of length 3328825 for bucket 168 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6355746 for bucket 166 bucket 176: 90% bucket 162: 100% Sorting block of length 6220215 for bucket 162 (Using difference cover) Getting block 193 of 205 Reserving size (6957365) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: Sorting block time: 00:00:00 Returning block of 1178062 for bucket 172 Getting block 194 of 205 Reserving size (6957365) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 185: 30% bucket 167: 100% Sorting block of length 3905876 for bucket 167 (Using difference cover) bucket 179: 90% bucket 190: 20% bucket 184: 50% bucket 173: 90% bucket 187: 20% bucket 175: 70% bucket 182: 50% Sorting block time: 00:00:01 Returning block of 3328826 for bucket 168 Getting block 195 of 205 Reserving size (6957365) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 189: 30% bucket 188: 20% bucket 191: 10% Sorting block time: 00:00:02 Returning block of 6220216 for bucket 162 Sorting block time: 00:00:01 Returning block of 3905877 for bucket 167 bucket 177: 90% Getting block 196 of 205 Reserving size (6957365) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: Getting block 197 of 205 Reserving size (6957365) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: bucket 171: 100% Sorting block of length 6211097 for bucket 171 (Using difference cover) bucket 180: 60% bucket 181: 60% bucket 178: 60% bucket 176: 100% Sorting block of length 5211733 for bucket 176 (Using difference cover) bucket 193: 10% bucket 194: 10% bucket 186: 30% bucket 183: 70% bucket 179: 100% Sorting block of length 2157474 for bucket 179 (Using difference cover) bucket 190: 30% bucket 174: 70% bucket 184: 60% bucket 169: 80% bucket 173: 100% Sorting block of length 6234729 for bucket 173 (Using difference cover) bucket 182: 60% Sorting block time: 00:00:02 Returning block of 6211098 for bucket 171 bucket 195: 10% Getting block 198 of 205 Reserving size (6957365) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 189: 40% Time to join reference sequences: 00:00:07 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 9276486 Using parameters --bmax 6957365 --dcv 1024 Doing ahead-of-time memory usage test Sorting block time: 00:00:01 Returning block of 2157475 for bucket 179 Getting block 199 of 205 Reserving size (6957365) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: Passed! Constructing with these parameters: --bmax 6957365 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime bucket 175: 80% bucket 191: 20% Sorting block time: 00:00:02 Returning block of 5211734 for bucket 176 Getting block 200 of 205 Reserving size (6957365) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 192: 10% Building sPrimeOrder V-Sorting samples bucket 185: 40% bucket 177: 100% Sorting block of length 6685339 for bucket 177 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6234730 for bucket 173 Getting block 201 of 205 Reserving size (6957365) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: bucket 193: 20% bucket 194: 20% bucket 187: 30% bucket 190: 40% bucket 184: 70% bucket 182: 70% bucket 188: 30% bucket 196: 10% bucket 197: 10% bucket 199: 10% bucket 189: 50% bucket 180: 70% Sorting block time: 00:00:02 Returning block of 6685340 for bucket 177 bucket 178: 70% bucket 198: 10% Getting block 202 of 205 Reserving size (6957365) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 191: 30% bucket 175: 90% bucket 181: 70% bucket 200: 10% bucket 195: 20% bucket 186: 40% bucket 183: 80% bucket 201: 10% bucket 174: 80% bucket 193: 30% bucket 194: 30% bucket 169: 90% bucket 190: 50% bucket 184: 80% bucket 192: 20% bucket 182: 80% bucket 199: 20% bucket 189: 60% bucket 202: 10% bucket 191: 40% bucket 198: 20% bucket 185: 50% bucket 175: 100% Sorting block of length 3158316 for bucket 175 (Using difference cover) bucket 178: 80% bucket 200: 20% bucket 187: 40% bucket 201: 20% bucket 193: 40% bucket 194: 40% bucket 188: 40% bucket 196: 20% bucket 197: 20% Sorting block time: 00:00:02 Returning block of 3158317 for bucket 175 bucket 180: 80% bucket 195: 30% Getting block 203 of 205 Reserving size (6957365) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: V-Sorting samples time: 00:00:09 Allocating rank array Ranking v-sort output bucket 189: 70% bucket 190: 60% bucket 184: 90% bucket 183: 90% bucket 182: 90% bucket 174: 90% bucket 181: 80% bucket 200: 30% bucket 186: 50% bucket 178: 90% bucket 199: 30% bucket 202: 20% bucket 191: 50% bucket 198: 30% bucket 169: 100% Sorting block of length 6385754 for bucket 169 (Using difference cover) bucket 192: 30% bucket 201: 30% bucket 193: 50% bucket 194: 50% bucket 187: 50% bucket 185: 60% bucket 203: 10% bucket 190: 70% bucket 189: 80% bucket 184: 100% Sorting block of length 6691266 for bucket 184 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6385755 for bucket 169 bucket 182: 100% Sorting block of length 5620090 for bucket 182 (Using difference cover) bucket 200: 40% bucket 199: 40% Getting block 204 of 205 Reserving size (6957365) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: bucket 202: 30% bucket 191: 60% bucket 178: 100% Sorting block of length 6098759 for bucket 178 (Using difference cover) bucket 198: 40% bucket 196: 30% bucket 188: 50% bucket 197: 30% bucket 180: 90% Ranking v-sort output time: 00:00:05 Invoking Larsson-Sadakane on ranks bucket 201: 40% bucket 193: 60% bucket 195: 40% bucket 194: 60% Sorting block time: 00:00:02 Returning block of 5620091 for bucket 182 Getting block 205 of 205 Reserving size (6957365) for bucket 205 Calculating Z arrays for bucket 205 Entering block accumulator loop for bucket 205: Sorting block time: 00:00:02 Returning block of 6691267 for bucket 184 bucket 183: 100% Sorting block of length 5934858 for bucket 183 (Using difference cover) bucket 174: 100% Sorting block of length 4869313 for bucket 174 (Using difference cover) bucket 181: 90% bucket 203: 20% bucket 186: 60% Sorting block time: 00:00:03 Returning block of 6098760 for bucket 178 bucket 190: 80% bucket 189: 90% Sorting block time: 00:00:02 Returning block of 4869314 for bucket 174 bucket 199: 50% bucket 202: 40% bucket 200: 50% Sorting block time: 00:00:02 Returning block of 5934859 for bucket 183 bucket 191: 70% bucket 192: 40% bucket 198: 50% bucket 205: 10% bucket 185: 70% bucket 187: 60% bucket 201: 50% bucket 196: 40% bucket 194: 70% bucket 193: 70% bucket 203: 30% bucket 195: 50% bucket 190: 90% bucket 204: 10% bucket 189: 100% Sorting block of length 5653115 for bucket 189 (Using difference cover) bucket 197: 40% bucket 188: 60% bucket 180: 100% Sorting block of length 5021875 for bucket 180 (Using difference cover) bucket 202: 50% bucket 205: 20% bucket 200: 60% bucket 191: 80% bucket 181: 100% Sorting block of length 2492090 for bucket 181 (Using difference cover) bucket 198: 60% bucket 186: 70% bucket 199: 60% Sorting block time: 00:00:02 Returning block of 5653116 for bucket 189 Sorting block time: 00:00:01 Returning block of 2492091 for bucket 181 bucket 201: 60% bucket 196: 50% Sorting block time: 00:00:02 Returning block of 5021876 for bucket 180 bucket 192: 50% bucket 194: 80% bucket 203: 40% bucket 195: 60% bucket 187: 70% bucket 205: 30% bucket 185: 80% bucket 190: 100% Sorting block of length 4351190 for bucket 190 (Using difference cover) bucket 193: 80% bucket 202: 60% Invoking Larsson-Sadakane on ranks time: 00:00:10 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 bucket 200: 70% bucket 191: 90% bucket 197: 50% bucket 201: 70% Sorting block time: 00:00:02 Returning block of 4351191 for bucket 190 bucket 198: 70% bucket 204: 20% bucket 192: 60% bucket 196: 60% bucket 205: 40% bucket 188: 70% bucket 203: 50% bucket 195: 70% bucket 194: 90% bucket 186: 80% bucket 199: 70% bucket 185: 90% bucket 192: 70% bucket 191: 100% Sorting block of length 5276006 for bucket 191 (Using difference cover) bucket 198: 80% bucket 202: 70% bucket 205: 50% bucket 200: 80% bucket 187: 80% bucket 193: 90% bucket 201: 80% bucket 196: 70% bucket 197: 60% bucket 194: 100% Sorting block of length 3479674 for bucket 194 (Using difference cover) bucket 203: 60% Sorting block time: 00:00:02 Returning block of 5276007 for bucket 191 bucket 204: 30% bucket 195: 80% bucket 205: 60% bucket 188: 80% bucket 202: 80% bucket 200: 90% Sorting block time: 00:00:01 Returning block of 3479675 for bucket 194 bucket 192: 80% bucket 198: 90% bucket 199: 80% bucket 185: 100% Sorting block of length 6865695 for bucket 185 (Using difference cover) Splitting and merging Splitting and merging time: 00:00:00 Split 45, merged 136; iterating... bucket 196: 80% bucket 186: 90% bucket 201: 90% bucket 193: 100% Sorting block of length 5481612 for bucket 193 (Using difference cover) bucket 187: 90% bucket 205: 70% bucket 195: 90% bucket 204: 40% bucket 203: 70% bucket 197: 70% bucket 188: 90% bucket 192: 90% bucket 200: 100% Sorting block of length 6604663 for bucket 200 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6865696 for bucket 185 bucket 202: 90% bucket 205: 80% bucket 199: 90% bucket 198: 100% Sorting block of length 4409580 for bucket 198 (Using difference cover) bucket 186: 100% Sorting block of length 6567781 for bucket 186 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5481613 for bucket 193 bucket 201: 100% Sorting block of length 4411002 for bucket 201 (Using difference cover) bucket 187: 100% Sorting block of length 6822354 for bucket 187 (Using difference cover) bucket 196: 90% bucket 203: 80% bucket 195: 100% Sorting block of length 5830377 for bucket 195 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4409581 for bucket 198 bucket 204: 50% Splitting and merging Splitting and merging time: 00:00:00 Split 22, merged 23; iterating... bucket 197: 80% bucket 188: 100% Sorting block of length 5724962 for bucket 188 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4411003 for bucket 201 bucket 192: 100% Sorting block of length 5221186 for bucket 192 (Using difference cover) bucket 199: 100% Sorting block of length 5980620 for bucket 199 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6567782 for bucket 186 bucket 202: 100% Sorting block of length 3490079 for bucket 202 (Using difference cover) bucket 205: 90% Sorting block time: 00:00:04 Returning block of 6604664 for bucket 200 Sorting block time: 00:00:04 Returning block of 6822355 for bucket 187 bucket 196: 100% Sorting block of length 3164569 for bucket 196 (Using difference cover) bucket 203: 90% Sorting block time: 00:00:01 Returning block of 3490080 for bucket 202 Sorting block time: 00:00:04 Returning block of 5830378 for bucket 195 Sorting block time: 00:00:03 Returning block of 5221187 for bucket 192 bucket 204: 60% bucket 197: 90% bucket 205: 100% Sorting block of length 4625068 for bucket 205 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3164570 for bucket 196 Sorting block time: 00:00:02 Returning block of 5980621 for bucket 199 Sorting block time: 00:00:04 Returning block of 5724963 for bucket 188 Sorting block time: 00:00:02 Returning block of 4625069 for bucket 205 bucket 203: 100% Sorting block of length 4794994 for bucket 203 (Using difference cover) bucket 204: 70% Splitting and merging Splitting and merging time: 00:00:00 Split 12, merged 13; iterating... bucket 197: 100% Sorting block of length 5747898 for bucket 197 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4794995 for bucket 203 bucket 204: 80% Sorting block time: 00:00:02 Returning block of 5747899 for bucket 197 bucket 204: 90% Splitting and merging Splitting and merging time: 00:00:00 Split 5, merged 9; iterating... bucket 204: 100% Sorting block of length 4981674 for bucket 204 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4981675 for bucket 204 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 2; iterating... Avg bucket size: 5.09297e+06 (target: 6957364) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 204 Reserving size (6957365) for bucket 1 Getting block 2 of 204 Calculating Z arrays for bucket 1 Reserving size (6957365) for bucket 2 Getting block 3 of 204 Getting block 4 of 204 Getting block 5 of 204 Getting block 6 of 204 Getting block 7 of 204 Getting block 8 of 204 Getting block 9 of 204 Getting block 10 of 204 Getting block 11 of 204 Getting block 12 of 204 Getting block 13 of 204 Getting block 14 of 204 Getting block 15 of 204 Getting block 16 of 204 Getting block 17 of 204 Getting block 18 of 204 Getting block 19 of 204 Getting block 20 of 204 Getting block 21 of 204 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 2 Reserving size (6957365) for bucket 3 Reserving size (6957365) for bucket 4 Getting block 22 of 204 Getting block 23 of 204 Reserving size (6957365) for bucket 5 Reserving size (6957365) for bucket 6 Reserving size (6957365) for bucket 7 Reserving size (6957365) for bucket 8 Reserving size (6957365) for bucket 9 Reserving size (6957365) for bucket 10 Reserving size (6957365) for bucket 11 Reserving size (6957365) for bucket 12 Reserving size (6957365) for bucket 13 Reserving size (6957365) for bucket 14 Reserving size (6957365) for bucket 15 Reserving size (6957365) for bucket 16 Reserving size (6957365) for bucket 17 Reserving size (6957365) for bucket 18 Reserving size (6957365) for bucket 19 Reserving size (6957365) for bucket 20 Reserving size (6957365) for bucket 21 Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 4 Reserving size (6957365) for bucket 22 Reserving size (6957365) for bucket 23 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 9 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 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 Getting block 24 of 204 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 23 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: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 10: Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 12: 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: Reserving size (6957365) for bucket 24 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 20: Entering block accumulator loop for bucket 23: Calculating Z arrays for bucket 24 Getting block 25 of 204 Entering block accumulator loop for bucket 24: Reserving size (6957365) for bucket 25 Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 25: Getting block 26 of 204 Reserving size (6957365) for bucket 26 Getting block 27 of 204 Calculating Z arrays for bucket 26 Reserving size (6957365) for bucket 27 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 27: bucket 1: 10% bucket 2: 10% bucket 3: 10% bucket 4: 10% bucket 5: 10% bucket 8: 10% bucket 9: 10% bucket 7: 10% bucket 12: 10% bucket 17: 10% bucket 19: 10% bucket 15: 10% bucket 6: 10% bucket 10: 10% bucket 22: 10% bucket 16: 10% bucket 21: 10% bucket 20: 10% bucket 13: 10% bucket 25: 10% bucket 11: 10% bucket 14: 10% bucket 18: 10% bucket 24: 10% bucket 26: 10% bucket 27: 10% bucket 23: 10% bucket 1: 20% bucket 2: 20% bucket 3: 20% bucket 4: 20% bucket 5: 20% bucket 9: 20% bucket 8: 20% bucket 7: 20% bucket 12: 20% bucket 6: 20% bucket 10: 20% bucket 17: 20% bucket 19: 20% bucket 15: 20% bucket 16: 20% bucket 13: 20% bucket 22: 20% bucket 11: 20% bucket 20: 20% bucket 21: 20% bucket 14: 20% bucket 18: 20% bucket 25: 20% bucket 24: 20% bucket 26: 20% bucket 27: 20% bucket 23: 20% bucket 1: 30% bucket 2: 30% bucket 3: 30% bucket 4: 30% bucket 5: 30% bucket 9: 30% bucket 8: 30% bucket 7: 30% bucket 6: 30% bucket 12: 30% bucket 10: 30% bucket 13: 30% bucket 17: 30% bucket 19: 30% bucket 15: 30% bucket 16: 30% bucket 11: 30% bucket 22: 30% bucket 14: 30% bucket 20: 30% bucket 21: 30% bucket 18: 30% bucket 25: 30% bucket 24: 30% bucket 26: 30% bucket 23: 30% bucket 27: 30% bucket 1: 40% bucket 2: 40% bucket 3: 40% bucket 5: 40% bucket 4: 40% bucket 9: 40% bucket 8: 40% bucket 7: 40% bucket 6: 40% bucket 10: 40% bucket 12: 40% bucket 13: 40% bucket 16: 40% bucket 17: 40% bucket 19: 40% bucket 15: 40% bucket 11: 40% bucket 22: 40% bucket 14: 40% bucket 20: 40% bucket 21: 40% bucket 18: 40% bucket 25: 40% bucket 26: 40% bucket 23: 40% bucket 24: 40% bucket 27: 40% bucket 1: 50% bucket 2: 50% bucket 3: 50% bucket 4: 50% bucket 5: 50% bucket 9: 50% bucket 8: 50% bucket 7: 50% bucket 6: 50% bucket 10: 50% bucket 12: 50% bucket 13: 50% bucket 16: 50% bucket 11: 50% bucket 17: 50% bucket 19: 50% bucket 15: 50% bucket 14: 50% bucket 22: 50% bucket 20: 50% bucket 18: 50% bucket 21: 50% bucket 23: 50% bucket 26: 50% bucket 25: 50% bucket 24: 50% bucket 1: 60% bucket 27: 50% bucket 2: 60% bucket 3: 60% bucket 4: 60% bucket 5: 60% bucket 9: 60% bucket 8: 60% bucket 7: 60% bucket 6: 60% bucket 10: 60% bucket 13: 60% bucket 12: 60% bucket 16: 60% bucket 11: 60% bucket 17: 60% bucket 19: 60% bucket 15: 60% bucket 14: 60% bucket 22: 60% bucket 18: 60% bucket 20: 60% bucket 21: 60% bucket 1: 70% bucket 23: 60% bucket 26: 60% bucket 24: 60% bucket 25: 60% bucket 27: 60% bucket 2: 70% bucket 3: 70% bucket 4: 70% bucket 5: 70% bucket 9: 70% bucket 8: 70% bucket 7: 70% bucket 6: 70% bucket 13: 70% bucket 10: 70% bucket 12: 70% bucket 11: 70% bucket 16: 70% bucket 17: 70% bucket 19: 70% bucket 15: 70% bucket 14: 70% bucket 1: 80% bucket 22: 70% bucket 18: 70% bucket 20: 70% bucket 21: 70% bucket 23: 70% bucket 2: 80% bucket 3: 80% bucket 26: 70% bucket 24: 70% bucket 25: 70% bucket 27: 70% bucket 4: 80% bucket 5: 80% bucket 9: 80% bucket 8: 80% bucket 7: 80% bucket 6: 80% bucket 13: 80% bucket 10: 80% bucket 12: 80% bucket 11: 80% bucket 16: 80% bucket 17: 80% bucket 19: 80% bucket 15: 80% bucket 1: 90% bucket 14: 80% bucket 22: 80% bucket 18: 80% bucket 20: 80% bucket 21: 80% bucket 2: 90% bucket 3: 90% bucket 23: 80% bucket 4: 90% bucket 5: 90% bucket 26: 80% bucket 24: 80% bucket 27: 80% bucket 25: 80% bucket 9: 90% bucket 7: 90% bucket 8: 90% bucket 6: 90% bucket 13: 90% bucket 10: 90% bucket 12: 90% bucket 1: 100% Sorting block of length 5583943 for bucket 1 (Using difference cover) bucket 11: 90% bucket 16: 90% bucket 17: 90% bucket 19: 90% bucket 15: 90% bucket 14: 90% bucket 22: 90% bucket 2: 100% Sorting block of length 4872096 for bucket 2 (Using difference cover) bucket 18: 90% bucket 3: 100% Sorting block of length 5298066 for bucket 3 (Using difference cover) bucket 20: 90% bucket 21: 90% bucket 4: 100% Sorting block of length 5968599 for bucket 4 (Using difference cover) bucket 5: 100% Sorting block of length 6939927 for bucket 5 (Using difference cover) bucket 23: 90% bucket 26: 90% bucket 24: 90% bucket 27: 90% bucket 25: 90% bucket 9: 100% Sorting block of length 4219583 for bucket 9 (Using difference cover) bucket 7: 100% Sorting block of length 6654660 for bucket 7 (Using difference cover) bucket 8: 100% Sorting block of length 4652258 for bucket 8 (Using difference cover) bucket 6: 100% Sorting block of length 6487358 for bucket 6 (Using difference cover) bucket 13: 100% Sorting block of length 2104768 for bucket 13 (Using difference cover) bucket 10: 100% Sorting block of length 6022469 for bucket 10 (Using difference cover) bucket 12: 100% Sorting block of length 5286685 for bucket 12 (Using difference cover) bucket 11: 100% Sorting block of length 4955987 for bucket 11 (Using difference cover) bucket 16: 100% Sorting block of length 3680370 for bucket 16 (Using difference cover) bucket 17: 100% Sorting block of length 3304620 for bucket 17 (Using difference cover) bucket 19: 100% Sorting block of length 2066938 for bucket 19 (Using difference cover) bucket 15: 100% Sorting block of length 3731633 for bucket 15 (Using difference cover) bucket 14: 100% Sorting block of length 6165499 for bucket 14 (Using difference cover) bucket 18: 100% Sorting block of length 5153658 for bucket 18 (Using difference cover) bucket 22: 100% Sorting block of length 3794494 for bucket 22 (Using difference cover) bucket 20: 100% Sorting block of length 6355044 for bucket 20 (Using difference cover) bucket 21: 100% Sorting block of length 5711446 for bucket 21 (Using difference cover) bucket 23: 100% Sorting block of length 4927633 for bucket 23 (Using difference cover) bucket 26: 100% Sorting block of length 6483039 for bucket 26 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2104769 for bucket 13 bucket 27: 100% Sorting block of length 6552190 for bucket 27 (Using difference cover) bucket 24: 100% Sorting block of length 6422134 for bucket 24 (Using difference cover) bucket 25: 100% Sorting block of length 4956527 for bucket 25 (Using difference cover) Getting block 28 of 204 Reserving size (6957365) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: Sorting block time: 00:00:02 Returning block of 5583944 for bucket 1 Sorting block time: 00:00:01 Returning block of 2066939 for bucket 19 Getting block 29 of 204 Reserving size (6957365) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: Getting block 30 of 204 Reserving size (6957365) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: Sorting block time: 00:00:02 Returning block of 4872097 for bucket 2 Getting block 31 of 204 Reserving size (6957365) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: Sorting block time: 00:00:02 Returning block of 3304621 for bucket 17 Sorting block time: 00:00:02 Returning block of 3680371 for bucket 16 Getting block 32 of 204 Reserving size (6957365) 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 5298067 for bucket 3 Getting block 33 of 204 Reserving size (6957365) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: Sorting block time: 00:00:02 Returning block of 4219584 for bucket 9 Getting block 34 of 204 Reserving size (6957365) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: Getting block 35 of 204 Reserving size (6957365) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: Sorting block time: 00:00:02 Returning block of 3731634 for bucket 15 Sorting block time: 00:00:02 Returning block of 4652259 for bucket 8 Getting block 36 of 204 Reserving size (6957365) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Sorting block time: 00:00:02 Returning block of 3794495 for bucket 22 bucket 28: 10% Sorting block time: 00:00:03 Returning block of 5968600 for bucket 4 Getting block 37 of 204 Reserving size (6957365) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: Sorting block time: 00:00:02 Returning block of 4955988 for bucket 11 Getting block 38 of 204 Reserving size (6957365) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: Sorting block time: 00:00:02 Returning block of 5286686 for bucket 12 Getting block 39 of 204 Reserving size (6957365) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Getting block 40 of 204 Reserving size (6957365) 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 6939928 for bucket 5 Getting block 41 of 204 Reserving size (6957365) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: bucket 30: 10% Sorting block time: 00:00:02 Returning block of 5153659 for bucket 18 bucket 29: 10% Getting block 42 of 204 Reserving size (6957365) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: Sorting block time: 00:00:03 Returning block of 6022470 for bucket 10 Sorting block time: 00:00:03 Returning block of 6487359 for bucket 6 Getting block 43 of 204 Reserving size (6957365) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: Getting block 44 of 204 Reserving size (6957365) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: Sorting block time: 00:00:02 Returning block of 4927634 for bucket 23 Sorting block time: 00:00:03 Returning block of 6654661 for bucket 7 Getting block 45 of 204 Reserving size (6957365) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Getting block 46 of 204 Reserving size (6957365) 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 5711447 for bucket 21 bucket 31: 10% Sorting block time: 00:00:02 Returning block of 4956528 for bucket 25 Sorting block time: 00:00:03 Returning block of 6165500 for bucket 14 Getting block 47 of 204 Reserving size (6957365) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 33: 10% Getting block 48 of 204 Reserving size (6957365) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Getting block 49 of 204 Reserving size (6957365) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: bucket 34: 10% bucket 32: 10% Sorting block time: 00:00:02 Returning block of 6355045 for bucket 20 Getting block 50 of 204 Reserving size (6957365) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: Getting block 51 of 204 Reserving size (6957365) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 35: 10% Sorting block time: 00:00:02 Returning block of 6483040 for bucket 26 Sorting block time: 00:00:02 Returning block of 6552191 for bucket 27 Sorting block time: 00:00:02 Returning block of 6422135 for bucket 24 bucket 28: 20% Getting block 52 of 204 Reserving size (6957365) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 36: 10% Getting block 53 of 204 Reserving size (6957365) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 38: 10% Getting block 54 of 204 Reserving size (6957365) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 37: 10% bucket 39: 10% bucket 40: 10% bucket 41: 10% bucket 30: 20% bucket 29: 20% bucket 42: 10% bucket 43: 10% bucket 44: 10% bucket 45: 10% bucket 46: 10% bucket 31: 20% bucket 33: 20% bucket 34: 20% bucket 32: 20% bucket 48: 10% bucket 47: 10% bucket 49: 10% bucket 35: 20% bucket 50: 10% bucket 51: 10% bucket 28: 30% bucket 38: 20% bucket 36: 20% bucket 52: 10% bucket 37: 20% bucket 39: 20% bucket 53: 10% bucket 54: 10% bucket 40: 20% bucket 29: 30% bucket 41: 20% bucket 30: 30% bucket 42: 20% bucket 43: 20% bucket 44: 20% bucket 31: 30% bucket 45: 20% bucket 46: 20% bucket 34: 30% bucket 33: 30% bucket 32: 30% bucket 48: 20% bucket 35: 30% bucket 49: 20% bucket 47: 20% bucket 28: 40% bucket 50: 20% bucket 38: 30% bucket 37: 30% bucket 39: 30% bucket 36: 30% bucket 51: 20% bucket 52: 20% bucket 29: 40% bucket 54: 20% bucket 40: 30% bucket 30: 40% bucket 41: 30% bucket 53: 20% bucket 42: 30% bucket 31: 40% bucket 43: 30% bucket 44: 30% bucket 45: 30% bucket 34: 40% bucket 32: 40% bucket 33: 40% bucket 46: 30% bucket 48: 30% bucket 35: 40% bucket 38: 40% bucket 39: 40% bucket 50: 30% bucket 37: 40% bucket 28: 50% bucket 36: 40% bucket 52: 30% bucket 47: 30% bucket 29: 50% bucket 49: 30% bucket 51: 30% bucket 40: 40% bucket 54: 30% bucket 30: 50% bucket 42: 40% bucket 41: 40% bucket 53: 30% bucket 31: 50% bucket 43: 40% bucket 44: 40% bucket 34: 50% bucket 45: 40% bucket 32: 50% bucket 33: 50% bucket 46: 40% bucket 48: 40% bucket 35: 50% bucket 39: 50% bucket 37: 50% bucket 38: 50% bucket 29: 60% bucket 36: 50% bucket 28: 60% bucket 52: 40% bucket 50: 40% bucket 47: 40% bucket 51: 40% bucket 40: 50% bucket 49: 40% bucket 54: 40% bucket 42: 50% bucket 30: 60% bucket 31: 60% bucket 41: 50% bucket 53: 40% bucket 43: 50% bucket 34: 60% bucket 44: 50% bucket 32: 60% bucket 33: 60% bucket 45: 50% bucket 48: 50% bucket 35: 60% bucket 46: 50% bucket 39: 60% bucket 37: 60% bucket 29: 70% bucket 38: 60% bucket 36: 60% bucket 28: 70% bucket 50: 50% bucket 52: 50% bucket 40: 60% bucket 49: 50% bucket 51: 50% bucket 30: 70% bucket 47: 50% bucket 42: 60% bucket 54: 50% bucket 31: 70% bucket 41: 60% bucket 53: 50% bucket 34: 70% bucket 43: 60% bucket 32: 70% bucket 44: 60% bucket 33: 70% bucket 35: 70% bucket 48: 60% bucket 45: 60% bucket 39: 70% bucket 46: 60% bucket 37: 70% bucket 29: 80% bucket 38: 70% bucket 36: 70% bucket 28: 80% bucket 52: 60% bucket 30: 80% bucket 50: 60% bucket 40: 70% bucket 42: 70% bucket 31: 80% bucket 47: 60% bucket 51: 60% bucket 49: 60% bucket 41: 70% bucket 34: 80% bucket 32: 80% bucket 53: 60% bucket 43: 70% bucket 44: 70% bucket 54: 60% bucket 33: 80% bucket 35: 80% bucket 48: 70% bucket 39: 80% bucket 29: 90% bucket 37: 80% bucket 45: 70% bucket 46: 70% bucket 28: 90% bucket 36: 80% bucket 38: 80% bucket 30: 90% bucket 31: 90% bucket 52: 70% bucket 42: 80% bucket 50: 70% bucket 47: 70% bucket 40: 80% bucket 41: 80% bucket 34: 90% bucket 49: 70% bucket 32: 90% bucket 51: 70% bucket 53: 70% bucket 33: 90% bucket 43: 80% bucket 54: 70% bucket 44: 80% bucket 35: 90% bucket 48: 80% bucket 29: 100% Sorting block of length 6225470 for bucket 29 (Using difference cover) bucket 39: 90% bucket 37: 90% bucket 46: 80% bucket 45: 80% bucket 28: 100% Sorting block of length 5742569 for bucket 28 (Using difference cover) bucket 38: 90% bucket 30: 100% Sorting block of length 6215673 for bucket 30 (Using difference cover) bucket 36: 90% bucket 31: 100% Sorting block of length 5356177 for bucket 31 (Using difference cover) bucket 42: 90% bucket 52: 80% bucket 50: 80% bucket 40: 90% bucket 47: 80% bucket 49: 80% bucket 41: 90% bucket 32: 100% Sorting block of length 5814979 for bucket 32 (Using difference cover) bucket 33: 100% Sorting block of length 6480589 for bucket 33 (Using difference cover) bucket 34: 100% Sorting block of length 4240268 for bucket 34 (Using difference cover) bucket 51: 80% bucket 53: 80% bucket 43: 90% bucket 54: 80% bucket 44: 90% bucket 35: 100% Sorting block of length 6743036 for bucket 35 (Using difference cover) bucket 48: 90% bucket 39: 100% Sorting block of length 6663032 for bucket 39 (Using difference cover) bucket 37: 100% Sorting block of length 3410824 for bucket 37 (Using difference cover) bucket 38: 100% Sorting block of length 6173332 for bucket 38 (Using difference cover) bucket 46: 90% bucket 45: 90% bucket 36: 100% Sorting block of length 6713121 for bucket 36 (Using difference cover) bucket 42: 100% Sorting block of length 6862626 for bucket 42 (Using difference cover) bucket 50: 90% bucket 40: 100% Sorting block of length 4974759 for bucket 40 (Using difference cover) bucket 52: 90% bucket 47: 90% bucket 41: 100% Sorting block of length 5054952 for bucket 41 (Using difference cover) bucket 49: 90% Sorting block time: 00:00:02 Returning block of 6225471 for bucket 29 bucket 53: 90% Sorting block time: 00:00:02 Returning block of 5742570 for bucket 28 bucket 43: 100% Sorting block of length 5218214 for bucket 43 (Using difference cover) bucket 51: 90% bucket 54: 90% Sorting block time: 00:00:02 Returning block of 5356178 for bucket 31 bucket 44: 100% Sorting block of length 5080930 for bucket 44 (Using difference cover) Getting block 55 of 204 Reserving size (6957365) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: Getting block 56 of 204 Reserving size (6957365) 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 4240269 for bucket 34 Getting block 57 of 204 Reserving size (6957365) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 48: 100% Sorting block of length 1019992 for bucket 48 (Using difference cover) Getting block 58 of 204 Reserving size (6957365) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: Sorting block time: 00:00:01 Returning block of 3410825 for bucket 37 Sorting block time: 00:00:02 Returning block of 6215674 for bucket 30 bucket 46: 100% Sorting block of length 5560577 for bucket 46 (Using difference cover) Getting block 59 of 204 Reserving size (6957365) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: Getting block 60 of 204 Reserving size (6957365) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 45: 100% Sorting block of length 6077859 for bucket 45 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1019993 for bucket 48 Sorting block time: 00:00:03 Returning block of 5814980 for bucket 32 Getting block 61 of 204 Reserving size (6957365) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: Getting block 62 of 204 Reserving size (6957365) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 50: 100% Sorting block of length 798737 for bucket 50 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6480590 for bucket 33 bucket 47: 100% Sorting block of length 6463073 for bucket 47 (Using difference cover) bucket 52: 100% Sorting block of length 1791551 for bucket 52 (Using difference cover) Getting block 63 of 204 Reserving size (6957365) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 49: 100% Sorting block of length 6605129 for bucket 49 (Using difference cover) Sorting block time: 00:00:00 Returning block of 798738 for bucket 50 Getting block 64 of 204 Reserving size (6957365) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 53: 100% Sorting block of length 5538598 for bucket 53 (Using difference cover) bucket 54: 100% Sorting block of length 3564164 for bucket 54 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6743037 for bucket 35 bucket 51: 100% Sorting block of length 6243948 for bucket 51 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6663033 for bucket 39 bucket 55: 10% bucket 56: 10% Sorting block time: 00:00:02 Returning block of 4974760 for bucket 40 Sorting block time: 00:00:02 Returning block of 5054953 for bucket 41 bucket 57: 10% Getting block 65 of 204 Reserving size (6957365) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: Getting block 66 of 204 Reserving size (6957365) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: Getting block 67 of 204 Reserving size (6957365) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: Sorting block time: 00:00:03 Returning block of 6173333 for bucket 38 Getting block 68 of 204 Reserving size (6957365) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 58: 10% bucket 59: 10% Sorting block time: 00:00:01 Returning block of 1791552 for bucket 52 Getting block 69 of 204 Reserving size (6957365) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: Sorting block time: 00:00:03 Returning block of 6713122 for bucket 36 Getting block 70 of 204 Reserving size (6957365) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: Sorting block time: 00:00:02 Returning block of 5218215 for bucket 43 bucket 60: 10% Getting block 71 of 204 Reserving size (6957365) 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 5080931 for bucket 44 Getting block 72 of 204 Reserving size (6957365) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 61: 10% Sorting block time: 00:00:03 Returning block of 6862627 for bucket 42 Getting block 73 of 204 Reserving size (6957365) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: bucket 62: 10% Getting block 74 of 204 Reserving size (6957365) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: Sorting block time: 00:00:02 Returning block of 5560578 for bucket 46 Sorting block time: 00:00:02 Returning block of 3564165 for bucket 54 bucket 64: 10% Getting block 75 of 204 Reserving size (6957365) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: Getting block 76 of 204 Reserving size (6957365) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 63: 10% Sorting block time: 00:00:02 Returning block of 6077860 for bucket 45 bucket 55: 20% bucket 56: 20% Getting block 77 of 204 Reserving size (6957365) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 57: 20% bucket 65: 10% bucket 66: 10% bucket 58: 20% Sorting block time: 00:00:02 Returning block of 5538599 for bucket 53 bucket 67: 10% bucket 68: 10% bucket 59: 20% bucket 69: 10% bucket 70: 10% Getting block 78 of 204 Reserving size (6957365) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 60: 20% Sorting block time: 00:00:02 Returning block of 6605130 for bucket 49 Sorting block time: 00:00:02 Returning block of 6463074 for bucket 47 bucket 71: 10% bucket 72: 10% bucket 61: 20% bucket 73: 10% Getting block 79 of 204 Reserving size (6957365) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 62: 20% Getting block 80 of 204 Reserving size (6957365) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: Sorting block time: 00:00:03 Returning block of 6243949 for bucket 51 bucket 74: 10% Getting block 81 of 204 Reserving size (6957365) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 64: 20% bucket 75: 10% bucket 63: 20% bucket 55: 30% bucket 76: 10% bucket 56: 30% bucket 77: 10% bucket 57: 30% bucket 58: 30% bucket 65: 20% bucket 66: 20% bucket 67: 20% bucket 68: 20% bucket 70: 20% bucket 69: 20% bucket 59: 30% bucket 78: 10% bucket 60: 30% bucket 72: 20% bucket 71: 20% bucket 62: 30% bucket 79: 10% bucket 61: 30% bucket 73: 20% bucket 74: 20% bucket 80: 10% bucket 81: 10% bucket 64: 30% bucket 75: 20% bucket 63: 30% bucket 55: 40% bucket 57: 40% bucket 76: 20% bucket 56: 40% bucket 58: 40% bucket 66: 30% bucket 65: 30% bucket 67: 30% bucket 77: 20% bucket 68: 30% bucket 70: 30% bucket 69: 30% bucket 59: 40% bucket 60: 40% bucket 62: 40% bucket 78: 20% bucket 71: 30% bucket 72: 30% bucket 79: 20% bucket 73: 30% bucket 74: 30% bucket 80: 20% bucket 61: 40% bucket 64: 40% bucket 63: 40% bucket 55: 50% bucket 81: 20% bucket 75: 30% bucket 57: 50% bucket 76: 30% bucket 58: 50% bucket 56: 50% bucket 66: 40% bucket 65: 40% bucket 67: 40% bucket 77: 30% bucket 68: 40% bucket 70: 40% bucket 60: 50% bucket 59: 50% bucket 69: 40% bucket 62: 50% bucket 71: 40% bucket 78: 30% bucket 79: 30% bucket 72: 40% bucket 74: 40% bucket 64: 50% bucket 61: 50% bucket 80: 30% bucket 55: 60% bucket 63: 50% bucket 75: 40% bucket 81: 30% bucket 73: 40% bucket 58: 60% bucket 57: 60% bucket 66: 50% bucket 67: 50% bucket 65: 50% bucket 76: 40% bucket 60: 60% bucket 68: 50% bucket 56: 60% bucket 70: 50% bucket 59: 60% bucket 69: 50% bucket 77: 40% bucket 62: 60% bucket 79: 40% bucket 71: 50% bucket 78: 40% bucket 74: 50% bucket 72: 50% bucket 64: 60% bucket 61: 60% bucket 80: 40% bucket 55: 70% bucket 63: 60% bucket 75: 50% bucket 81: 40% bucket 73: 50% bucket 58: 70% bucket 66: 60% bucket 67: 60% bucket 57: 70% bucket 65: 60% bucket 60: 70% bucket 56: 70% bucket 68: 60% bucket 59: 70% bucket 62: 70% bucket 70: 60% bucket 77: 50% bucket 76: 50% bucket 69: 60% bucket 79: 50% bucket 71: 60% bucket 74: 60% bucket 78: 50% bucket 64: 70% bucket 72: 60% bucket 55: 80% bucket 63: 70% bucket 80: 50% bucket 61: 70% bucket 75: 60% bucket 58: 80% bucket 81: 50% bucket 73: 60% bucket 66: 70% bucket 67: 70% bucket 60: 80% bucket 65: 70% bucket 57: 80% bucket 56: 80% bucket 62: 80% bucket 59: 80% bucket 68: 70% bucket 70: 70% bucket 77: 60% bucket 76: 60% bucket 79: 60% bucket 69: 70% bucket 71: 70% bucket 64: 80% bucket 74: 70% bucket 78: 60% bucket 55: 90% bucket 63: 80% bucket 72: 70% bucket 61: 80% bucket 80: 60% bucket 58: 90% bucket 75: 70% bucket 73: 70% bucket 81: 60% bucket 60: 90% bucket 66: 80% bucket 67: 80% bucket 65: 80% bucket 56: 90% bucket 62: 90% bucket 59: 90% bucket 68: 80% bucket 57: 90% bucket 70: 80% bucket 77: 70% bucket 79: 70% bucket 64: 90% bucket 76: 70% bucket 71: 80% bucket 55: 100% Sorting block of length 6164032 for bucket 55 (Using difference cover) bucket 69: 80% bucket 63: 90% bucket 74: 80% bucket 72: 80% bucket 78: 70% bucket 61: 90% bucket 80: 70% bucket 58: 100% Sorting block of length 5383337 for bucket 58 (Using difference cover) bucket 75: 80% bucket 81: 70% bucket 73: 80% bucket 60: 100% Sorting block of length 6282143 for bucket 60 (Using difference cover) bucket 67: 90% bucket 66: 90% bucket 65: 90% bucket 62: 100% Sorting block of length 4785427 for bucket 62 (Using difference cover) bucket 56: 100% Sorting block of length 5732101 for bucket 56 (Using difference cover) bucket 59: 100% Sorting block of length 3666728 for bucket 59 (Using difference cover) bucket 57: 100% Sorting block of length 5740029 for bucket 57 (Using difference cover) bucket 68: 90% bucket 70: 90% bucket 77: 80% bucket 64: 100% Sorting block of length 3315734 for bucket 64 (Using difference cover) bucket 79: 80% bucket 76: 80% bucket 71: 90% bucket 63: 100% Sorting block of length 6263154 for bucket 63 (Using difference cover) bucket 69: 90% bucket 72: 90% bucket 74: 90% bucket 61: 100% Sorting block of length 4001160 for bucket 61 (Using difference cover) bucket 78: 80% bucket 80: 80% bucket 81: 80% bucket 73: 90% bucket 75: 90% bucket 67: 100% Sorting block of length 5054145 for bucket 67 (Using difference cover) bucket 66: 100% Sorting block of length 6667399 for bucket 66 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3666729 for bucket 59 bucket 65: 100% Sorting block of length 5756473 for bucket 65 (Using difference cover) Getting block 82 of 204 Reserving size (6957365) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 70: 100% Sorting block of length 2999296 for bucket 70 (Using difference cover) bucket 77: 90% bucket 68: 100% Sorting block of length 6531286 for bucket 68 (Using difference cover) Sorting block time: 00:00:02 Returning block of 5383338 for bucket 58 Sorting block time: 00:00:02 Returning block of 6164033 for bucket 55 Sorting block time: 00:00:01 Returning block of 3315735 for bucket 64 Getting block 83 of 204 Reserving size (6957365) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: Getting block 84 of 204 Reserving size (6957365) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: Sorting block time: 00:00:01 Returning block of 4785428 for bucket 62 Getting block 85 of 204 Reserving size (6957365) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 79: 90% Getting block 86 of 204 Reserving size (6957365) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: Sorting block time: 00:00:02 Returning block of 5740030 for bucket 57 bucket 71: 100% Sorting block of length 6660255 for bucket 71 (Using difference cover) bucket 76: 90% Getting block 87 of 204 Reserving size (6957365) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 69: 100% Sorting block of length 5302160 for bucket 69 (Using difference cover) bucket 74: 100% Sorting block of length 3448960 for bucket 74 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4001161 for bucket 61 bucket 72: 100% Sorting block of length 2720949 for bucket 72 (Using difference cover) bucket 80: 90% Getting block 88 of 204 Reserving size (6957365) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: Sorting block time: 00:00:02 Returning block of 5732102 for bucket 56 Sorting block time: 00:00:03 Returning block of 6282144 for bucket 60 bucket 78: 90% Getting block 89 of 204 Reserving size (6957365) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: Getting block 90 of 204 Reserving size (6957365) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 73: 100% Sorting block of length 6904903 for bucket 73 (Using difference cover) bucket 81: 90% bucket 75: 100% Sorting block of length 5619021 for bucket 75 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2999297 for bucket 70 bucket 82: 10% Getting block 91 of 204 Reserving size (6957365) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 77: 100% Sorting block of length 2680225 for bucket 77 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6263155 for bucket 63 Getting block 92 of 204 Reserving size (6957365) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: Sorting block time: 00:00:01 Returning block of 2720950 for bucket 72 bucket 83: 10% Getting block 93 of 204 Reserving size (6957365) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 85: 10% bucket 84: 10% Sorting block time: 00:00:02 Returning block of 5054146 for bucket 67 bucket 79: 100% Sorting block of length 5888175 for bucket 79 (Using difference cover) Getting block 94 of 204 Reserving size (6957365) 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 5756474 for bucket 65 bucket 86: 10% bucket 76: 100% Sorting block of length 5509538 for bucket 76 (Using difference cover) Getting block 95 of 204 Reserving size (6957365) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 87: 10% Sorting block time: 00:00:01 Returning block of 3448961 for bucket 74 bucket 80: 100% Sorting block of length 6558767 for bucket 80 (Using difference cover) Getting block 96 of 204 Reserving size (6957365) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 78: 100% Sorting block of length 6824320 for bucket 78 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6667400 for bucket 66 Sorting block time: 00:00:03 Returning block of 6531287 for bucket 68 bucket 88: 10% bucket 81: 100% Sorting block of length 5610298 for bucket 81 (Using difference cover) bucket 89: 10% bucket 90: 10% Getting block 97 of 204 Reserving size (6957365) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: Getting block 98 of 204 Reserving size (6957365) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: Sorting block time: 00:00:01 Returning block of 2680226 for bucket 77 Getting block 99 of 204 Reserving size (6957365) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: Sorting block time: 00:00:02 Returning block of 5302161 for bucket 69 bucket 82: 20% Getting block 100 of 204 Reserving size (6957365) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: bucket 91: 10% bucket 92: 10% bucket 85: 20% bucket 83: 20% bucket 84: 20% bucket 93: 10% Sorting block time: 00:00:03 Returning block of 6660256 for bucket 71 Sorting block time: 00:00:03 Returning block of 5619022 for bucket 75 bucket 94: 10% bucket 86: 20% Sorting block time: 00:00:03 Returning block of 6904904 for bucket 73 Getting block 101 of 204 Reserving size (6957365) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: Getting block 102 of 204 Reserving size (6957365) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 87: 20% bucket 95: 10% Getting block 103 of 204 Reserving size (6957365) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: bucket 96: 10% bucket 88: 20% bucket 90: 20% bucket 89: 20% Sorting block time: 00:00:02 Returning block of 5888176 for bucket 79 Sorting block time: 00:00:02 Returning block of 5509539 for bucket 76 Getting block 104 of 204 Reserving size (6957365) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: Getting block 105 of 204 Reserving size (6957365) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 82: 30% bucket 97: 10% bucket 98: 10% bucket 99: 10% Sorting block time: 00:00:02 Returning block of 5610299 for bucket 81 bucket 100: 10% Sorting block time: 00:00:03 Returning block of 6558768 for bucket 80 bucket 91: 20% Getting block 106 of 204 Reserving size (6957365) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: Getting block 107 of 204 Reserving size (6957365) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 83: 30% bucket 85: 30% bucket 84: 30% bucket 93: 20% bucket 101: 10% Sorting block time: 00:00:03 Returning block of 6824321 for bucket 78 bucket 94: 20% bucket 86: 30% Getting block 108 of 204 Reserving size (6957365) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 102: 10% bucket 87: 30% bucket 92: 20% bucket 95: 20% bucket 103: 10% bucket 90: 30% bucket 88: 30% bucket 96: 20% bucket 104: 10% bucket 89: 30% bucket 105: 10% bucket 82: 40% bucket 97: 20% bucket 98: 20% bucket 100: 20% bucket 99: 20% bucket 91: 30% bucket 107: 10% bucket 85: 40% bucket 83: 40% bucket 106: 10% bucket 101: 20% bucket 84: 40% bucket 93: 30% bucket 108: 10% bucket 94: 30% bucket 86: 40% bucket 102: 20% bucket 103: 20% bucket 92: 30% bucket 87: 40% bucket 104: 20% bucket 105: 20% bucket 95: 30% bucket 90: 40% bucket 88: 40% bucket 89: 40% bucket 96: 30% bucket 82: 50% bucket 107: 20% bucket 100: 30% bucket 97: 30% bucket 98: 30% bucket 91: 40% bucket 101: 30% bucket 85: 50% bucket 106: 20% bucket 99: 30% bucket 84: 50% bucket 83: 50% bucket 108: 20% bucket 94: 40% bucket 93: 40% bucket 86: 50% bucket 102: 30% bucket 103: 30% bucket 105: 30% bucket 104: 30% bucket 92: 40% bucket 90: 50% bucket 87: 50% bucket 89: 50% bucket 88: 50% bucket 96: 40% bucket 95: 40% bucket 107: 30% bucket 82: 60% bucket 100: 40% bucket 101: 40% bucket 108: 30% bucket 85: 60% bucket 91: 50% bucket 97: 40% bucket 98: 40% bucket 106: 30% bucket 84: 60% bucket 83: 60% bucket 99: 40% bucket 94: 50% bucket 103: 40% bucket 105: 40% bucket 93: 50% bucket 104: 40% bucket 86: 60% bucket 102: 40% bucket 92: 50% bucket 90: 60% bucket 87: 60% bucket 89: 60% bucket 107: 40% bucket 101: 50% bucket 96: 50% bucket 88: 60% bucket 82: 70% bucket 100: 50% bucket 108: 40% bucket 85: 70% bucket 106: 40% bucket 95: 50% bucket 84: 70% bucket 91: 60% bucket 97: 50% bucket 98: 50% bucket 83: 70% bucket 105: 50% bucket 104: 50% bucket 99: 50% bucket 94: 60% bucket 102: 50% bucket 93: 60% bucket 86: 70% bucket 103: 50% bucket 92: 60% bucket 90: 70% bucket 101: 60% bucket 87: 70% bucket 107: 50% bucket 108: 50% bucket 89: 70% bucket 82: 80% bucket 88: 70% bucket 100: 60% bucket 96: 60% bucket 85: 80% bucket 106: 50% bucket 91: 70% bucket 95: 60% bucket 84: 80% bucket 83: 80% bucket 105: 60% bucket 104: 60% bucket 97: 60% bucket 98: 60% bucket 102: 60% bucket 103: 60% bucket 94: 70% bucket 99: 60% bucket 86: 80% bucket 93: 70% bucket 101: 70% bucket 108: 60% bucket 92: 70% bucket 90: 80% bucket 87: 80% bucket 82: 90% bucket 107: 60% bucket 89: 80% bucket 100: 70% bucket 85: 90% bucket 88: 80% bucket 96: 70% bucket 106: 60% bucket 105: 70% bucket 104: 70% bucket 91: 80% bucket 84: 90% bucket 95: 70% bucket 98: 70% bucket 97: 70% bucket 83: 90% bucket 102: 70% bucket 103: 70% bucket 94: 80% bucket 86: 90% bucket 99: 70% bucket 101: 80% bucket 108: 70% bucket 93: 80% bucket 90: 90% bucket 92: 80% bucket 82: 100% Sorting block of length 6710980 for bucket 82 (Using difference cover) bucket 107: 70% bucket 87: 90% bucket 100: 80% bucket 85: 100% Sorting block of length 4103583 for bucket 85 (Using difference cover) bucket 89: 90% bucket 105: 80% bucket 88: 90% bucket 104: 80% bucket 106: 70% bucket 96: 80% bucket 91: 90% bucket 84: 100% Sorting block of length 4830764 for bucket 84 (Using difference cover) bucket 102: 80% bucket 103: 80% bucket 83: 100% Sorting block of length 4608771 for bucket 83 (Using difference cover) bucket 95: 80% bucket 98: 80% bucket 97: 80% bucket 94: 90% bucket 101: 90% bucket 108: 80% bucket 86: 100% Sorting block of length 6801265 for bucket 86 (Using difference cover) bucket 99: 80% bucket 93: 90% bucket 107: 80% bucket 90: 100% Sorting block of length 4531738 for bucket 90 (Using difference cover) bucket 105: 90% bucket 100: 90% bucket 92: 90% bucket 104: 90% Sorting block time: 00:00:01 Returning block of 4103584 for bucket 85 bucket 87: 100% Sorting block of length 6555712 for bucket 87 (Using difference cover) bucket 89: 100% Sorting block of length 6419221 for bucket 89 (Using difference cover) bucket 106: 80% Getting block 109 of 204 Reserving size (6957365) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 88: 100% Sorting block of length 4973731 for bucket 88 (Using difference cover) bucket 96: 90% bucket 102: 90% bucket 91: 100% Sorting block of length 6889399 for bucket 91 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4830765 for bucket 84 bucket 103: 90% Getting block 110 of 204 Reserving size (6957365) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: Sorting block time: 00:00:02 Returning block of 6710981 for bucket 82 Sorting block time: 00:00:01 Returning block of 4608772 for bucket 83 bucket 101: 100% Sorting block of length 5822888 for bucket 101 (Using difference cover) bucket 108: 90% bucket 95: 90% Getting block 111 of 204 Reserving size (6957365) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: Getting block 112 of 204 Reserving size (6957365) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 97: 90% bucket 94: 100% Sorting block of length 4868262 for bucket 94 (Using difference cover) bucket 98: 90% bucket 99: 90% bucket 107: 90% bucket 93: 100% Sorting block of length 2803861 for bucket 93 (Using difference cover) bucket 105: 100% Sorting block of length 5539626 for bucket 105 (Using difference cover) bucket 104: 100% Sorting block of length 6066163 for bucket 104 (Using difference cover) bucket 100: 100% Sorting block of length 5139973 for bucket 100 (Using difference cover) bucket 109: 10% bucket 106: 90% bucket 92: 100% Sorting block of length 6426773 for bucket 92 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4531739 for bucket 90 Getting block 113 of 204 Reserving size (6957365) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: Sorting block time: 00:00:01 Returning block of 4973732 for bucket 88 bucket 102: 100% Sorting block of length 5960741 for bucket 102 (Using difference cover) bucket 96: 100% Sorting block of length 6671469 for bucket 96 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6801266 for bucket 86 Getting block 114 of 204 Reserving size (6957365) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 103: 100% Sorting block of length 5109140 for bucket 103 (Using difference cover) bucket 110: 10% bucket 108: 100% Sorting block of length 4879183 for bucket 108 (Using difference cover) bucket 111: 10% Getting block 115 of 204 Reserving size (6957365) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 112: 10% bucket 95: 100% Sorting block of length 4068078 for bucket 95 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6555713 for bucket 87 bucket 97: 100% Sorting block of length 6356307 for bucket 97 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2803862 for bucket 93 Getting block 116 of 204 Reserving size (6957365) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: Getting block 117 of 204 Reserving size (6957365) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: bucket 107: 100% Sorting block of length 6033408 for bucket 107 (Using difference cover) bucket 98: 100% Sorting block of length 4090040 for bucket 98 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6419222 for bucket 89 bucket 99: 100% Sorting block of length 3601916 for bucket 99 (Using difference cover) Getting block 118 of 204 Reserving size (6957365) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: bucket 109: 20% bucket 106: 100% Sorting block of length 5870249 for bucket 106 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4868263 for bucket 94 bucket 113: 10% Getting block 119 of 204 Reserving size (6957365) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: Sorting block time: 00:00:03 Returning block of 5822889 for bucket 101 Getting block 120 of 204 Reserving size (6957365) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 110: 20% Sorting block time: 00:00:03 Returning block of 6889400 for bucket 91 bucket 114: 10% Sorting block time: 00:00:02 Returning block of 5539627 for bucket 105 bucket 111: 20% bucket 112: 20% Getting block 121 of 204 Reserving size (6957365) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: Getting block 122 of 204 Reserving size (6957365) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 115: 10% bucket 117: 10% bucket 116: 10% Sorting block time: 00:00:02 Returning block of 6066164 for bucket 104 Sorting block time: 00:00:01 Returning block of 4068079 for bucket 95 Sorting block time: 00:00:02 Returning block of 5139974 for bucket 100 Sorting block time: 00:00:02 Returning block of 5109141 for bucket 103 Getting block 123 of 204 Reserving size (6957365) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: Sorting block time: 00:00:02 Returning block of 4879184 for bucket 108 bucket 118: 10% Getting block 124 of 204 Reserving size (6957365) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: Getting block 125 of 204 Reserving size (6957365) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: Sorting block time: 00:00:01 Returning block of 4090041 for bucket 98 Getting block 126 of 204 Reserving size (6957365) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: Sorting block time: 00:00:02 Returning block of 6426774 for bucket 92 Getting block 127 of 204 Reserving size (6957365) 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 5960742 for bucket 102 bucket 109: 30% Sorting block time: 00:00:02 Returning block of 3601917 for bucket 99 Getting block 128 of 204 Reserving size (6957365) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: Getting block 129 of 204 Reserving size (6957365) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: Getting block 130 of 204 Reserving size (6957365) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: bucket 113: 20% Getting block 131 of 204 Reserving size (6957365) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 119: 10% Sorting block time: 00:00:03 Returning block of 6671470 for bucket 96 bucket 120: 10% Sorting block time: 00:00:02 Returning block of 6033409 for bucket 107 Getting block 132 of 204 Reserving size (6957365) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 110: 30% Sorting block time: 00:00:02 Returning block of 6356308 for bucket 97 Getting block 133 of 204 Reserving size (6957365) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 111: 30% Getting block 134 of 204 Reserving size (6957365) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: Sorting block time: 00:00:02 Returning block of 5870250 for bucket 106 bucket 122: 10% bucket 114: 20% bucket 112: 30% bucket 121: 10% Getting block 135 of 204 Reserving size (6957365) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 115: 20% bucket 117: 20% bucket 116: 20% bucket 123: 10% bucket 118: 20% bucket 125: 10% bucket 124: 10% bucket 126: 10% bucket 109: 40% bucket 128: 10% bucket 127: 10% bucket 129: 10% bucket 113: 30% bucket 130: 10% bucket 119: 20% bucket 131: 10% bucket 120: 20% bucket 132: 10% bucket 111: 40% bucket 122: 20% bucket 133: 10% bucket 134: 10% bucket 110: 40% bucket 121: 20% bucket 114: 30% bucket 112: 40% bucket 135: 10% bucket 117: 30% bucket 115: 30% bucket 118: 30% bucket 123: 20% bucket 124: 20% bucket 125: 20% bucket 116: 30% bucket 109: 50% bucket 128: 20% bucket 126: 20% bucket 127: 20% bucket 129: 20% bucket 113: 40% bucket 119: 30% bucket 130: 20% bucket 131: 20% bucket 120: 30% bucket 111: 50% bucket 121: 30% bucket 110: 50% bucket 133: 20% bucket 132: 20% bucket 134: 20% bucket 122: 30% bucket 112: 50% bucket 117: 40% bucket 118: 40% bucket 123: 30% bucket 115: 40% bucket 135: 20% bucket 114: 40% Exited Ebwt loop fchr[A]: 0 fchr[C]: 329461670 fchr[G]: 329461670 fchr[T]: 519415916 fchr[$]: 1038966499 bucket 124: 30% Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 356457280 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 259741632 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 1038966499 bwtLen: 1038966500 sz: 259741625 bwtSz: 259741625 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 64935407 offsSz: 259741628 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 5411284 numLines: 5411284 ebwtTotLen: 346322176 ebwtTotSz: 346322176 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:07:44 Reading reference sizes bucket 109: 60% bucket 116: 40% bucket 125: 30% bucket 128: 30% bucket 126: 30% bucket 119: 40% bucket 127: 30% bucket 113: 50% bucket 129: 30% bucket 130: 30% bucket 131: 30% bucket 120: 40% bucket 121: 40% bucket 111: 60% bucket 133: 30% bucket 122: 40% bucket 110: 60% bucket 132: 30% bucket 118: 50% bucket 117: 50% bucket 134: 30% bucket 123: 40% bucket 112: 60% bucket 115: 50% bucket 114: 50% bucket 135: 30% bucket 124: 40% bucket 109: 70% bucket 119: 50% bucket 128: 40% bucket 126: 40% bucket 127: 40% bucket 116: 50% bucket 125: 40% bucket 113: 60% bucket 129: 40% bucket 131: 40% bucket 120: 50% bucket 130: 40% bucket 121: 50% bucket 111: 70% bucket 133: 40% bucket 122: 50% bucket 110: 70% bucket 118: 60% bucket 123: 50% bucket 117: 60% bucket 132: 40% bucket 134: 40% bucket 115: 60% bucket 109: 80% bucket 112: 70% bucket 114: 60% bucket 124: 50% bucket 119: 60% bucket 135: 40% bucket 128: 50% bucket 126: 50% bucket 127: 50% bucket 113: 70% bucket 116: 60% bucket 129: 50% bucket 125: 50% bucket 131: 50% bucket 120: 60% bucket 121: 60% bucket 130: 50% bucket 111: 80% bucket 133: 50% bucket 118: 70% bucket 123: 60% bucket 117: 70% bucket 122: 60% bucket 110: 80% bucket 132: 50% bucket 134: 50% bucket 109: 90% bucket 119: 70% bucket 124: 60% bucket 115: 70% bucket 128: 60% bucket 135: 50% bucket 112: 80% bucket 127: 60% bucket 126: 60% bucket 113: 80% bucket 129: 60% bucket 114: 70% bucket 116: 70% bucket 125: 60% bucket 121: 70% bucket 131: 60% bucket 120: 70% bucket 130: 60% bucket 111: 90% bucket 118: 80% bucket 133: 60% bucket 123: 70% bucket 117: 80% bucket 122: 70% bucket 110: 90% bucket 109: 100% Sorting block of length 6536368 for bucket 109 (Using difference cover) bucket 119: 80% bucket 132: 60% bucket 124: 70% bucket 115: 80% bucket 134: 60% bucket 128: 70% bucket 127: 70% bucket 135: 60% bucket 113: 90% bucket 126: 70% bucket 129: 70% bucket 121: 80% bucket 114: 80% bucket 116: 80% bucket 112: 90% bucket 125: 70% bucket 131: 70% bucket 120: 80% bucket 118: 90% bucket 111: 100% Sorting block of length 1636326 for bucket 111 (Using difference cover) bucket 130: 70% bucket 123: 80% bucket 133: 70% bucket 117: 90% bucket 122: 80% bucket 119: 90% Sorting block time: 00:00:00 Returning block of 1636327 for bucket 111 Getting block 136 of 204 Reserving size (6957365) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 110: 100% Sorting block of length 6685488 for bucket 110 (Using difference cover) bucket 124: 80% bucket 132: 70% bucket 134: 70% bucket 115: 90% bucket 128: 80% bucket 127: 80% bucket 113: 100% Sorting block of length 5310317 for bucket 113 (Using difference cover) bucket 135: 70% bucket 121: 90% bucket 129: 80% bucket 126: 80% bucket 114: 90% bucket 112: 100% Sorting block of length 5623017 for bucket 112 (Using difference cover) bucket 116: 90% bucket 131: 80% bucket 125: 80% bucket 118: 100% Sorting block of length 1942351 for bucket 118 (Using difference cover) bucket 120: 90% bucket 123: 90% Sorting block time: 00:00:02 Returning block of 6536369 for bucket 109 bucket 130: 80% bucket 133: 80% bucket 117: 100% Sorting block of length 5652575 for bucket 117 (Using difference cover) Getting block 137 of 204 Reserving size (6957365) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 122: 90% bucket 119: 100% Sorting block of length 5119292 for bucket 119 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1942352 for bucket 118 Getting block 138 of 204 Reserving size (6957365) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 124: 90% bucket 132: 80% bucket 115: 100% Sorting block of length 5055039 for bucket 115 (Using difference cover) bucket 134: 80% bucket 128: 90% bucket 136: 10% bucket 127: 90% bucket 121: 100% Sorting block of length 6535132 for bucket 121 (Using difference cover) bucket 135: 80% bucket 129: 90% Time reading reference sizes: 00:00:08 Calculating joined length Writing header Reserving space for joined string Joining reference sequences bucket 114: 100% Sorting block of length 5781282 for bucket 114 (Using difference cover) bucket 126: 90% bucket 131: 90% bucket 116: 100% Sorting block of length 6124571 for bucket 116 (Using difference cover) bucket 125: 90% bucket 120: 100% Sorting block of length 5110328 for bucket 120 (Using difference cover) bucket 123: 100% Sorting block of length 6513401 for bucket 123 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6685489 for bucket 110 Sorting block time: 00:00:02 Returning block of 5310318 for bucket 113 bucket 130: 90% Getting block 139 of 204 Reserving size (6957365) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 133: 90% Getting block 140 of 204 Reserving size (6957365) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: bucket 122: 100% Sorting block of length 3650312 for bucket 122 (Using difference cover) Sorting block time: 00:00:02 Returning block of 5623018 for bucket 112 bucket 137: 10% Getting block 141 of 204 Reserving size (6957365) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 124: 100% Sorting block of length 5937170 for bucket 124 (Using difference cover) bucket 138: 10% bucket 128: 100% Sorting block of length 5469196 for bucket 128 (Using difference cover) bucket 132: 90% bucket 127: 100% Sorting block of length 6217462 for bucket 127 (Using difference cover) bucket 134: 90% bucket 129: 100% Sorting block of length 6488275 for bucket 129 (Using difference cover) bucket 135: 90% Sorting block time: 00:00:02 Returning block of 5119293 for bucket 119 Sorting block time: 00:00:02 Returning block of 5652576 for bucket 117 Sorting block time: 00:00:01 Returning block of 5055040 for bucket 115 bucket 136: 20% bucket 126: 100% Sorting block of length 6902437 for bucket 126 (Using difference cover) Getting block 142 of 204 Reserving size (6957365) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 131: 100% Sorting block of length 4304234 for bucket 131 (Using difference cover) Getting block 143 of 204 Reserving size (6957365) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: Getting block 144 of 204 Reserving size (6957365) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 125: 100% Sorting block of length 3384572 for bucket 125 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3650313 for bucket 122 bucket 133: 100% Sorting block of length 6227277 for bucket 133 (Using difference cover) bucket 130: 100% Sorting block of length 6905193 for bucket 130 (Using difference cover) bucket 140: 10% Getting block 145 of 204 Reserving size (6957365) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 139: 10% Sorting block time: 00:00:02 Returning block of 5110329 for bucket 120 Getting block 146 of 204 Reserving size (6957365) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: Sorting block time: 00:00:02 Returning block of 5781283 for bucket 114 Sorting block time: 00:00:02 Returning block of 6124572 for bucket 116 Sorting block time: 00:00:02 Returning block of 6535133 for bucket 121 Getting block 147 of 204 Reserving size (6957365) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 137: 20% Getting block 148 of 204 Reserving size (6957365) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 138: 20% bucket 132: 100% Sorting block of length 4847927 for bucket 132 (Using difference cover) bucket 134: 100% Sorting block of length 5315199 for bucket 134 (Using difference cover) Getting block 149 of 204 Reserving size (6957365) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: bucket 141: 10% Sorting block time: 00:00:03 Returning block of 6513402 for bucket 123 bucket 135: 100% Sorting block of length 2998476 for bucket 135 (Using difference cover) Getting block 150 of 204 Reserving size (6957365) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 142: 10% Sorting block time: 00:00:01 Returning block of 3384573 for bucket 125 bucket 136: 30% Sorting block time: 00:00:02 Returning block of 4304235 for bucket 131 Getting block 151 of 204 Reserving size (6957365) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 144: 10% Getting block 152 of 204 Reserving size (6957365) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: bucket 143: 10% Sorting block time: 00:00:02 Returning block of 5937171 for bucket 124 Sorting block time: 00:00:02 Returning block of 5469197 for bucket 128 bucket 140: 20% bucket 139: 20% Getting block 153 of 204 Reserving size (6957365) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: Getting block 154 of 204 Reserving size (6957365) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 145: 10% Sorting block time: 00:00:03 Returning block of 6217463 for bucket 127 bucket 146: 10% Getting block 155 of 204 Reserving size (6957365) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: Sorting block time: 00:00:01 Returning block of 2998477 for bucket 135 Sorting block time: 00:00:03 Returning block of 6902438 for bucket 126 Sorting block time: 00:00:03 Returning block of 6488276 for bucket 129 bucket 148: 10% Getting block 156 of 204 Reserving size (6957365) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 138: 30% bucket 147: 10% Getting block 157 of 204 Reserving size (6957365) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 137: 30% bucket 149: 10% Getting block 158 of 204 Reserving size (6957365) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: bucket 141: 20% Sorting block time: 00:00:01 Returning block of 4847928 for bucket 132 Sorting block time: 00:00:02 Returning block of 6905194 for bucket 130 Sorting block time: 00:00:02 Returning block of 6227278 for bucket 133 Getting block 159 of 204 Reserving size (6957365) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 150: 10% Getting block 160 of 204 Reserving size (6957365) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: Getting block 161 of 204 Reserving size (6957365) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 142: 20% Sorting block time: 00:00:01 Returning block of 5315200 for bucket 134 bucket 151: 10% Getting block 162 of 204 Reserving size (6957365) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 144: 20% bucket 136: 40% bucket 152: 10% bucket 143: 20% bucket 153: 10% bucket 140: 30% bucket 154: 10% bucket 139: 30% bucket 145: 20% bucket 146: 20% bucket 155: 10% bucket 148: 20% bucket 157: 10% bucket 138: 40% bucket 156: 10% bucket 149: 20% bucket 137: 40% bucket 141: 30% bucket 159: 10% bucket 147: 20% bucket 161: 10% bucket 150: 20% bucket 158: 10% bucket 142: 30% bucket 160: 10% bucket 151: 20% bucket 162: 10% bucket 144: 30% bucket 143: 30% bucket 152: 20% bucket 153: 20% bucket 136: 50% bucket 154: 20% bucket 140: 40% bucket 139: 40% bucket 146: 30% bucket 145: 30% bucket 155: 20% bucket 148: 30% Time to join reference sequences: 00:00:06 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 9276486 Using parameters --bmax 6957365 --dcv 1024 Doing ahead-of-time memory usage test bucket 157: 20% bucket 138: 50% bucket 149: 30% bucket 156: 20% bucket 137: 50% Passed! Constructing with these parameters: --bmax 6957365 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime bucket 161: 20% bucket 159: 20% bucket 141: 40% bucket 160: 20% bucket 142: 40% bucket 147: 30% bucket 151: 30% bucket 158: 20% bucket 150: 30% Building sPrimeOrder V-Sorting samples bucket 162: 20% bucket 143: 40% bucket 153: 30% bucket 154: 30% bucket 140: 50% bucket 144: 40% bucket 152: 30% bucket 139: 50% bucket 136: 60% bucket 146: 40% bucket 155: 30% bucket 148: 40% bucket 145: 40% bucket 157: 30% bucket 149: 40% bucket 138: 60% bucket 161: 30% bucket 159: 30% bucket 156: 30% bucket 141: 50% bucket 137: 60% bucket 160: 30% bucket 142: 50% bucket 147: 40% bucket 151: 40% bucket 150: 40% bucket 153: 40% bucket 143: 50% bucket 158: 30% bucket 162: 30% bucket 154: 40% bucket 140: 60% bucket 144: 50% bucket 139: 60% bucket 148: 50% bucket 152: 40% bucket 146: 50% bucket 155: 40% bucket 136: 70% bucket 157: 40% bucket 145: 50% bucket 149: 50% bucket 161: 40% bucket 138: 70% bucket 159: 40% bucket 141: 60% bucket 156: 40% bucket 137: 70% bucket 160: 40% bucket 147: 50% bucket 142: 60% bucket 150: 50% bucket 151: 50% bucket 153: 50% bucket 143: 60% bucket 162: 40% bucket 158: 40% bucket 154: 50% bucket 140: 70% bucket 144: 60% bucket 139: 70% bucket 148: 60% bucket 146: 60% bucket 155: 50% bucket 152: 50% bucket 157: 50% bucket 136: 80% bucket 161: 50% bucket 149: 60% bucket 145: 60% bucket 138: 80% bucket 159: 50% bucket 156: 50% bucket 141: 70% bucket 160: 50% bucket 137: 80% bucket 150: 60% bucket 147: 60% bucket 153: 60% bucket 142: 70% bucket 143: 70% bucket 151: 60% bucket 140: 80% bucket 154: 60% bucket 158: 50% bucket 162: 50% bucket 148: 70% bucket 144: 70% bucket 139: 80% bucket 155: 60% bucket 146: 70% bucket 161: 60% bucket 157: 60% bucket 149: 70% bucket 152: 60% bucket 136: 90% bucket 138: 90% bucket 145: 70% bucket 141: 80% bucket 160: 60% bucket 159: 60% bucket 156: 60% bucket 137: 90% bucket 153: 70% bucket 150: 70% bucket 147: 70% bucket 142: 80% bucket 143: 80% bucket 140: 90% bucket 154: 70% bucket 158: 60% bucket 151: 70% bucket 148: 80% bucket 162: 60% bucket 155: 70% bucket 146: 80% bucket 161: 70% bucket 139: 90% bucket 157: 70% bucket 144: 80% bucket 149: 80% bucket 152: 70% bucket 138: 100% Sorting block of length 5301663 for bucket 138 (Using difference cover) bucket 136: 100% Sorting block of length 4101600 for bucket 136 (Using difference cover) bucket 145: 80% bucket 159: 70% bucket 160: 70% bucket 141: 90% bucket 137: 100% Sorting block of length 6454376 for bucket 137 (Using difference cover) bucket 156: 70% bucket 150: 80% bucket 147: 80% bucket 143: 90% bucket 153: 80% bucket 158: 70% bucket 148: 90% bucket 162: 70% bucket 154: 80% bucket 142: 90% bucket 149: 90% bucket 140: 100% Sorting block of length 4948543 for bucket 140 (Using difference cover) bucket 151: 80% bucket 146: 90% bucket 155: 80% bucket 161: 80% bucket 157: 80% bucket 145: 90% bucket 159: 80% bucket 139: 100% Sorting block of length 6844254 for bucket 139 (Using difference cover) bucket 144: 90% bucket 160: 80% V-Sorting samples time: 00:00:09 Allocating rank array Ranking v-sort output bucket 152: 80% bucket 158: 80% bucket 148: 100% Sorting block of length 3960065 for bucket 148 (Using difference cover) bucket 143: 100% Sorting block of length 5299468 for bucket 143 (Using difference cover) bucket 156: 80% bucket 147: 90% bucket 150: 90% Sorting block time: 00:00:02 Returning block of 4101601 for bucket 136 Getting block 163 of 204 Reserving size (6957365) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: bucket 153: 90% bucket 141: 100% Sorting block of length 3810378 for bucket 141 (Using difference cover) bucket 162: 80% bucket 142: 100% Sorting block of length 5710064 for bucket 142 (Using difference cover) bucket 149: 100% Sorting block of length 6076269 for bucket 149 (Using difference cover) bucket 154: 90% Sorting block time: 00:00:03 Returning block of 5301664 for bucket 138 bucket 151: 90% Sorting block time: 00:00:03 Returning block of 6454377 for bucket 137 bucket 161: 90% Getting block 164 of 204 Reserving size (6957365) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 155: 90% bucket 146: 100% Sorting block of length 3887926 for bucket 146 (Using difference cover) bucket 157: 90% Getting block 165 of 204 Reserving size (6957365) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 159: 90% bucket 160: 90% bucket 145: 100% Sorting block of length 3234195 for bucket 145 (Using difference cover) bucket 144: 100% Sorting block of length 5352167 for bucket 144 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4948544 for bucket 140 bucket 152: 90% bucket 158: 90% Getting block 166 of 204 Reserving size (6957365) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 150: 100% Sorting block of length 6386531 for bucket 150 (Using difference cover) bucket 147: 100% Sorting block of length 4469220 for bucket 147 (Using difference cover) bucket 163: 10% Sorting block time: 00:00:02 Returning block of 3960066 for bucket 148 bucket 156: 90% bucket 162: 90% bucket 153: 100% Sorting block of length 3130828 for bucket 153 (Using difference cover) Getting block 167 of 204 Reserving size (6957365) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: Sorting block time: 00:00:01 Returning block of 3810379 for bucket 141 Sorting block time: 00:00:02 Returning block of 5299469 for bucket 143 Getting block 168 of 204 Reserving size (6957365) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 154: 100% Sorting block of length 6261335 for bucket 154 (Using difference cover) bucket 151: 100% Sorting block of length 1021545 for bucket 151 (Using difference cover) bucket 161: 100% Sorting block of length 1304414 for bucket 161 (Using difference cover) Getting block 169 of 204 Reserving size (6957365) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: Sorting block time: 00:00:02 Returning block of 3234196 for bucket 145 bucket 155: 100% Sorting block of length 2284452 for bucket 155 (Using difference cover) Getting block 170 of 204 Reserving size (6957365) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 164: 10% Sorting block time: 00:00:02 Returning block of 3887927 for bucket 146 bucket 159: 100% Sorting block of length 5612602 for bucket 159 (Using difference cover) bucket 165: 10% bucket 157: 100% Sorting block of length 2294120 for bucket 157 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6844255 for bucket 139 bucket 160: 100% Sorting block of length 5699920 for bucket 160 (Using difference cover) Getting block 171 of 204 Reserving size (6957365) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: Sorting block time: 00:00:01 Returning block of 1021546 for bucket 151 Getting block 172 of 204 Reserving size (6957365) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: Getting block 173 of 204 Reserving size (6957365) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: Sorting block time: 00:00:02 Returning block of 5710065 for bucket 142 Sorting block time: 00:00:01 Returning block of 1304415 for bucket 161 Getting block 174 of 204 Reserving size (6957365) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: Getting block 175 of 204 Reserving size (6957365) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 166: 10% bucket 152: 100% Sorting block of length 6726730 for bucket 152 (Using difference cover) bucket 158: 100% Sorting block of length 5590166 for bucket 158 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6076270 for bucket 149 Sorting block time: 00:00:01 Returning block of 3130829 for bucket 153 Getting block 176 of 204 Reserving size (6957365) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: Sorting block time: 00:00:01 Returning block of 5352168 for bucket 144 Getting block 177 of 204 Reserving size (6957365) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 163: 20% bucket 162: 100% Sorting block of length 5660673 for bucket 162 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2284453 for bucket 155 bucket 167: 10% Getting block 178 of 204 Reserving size (6957365) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: Sorting block time: 00:00:01 Returning block of 4469221 for bucket 147 bucket 156: 100% Sorting block of length 5350434 for bucket 156 (Using difference cover) Getting block 179 of 204 Reserving size (6957365) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: Sorting block time: 00:00:01 Returning block of 2294121 for bucket 157 Getting block 180 of 204 Reserving size (6957365) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: Getting block 181 of 204 Reserving size (6957365) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: bucket 168: 10% bucket 169: 10% Sorting block time: 00:00:02 Returning block of 6386532 for bucket 150 bucket 170: 10% bucket 164: 20% bucket 165: 20% bucket 171: 10% Getting block 182 of 204 Reserving size (6957365) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 173: 10% bucket 174: 10% bucket 175: 10% bucket 172: 10% bucket 166: 20% Sorting block time: 00:00:02 Returning block of 6261336 for bucket 154 bucket 176: 10% Getting block 183 of 204 Reserving size (6957365) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: Sorting block time: 00:00:02 Returning block of 5612603 for bucket 159 bucket 167: 20% bucket 178: 10% bucket 177: 10% Sorting block time: 00:00:02 Returning block of 5699921 for bucket 160 bucket 163: 30% Getting block 184 of 204 Reserving size (6957365) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 180: 10% bucket 179: 10% bucket 181: 10% Getting block 185 of 204 Reserving size (6957365) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 168: 20% Sorting block time: 00:00:02 Returning block of 5590167 for bucket 158 bucket 169: 20% Getting block 186 of 204 Reserving size (6957365) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: bucket 164: 30% bucket 170: 20% bucket 165: 30% bucket 171: 20% Sorting block time: 00:00:01 Returning block of 5350435 for bucket 156 Sorting block time: 00:00:02 Returning block of 5660674 for bucket 162 bucket 173: 20% bucket 182: 10% Getting block 187 of 204 Reserving size (6957365) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: Getting block 188 of 204 Reserving size (6957365) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: Sorting block time: 00:00:03 Returning block of 6726731 for bucket 152 bucket 174: 20% bucket 175: 20% Getting block 189 of 204 Reserving size (6957365) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: Ranking v-sort output time: 00:00:06 Invoking Larsson-Sadakane on ranks bucket 172: 20% bucket 166: 30% bucket 176: 20% bucket 183: 10% bucket 178: 20% bucket 167: 30% bucket 184: 10% bucket 177: 20% bucket 163: 40% bucket 180: 20% bucket 181: 20% bucket 185: 10% bucket 168: 30% bucket 179: 20% bucket 186: 10% bucket 169: 30% bucket 164: 40% bucket 170: 30% bucket 171: 30% bucket 165: 40% bucket 173: 30% bucket 187: 10% bucket 182: 20% bucket 188: 10% bucket 174: 30% bucket 175: 30% bucket 189: 10% bucket 166: 40% bucket 176: 30% bucket 172: 30% bucket 183: 20% bucket 178: 30% bucket 167: 40% bucket 177: 30% bucket 184: 20% bucket 185: 20% bucket 179: 30% bucket 181: 30% bucket 180: 30% bucket 168: 40% bucket 163: 50% bucket 186: 20% bucket 169: 40% bucket 164: 50% bucket 171: 40% bucket 170: 40% bucket 173: 40% bucket 187: 20% bucket 165: 50% bucket 182: 30% bucket 175: 40% bucket 188: 20% bucket 174: 40% bucket 166: 50% bucket 189: 20% bucket 172: 40% bucket 183: 30% bucket 176: 40% bucket 167: 50% bucket 178: 40% bucket 184: 30% bucket 177: 40% bucket 185: 30% bucket 179: 40% bucket 180: 40% bucket 168: 50% bucket 163: 60% bucket 186: 30% bucket 181: 40% bucket 171: 50% bucket 169: 50% bucket 173: 50% bucket 182: 40% bucket 187: 30% bucket 170: 50% bucket 164: 60% bucket 188: 30% bucket 165: 60% bucket 175: 50% bucket 166: 60% bucket 172: 50% bucket 183: 40% bucket 174: 50% bucket 189: 30% bucket 167: 60% bucket 184: 40% bucket 176: 50% bucket 177: 50% bucket 185: 40% bucket 178: 50% bucket 180: 50% bucket 179: 50% bucket 168: 60% bucket 186: 40% bucket 163: 70% bucket 173: 60% bucket 171: 60% bucket 169: 60% bucket 181: 50% bucket 182: 50% bucket 187: 40% bucket 188: 40% bucket 164: 70% bucket 165: 70% bucket 170: 60% bucket 175: 60% bucket 183: 50% bucket 172: 60% bucket 166: 70% bucket 189: 40% bucket 167: 70% bucket 184: 50% bucket 176: 60% bucket 174: 60% bucket 185: 50% bucket 177: 60% bucket 178: 60% bucket 179: 60% bucket 180: 60% bucket 186: 50% bucket 168: 70% bucket 163: 80% bucket 173: 70% bucket 171: 70% bucket 182: 60% bucket 169: 70% bucket 181: 60% bucket 187: 50% bucket 164: 80% bucket 188: 50% bucket 165: 80% bucket 170: 70% bucket 175: 70% bucket 183: 60% bucket 189: 50% bucket 166: 80% bucket 172: 70% bucket 167: 80% bucket 176: 70% bucket 185: 60% bucket 184: 60% bucket 178: 70% bucket 179: 70% bucket 177: 70% bucket 174: 70% bucket 180: 70% bucket 186: 60% bucket 173: 80% bucket 168: 80% bucket 163: 90% bucket 171: 80% bucket 182: 70% bucket 169: 80% bucket 187: 60% bucket 181: 70% bucket 188: 60% bucket 164: 90% bucket 165: 90% bucket 175: 80% bucket 170: 80% bucket 183: 70% bucket 189: 60% bucket 166: 90% bucket 185: 70% bucket 176: 80% bucket 167: 90% bucket 172: 80% bucket 178: 80% bucket 184: 70% bucket 179: 80% bucket 186: 70% bucket 173: 90% bucket 180: 80% bucket 163: 100% Sorting block of length 6718712 for bucket 163 (Using difference cover) bucket 177: 80% bucket 168: 90% bucket 171: 90% bucket 174: 80% bucket 187: 70% bucket 169: 90% bucket 182: 80% bucket 181: 80% bucket 188: 70% bucket 164: 100% Sorting block of length 2813606 for bucket 164 (Using difference cover) bucket 175: 90% bucket 165: 100% Sorting block of length 5318343 for bucket 165 (Using difference cover) bucket 183: 80% bucket 170: 90% bucket 189: 70% bucket 166: 100% Sorting block of length 3849606 for bucket 166 (Using difference cover) bucket 185: 80% bucket 176: 90% Invoking Larsson-Sadakane on ranks time: 00:00:10 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 bucket 167: 100% Sorting block of length 3702381 for bucket 167 (Using difference cover) bucket 172: 90% bucket 184: 80% bucket 178: 90% bucket 179: 90% bucket 168: 100% Sorting block of length 5256955 for bucket 168 (Using difference cover) bucket 186: 80% bucket 180: 90% bucket 173: 100% Sorting block of length 2124709 for bucket 173 (Using difference cover) bucket 177: 90% bucket 174: 90% bucket 188: 80% bucket 171: 100% Sorting block of length 5233177 for bucket 171 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2813607 for bucket 164 bucket 187: 80% bucket 182: 90% bucket 169: 100% Sorting block of length 4799274 for bucket 169 (Using difference cover) Getting block 190 of 204 Reserving size (6957365) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 175: 100% Sorting block of length 3147441 for bucket 175 (Using difference cover) bucket 170: 100% Sorting block of length 5751380 for bucket 170 (Using difference cover) bucket 181: 90% bucket 183: 90% bucket 172: 100% Sorting block of length 6072544 for bucket 172 (Using difference cover) bucket 189: 80% Sorting block time: 00:00:01 Returning block of 2124710 for bucket 173 bucket 185: 90% Getting block 191 of 204 Reserving size (6957365) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: bucket 184: 90% Sorting block time: 00:00:03 Returning block of 3849607 for bucket 166 bucket 176: 100% Sorting block of length 4033299 for bucket 176 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3702382 for bucket 167 bucket 179: 100% Sorting block of length 5866460 for bucket 179 (Using difference cover) bucket 186: 90% Getting block 192 of 204 Reserving size (6957365) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: Getting block 193 of 204 Reserving size (6957365) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: bucket 178: 100% Sorting block of length 4233052 for bucket 178 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5318344 for bucket 165 bucket 182: 100% Sorting block of length 2904054 for bucket 182 (Using difference cover) Getting block 194 of 204 Reserving size (6957365) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 180: 100% Sorting block of length 6917368 for bucket 180 (Using difference cover) Sorting block time: 00:00:03 Returning block of 5256956 for bucket 168 bucket 174: 100% Sorting block of length 6559851 for bucket 174 (Using difference cover) Sorting block time: 00:00:04 Returning block of 6718713 for bucket 163 bucket 188: 90% bucket 177: 100% Sorting block of length 5385272 for bucket 177 (Using difference cover) Getting block 195 of 204 Reserving size (6957365) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: Getting block 196 of 204 Reserving size (6957365) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 190: 10% bucket 183: 100% Sorting block of length 4786374 for bucket 183 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4799275 for bucket 169 bucket 187: 90% Getting block 197 of 204 Reserving size (6957365) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: Sorting block time: 00:00:03 Returning block of 3147442 for bucket 175 Getting block 198 of 204 Reserving size (6957365) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 185: 100% Sorting block of length 4795961 for bucket 185 (Using difference cover) bucket 186: 100% Sorting block of length 4670941 for bucket 186 (Using difference cover) bucket 181: 100% Sorting block of length 4961479 for bucket 181 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2904055 for bucket 182 Sorting block time: 00:00:04 Returning block of 5233178 for bucket 171 Getting block 199 of 204 Reserving size (6957365) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: Getting block 200 of 204 Reserving size (6957365) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 189: 90% bucket 191: 10% bucket 184: 100% Sorting block of length 5285977 for bucket 184 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6072545 for bucket 172 Sorting block time: 00:00:02 Returning block of 4033300 for bucket 176 bucket 193: 10% bucket 194: 10% Getting block 201 of 204 Reserving size (6957365) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: Getting block 202 of 204 Reserving size (6957365) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 192: 10% bucket 196: 10% bucket 195: 10% Sorting block time: 00:00:03 Returning block of 5385273 for bucket 177 Sorting block time: 00:00:03 Returning block of 5866461 for bucket 179 bucket 188: 100% Sorting block of length 5501000 for bucket 188 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5751381 for bucket 170 bucket 198: 10% Getting block 203 of 204 Reserving size (6957365) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: Sorting block time: 00:00:03 Returning block of 4233053 for bucket 178 Getting block 204 of 204 Reserving size (6957365) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: bucket 197: 10% bucket 187: 100% Sorting block of length 2994934 for bucket 187 (Using difference cover) bucket 190: 20% Sorting block time: 00:00:04 Returning block of 6559852 for bucket 174 Sorting block time: 00:00:03 Returning block of 4786375 for bucket 183 Sorting block time: 00:00:03 Returning block of 4670942 for bucket 186 bucket 191: 20% bucket 199: 10% Sorting block time: 00:00:03 Returning block of 4795962 for bucket 185 bucket 200: 10% bucket 201: 10% Sorting block time: 00:00:05 Returning block of 6917369 for bucket 180 bucket 203: 10% bucket 202: 10% bucket 196: 20% bucket 189: 100% Sorting block of length 4946016 for bucket 189 (Using difference cover) bucket 193: 20% bucket 204: 10% Sorting block time: 00:00:03 Returning block of 5285978 for bucket 184 bucket 192: 20% bucket 194: 20% bucket 198: 20% bucket 195: 20% Sorting block time: 00:00:04 Returning block of 4961480 for bucket 181 bucket 197: 20% Splitting and merging Splitting and merging time: 00:00:00 Split 44, merged 131; iterating... Sorting block time: 00:00:01 Returning block of 2994935 for bucket 187 bucket 199: 20% bucket 191: 30% bucket 204: 20% bucket 190: 30% Sorting block time: 00:00:03 Returning block of 5501001 for bucket 188 bucket 201: 20% bucket 203: 20% bucket 200: 20% bucket 196: 30% bucket 198: 30% bucket 195: 30% bucket 192: 30% bucket 194: 30% bucket 197: 30% bucket 202: 20% bucket 193: 30% bucket 204: 30% Sorting block time: 00:00:02 Returning block of 4946017 for bucket 189 bucket 199: 30% bucket 201: 30% bucket 191: 40% bucket 196: 40% bucket 203: 30% bucket 190: 40% bucket 200: 30% bucket 204: 40% bucket 198: 40% bucket 193: 40% bucket 195: 40% bucket 202: 30% bucket 192: 40% bucket 194: 40% bucket 197: 40% bucket 199: 40% bucket 201: 40% bucket 190: 50% bucket 204: 50% bucket 193: 50% bucket 203: 40% bucket 196: 50% bucket 191: 50% bucket 200: 40% bucket 202: 40% bucket 198: 50% bucket 195: 50% bucket 194: 50% bucket 201: 50% bucket 204: 60% bucket 192: 50% bucket 197: 50% bucket 193: 60% bucket 199: 50% Splitting and merging Splitting and merging time: 00:00:00 Split 24, merged 22; iterating... bucket 190: 60% bucket 203: 50% bucket 200: 50% bucket 196: 60% bucket 202: 50% bucket 198: 60% bucket 195: 60% bucket 204: 70% bucket 191: 60% bucket 201: 60% bucket 192: 60% bucket 194: 60% bucket 197: 60% bucket 203: 60% bucket 193: 70% bucket 199: 60% bucket 190: 70% bucket 200: 60% bucket 196: 70% bucket 204: 80% bucket 195: 70% bucket 202: 60% bucket 198: 70% bucket 201: 70% bucket 191: 70% bucket 194: 70% bucket 192: 70% bucket 197: 70% bucket 204: 90% bucket 202: 70% bucket 203: 70% bucket 199: 70% bucket 193: 80% bucket 196: 80% bucket 201: 80% bucket 198: 80% bucket 190: 80% bucket 195: 80% bucket 200: 70% bucket 204: 100% Sorting block of length 4931338 for bucket 204 (Using difference cover) bucket 194: 80% bucket 202: 80% bucket 191: 80% bucket 193: 90% bucket 197: 80% bucket 201: 90% bucket 192: 80% bucket 203: 80% bucket 199: 80% bucket 198: 90% bucket 196: 90% bucket 194: 90% bucket 190: 90% bucket 200: 80% bucket 195: 90% Sorting block time: 00:00:02 Returning block of 4931339 for bucket 204 Splitting and merging Splitting and merging time: 00:00:00 Split 11, merged 16; iterating... bucket 201: 100% Sorting block of length 1210949 for bucket 201 (Using difference cover) bucket 191: 90% bucket 197: 90% bucket 203: 90% bucket 192: 90% bucket 193: 100% Sorting block of length 6415343 for bucket 193 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1210950 for bucket 201 bucket 202: 90% bucket 195: 100% Sorting block of length 6904643 for bucket 195 (Using difference cover) bucket 200: 90% bucket 199: 90% bucket 198: 100% Sorting block of length 6623231 for bucket 198 (Using difference cover) bucket 194: 100% Sorting block of length 4479324 for bucket 194 (Using difference cover) bucket 190: 100% Sorting block of length 6359862 for bucket 190 (Using difference cover) bucket 196: 100% Sorting block of length 2080643 for bucket 196 (Using difference cover) bucket 191: 100% Sorting block of length 6698132 for bucket 191 (Using difference cover) bucket 197: 100% Sorting block of length 5682248 for bucket 197 (Using difference cover) bucket 202: 100% Sorting block of length 7078100 for bucket 202 (Using difference cover) bucket 192: 100% Sorting block of length 6515681 for bucket 192 (Using difference cover) bucket 203: 100% Sorting block of length 2341307 for bucket 203 (Using difference cover) bucket 199: 100% Sorting block of length 6619988 for bucket 199 (Using difference cover) bucket 200: 100% Sorting block of length 559127 for bucket 200 (Using difference cover) Sorting block time: 00:00:00 Returning block of 559128 for bucket 200 Sorting block time: 00:00:02 Returning block of 2080644 for bucket 196 Sorting block time: 00:00:01 Returning block of 2341308 for bucket 203 Sorting block time: 00:00:03 Returning block of 4479325 for bucket 194 Sorting block time: 00:00:03 Returning block of 6904644 for bucket 195 Sorting block time: 00:00:04 Returning block of 6415344 for bucket 193 Sorting block time: 00:00:02 Returning block of 5682249 for bucket 197 Sorting block time: 00:00:04 Returning block of 6623232 for bucket 198 Sorting block time: 00:00:04 Returning block of 6359863 for bucket 190 Sorting block time: 00:00:03 Returning block of 6698133 for bucket 191 Sorting block time: 00:00:03 Returning block of 6515682 for bucket 192 Sorting block time: 00:00:02 Returning block of 6619989 for bucket 199 Splitting and merging Splitting and merging time: 00:00:00 Split 5, merged 7; iterating... Sorting block time: 00:00:04 Returning block of 7078101 for bucket 202 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 2; iterating... Avg bucket size: 4.97113e+06 (target: 6957364) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 209 Reserving size (6957365) for bucket 1 Getting block 2 of 209 Getting block 3 of 209 Getting block 4 of 209 Getting block 5 of 209 Getting block 6 of 209 Getting block 7 of 209 Getting block 8 of 209 Getting block 9 of 209 Getting block 10 of 209 Getting block 11 of 209 Getting block 12 of 209 Getting block 13 of 209 Getting block 14 of 209 Getting block 15 of 209 Getting block 16 of 209 Getting block 17 of 209 Getting block 18 of 209 Getting block 19 of 209 Getting block 20 of 209 Getting block 21 of 209 Getting block 22 of 209 Calculating Z arrays for bucket 1 Reserving size (6957365) for bucket 2 Getting block 23 of 209 Reserving size (6957365) for bucket 3 Getting block 24 of 209 Getting block 25 of 209 Reserving size (6957365) for bucket 4 Reserving size (6957365) for bucket 5 Reserving size (6957365) for bucket 6 Reserving size (6957365) for bucket 7 Reserving size (6957365) for bucket 8 Reserving size (6957365) for bucket 9 Reserving size (6957365) for bucket 10 Reserving size (6957365) for bucket 11 Reserving size (6957365) for bucket 12 Reserving size (6957365) for bucket 13 Reserving size (6957365) for bucket 14 Reserving size (6957365) for bucket 15 Reserving size (6957365) for bucket 16 Reserving size (6957365) for bucket 17 Reserving size (6957365) for bucket 18 Reserving size (6957365) for bucket 19 Reserving size (6957365) for bucket 20 Reserving size (6957365) for bucket 21 Reserving size (6957365) for bucket 22 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 1: Reserving size (6957365) for bucket 23 Calculating Z arrays for bucket 3 Reserving size (6957365) for bucket 24 Reserving size (6957365) for bucket 25 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 8 Calculating Z arrays for bucket 9 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 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 Getting block 26 of 209 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 Getting block 27 of 209 Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 24 Entering block accumulator loop for bucket 3: Calculating Z arrays for bucket 25 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 8: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 10: Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 14: 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 15: Reserving size (6957365) for bucket 26 Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 22: Reserving size (6957365) for bucket 27 Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 25: 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 1: 10% bucket 2: 10% bucket 4: 10% bucket 5: 10% bucket 6: 10% bucket 10: 10% bucket 7: 10% bucket 8: 10% bucket 11: 10% bucket 9: 10% bucket 3: 10% bucket 12: 10% bucket 13: 10% bucket 15: 10% bucket 19: 10% bucket 14: 10% bucket 18: 10% bucket 20: 10% bucket 21: 10% bucket 23: 10% bucket 24: 10% bucket 26: 10% bucket 17: 10% bucket 16: 10% bucket 22: 10% bucket 25: 10% bucket 27: 10% bucket 1: 20% bucket 2: 20% bucket 5: 20% bucket 4: 20% bucket 3: 20% bucket 6: 20% bucket 10: 20% bucket 8: 20% bucket 7: 20% bucket 11: 20% bucket 9: 20% bucket 12: 20% bucket 13: 20% bucket 14: 20% bucket 15: 20% bucket 19: 20% bucket 18: 20% bucket 17: 20% bucket 20: 20% bucket 21: 20% bucket 23: 20% bucket 16: 20% bucket 24: 20% bucket 26: 20% bucket 25: 20% bucket 22: 20% bucket 27: 20% Exited Ebwt loop fchr[A]: 0 fchr[C]: 519415916 fchr[G]: 709360996 fchr[T]: 709360996 fchr[$]: 1038966499 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 356457280 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 259741632 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 1038966499 bwtLen: 1038966500 sz: 259741625 bwtSz: 259741625 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 64935407 offsSz: 259741628 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 5411284 numLines: 5411284 ebwtTotLen: 346322176 ebwtTotSz: 346322176 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:03:31 bucket 1: 30% bucket 2: 30% bucket 5: 30% bucket 4: 30% bucket 3: 30% bucket 10: 30% bucket 8: 30% bucket 7: 30% bucket 11: 30% bucket 9: 30% bucket 6: 30% bucket 12: 30% bucket 14: 30% bucket 13: 30% bucket 15: 30% bucket 19: 30% bucket 17: 30% bucket 16: 30% bucket 23: 30% bucket 21: 30% bucket 18: 30% bucket 20: 30% bucket 24: 30% bucket 26: 30% bucket 25: 30% bucket 1: 40% bucket 22: 30% bucket 27: 30% bucket 2: 40% bucket 5: 40% bucket 4: 40% bucket 3: 40% bucket 10: 40% bucket 8: 40% bucket 7: 40% bucket 11: 40% bucket 9: 40% bucket 12: 40% bucket 6: 40% bucket 14: 40% bucket 15: 40% bucket 13: 40% bucket 17: 40% bucket 19: 40% bucket 1: 50% bucket 16: 40% bucket 18: 40% bucket 23: 40% bucket 21: 40% bucket 20: 40% bucket 24: 40% bucket 2: 50% bucket 26: 40% bucket 25: 40% bucket 22: 40% bucket 5: 50% bucket 4: 50% bucket 3: 50% bucket 27: 40% bucket 10: 50% bucket 8: 50% bucket 7: 50% bucket 9: 50% bucket 11: 50% bucket 12: 50% bucket 14: 50% bucket 1: 60% bucket 6: 50% bucket 13: 50% bucket 15: 50% bucket 17: 50% bucket 19: 50% bucket 16: 50% bucket 2: 60% bucket 18: 50% bucket 23: 50% bucket 21: 50% bucket 20: 50% bucket 24: 50% bucket 5: 60% bucket 26: 50% bucket 4: 60% bucket 3: 60% bucket 25: 50% bucket 22: 50% bucket 10: 60% bucket 7: 60% bucket 8: 60% bucket 9: 60% bucket 11: 60% bucket 1: 70% bucket 14: 60% bucket 12: 60% bucket 27: 50% bucket 6: 60% bucket 13: 60% bucket 15: 60% bucket 2: 70% bucket 17: 60% bucket 19: 60% bucket 16: 60% bucket 18: 60% bucket 3: 70% bucket 23: 60% bucket 4: 70% bucket 21: 60% bucket 5: 70% bucket 20: 60% bucket 24: 60% bucket 26: 60% bucket 25: 60% bucket 10: 70% bucket 7: 70% bucket 8: 70% bucket 1: 80% bucket 22: 60% bucket 9: 70% bucket 11: 70% bucket 14: 70% bucket 12: 70% bucket 6: 70% bucket 27: 60% bucket 13: 70% bucket 15: 70% bucket 2: 80% bucket 17: 70% bucket 3: 80% bucket 19: 70% bucket 16: 70% bucket 4: 80% bucket 5: 80% bucket 18: 70% bucket 23: 70% bucket 21: 70% bucket 20: 70% bucket 1: 90% bucket 24: 70% bucket 7: 80% bucket 8: 80% bucket 25: 70% bucket 26: 70% bucket 9: 80% bucket 11: 80% bucket 10: 80% bucket 14: 80% bucket 22: 70% bucket 12: 80% bucket 6: 80% bucket 13: 80% bucket 2: 90% bucket 27: 70% bucket 15: 80% bucket 3: 90% bucket 4: 90% bucket 5: 90% bucket 17: 80% bucket 16: 80% bucket 19: 80% bucket 1: 100% Sorting block of length 5047123 for bucket 1 (Using difference cover) bucket 18: 80% bucket 23: 80% bucket 20: 80% bucket 21: 80% bucket 7: 90% bucket 8: 90% bucket 9: 90% bucket 11: 90% bucket 24: 80% bucket 10: 90% bucket 25: 80% bucket 26: 80% bucket 14: 90% bucket 12: 90% bucket 6: 90% bucket 2: 100% Sorting block of length 6588099 for bucket 2 (Using difference cover) bucket 22: 80% bucket 13: 90% bucket 3: 100% Sorting block of length 3439776 for bucket 3 (Using difference cover) bucket 4: 100% Sorting block of length 6133801 for bucket 4 (Using difference cover) bucket 5: 100% Sorting block of length 4592500 for bucket 5 (Using difference cover) bucket 15: 90% bucket 27: 80% bucket 17: 90% bucket 16: 90% bucket 19: 90% bucket 18: 90% bucket 7: 100% Sorting block of length 5116671 for bucket 7 (Using difference cover) bucket 8: 100% Sorting block of length 6295421 for bucket 8 (Using difference cover) bucket 9: 100% Sorting block of length 4509404 for bucket 9 (Using difference cover) bucket 11: 100% Sorting block of length 5595714 for bucket 11 (Using difference cover) bucket 20: 90% bucket 23: 90% bucket 10: 100% Sorting block of length 4180385 for bucket 10 (Using difference cover) bucket 14: 100% Sorting block of length 5071856 for bucket 14 (Using difference cover) bucket 21: 90% bucket 24: 90% bucket 25: 90% bucket 6: 100% Sorting block of length 4505391 for bucket 6 (Using difference cover) bucket 12: 100% Sorting block of length 4709054 for bucket 12 (Using difference cover) bucket 26: 90% bucket 13: 100% Sorting block of length 6424818 for bucket 13 (Using difference cover) Sorting block time: 00:00:02 Returning block of 5047124 for bucket 1 bucket 22: 90% Getting block 28 of 209 Reserving size (6957365) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 15: 100% Sorting block of length 6915061 for bucket 15 (Using difference cover) bucket 17: 100% Sorting block of length 4989222 for bucket 17 (Using difference cover) bucket 27: 90% Sorting block time: 00:00:01 Returning block of 3439777 for bucket 3 Getting block 29 of 209 Reserving size (6957365) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 16: 100% Sorting block of length 6634554 for bucket 16 (Using difference cover) bucket 19: 100% Sorting block of length 3644787 for bucket 19 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4592501 for bucket 5 bucket 18: 100% Sorting block of length 6786029 for bucket 18 (Using difference cover) Getting block 30 of 209 Reserving size (6957365) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 20: 100% Sorting block of length 4896749 for bucket 20 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6133802 for bucket 4 Sorting block time: 00:00:02 Returning block of 4180386 for bucket 10 Sorting block time: 00:00:02 Returning block of 4509405 for bucket 9 Sorting block time: 00:00:02 Returning block of 6588100 for bucket 2 Getting block 31 of 209 Reserving size (6957365) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: Getting block 32 of 209 Reserving size (6957365) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: Getting block 33 of 209 Reserving size (6957365) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: Sorting block time: 00:00:02 Returning block of 5116672 for bucket 7 Getting block 34 of 209 Reserving size (6957365) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: Sorting block time: 00:00:02 Returning block of 5595715 for bucket 11 Getting block 35 of 209 Reserving size (6957365) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: Sorting block time: 00:00:02 Returning block of 5071857 for bucket 14 Sorting block time: 00:00:01 Returning block of 4709055 for bucket 12 Sorting block time: 00:00:01 Returning block of 4505392 for bucket 6 Getting block 36 of 209 Reserving size (6957365) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Getting block 37 of 209 Reserving size (6957365) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: Getting block 38 of 209 Reserving size (6957365) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: Getting block 39 of 209 Reserving size (6957365) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: bucket 24: 100% Sorting block of length 5397013 for bucket 24 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6295422 for bucket 8 Sorting block time: 00:00:02 Returning block of 3644788 for bucket 19 bucket 25: 100% Sorting block of length 4840407 for bucket 25 (Using difference cover) Getting block 40 of 209 Reserving size (6957365) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: Getting block 41 of 209 Reserving size (6957365) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: Sorting block time: 00:00:02 Returning block of 4989223 for bucket 17 Getting block 42 of 209 Reserving size (6957365) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: bucket 23: 100% Sorting block of length 4975348 for bucket 23 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6424819 for bucket 13 Getting block 43 of 209 Reserving size (6957365) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: Sorting block time: 00:00:02 Returning block of 6915062 for bucket 15 bucket 28: 10% Getting block 44 of 209 Reserving size (6957365) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: Sorting block time: 00:00:03 Returning block of 6634555 for bucket 16 bucket 27: 100% Sorting block of length 4745968 for bucket 27 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4896750 for bucket 20 Getting block 45 of 209 Reserving size (6957365) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Getting block 46 of 209 Reserving size (6957365) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: bucket 21: 100% Sorting block of length 4004246 for bucket 21 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6786030 for bucket 18 Getting block 47 of 209 Reserving size (6957365) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 30: 10% Sorting block time: 00:00:01 Returning block of 4840408 for bucket 25 Sorting block time: 00:00:02 Returning block of 5397014 for bucket 24 Getting block 48 of 209 Reserving size (6957365) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Getting block 49 of 209 Reserving size (6957365) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: Sorting block time: 00:00:02 Returning block of 4975349 for bucket 23 Getting block 50 of 209 Reserving size (6957365) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 34: 10% bucket 26: 100% Sorting block of length 5412893 for bucket 26 (Using difference cover) bucket 31: 10% bucket 37: 10% Sorting block time: 00:00:01 Returning block of 4745969 for bucket 27 bucket 38: 10% Getting block 51 of 209 Reserving size (6957365) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: Sorting block time: 00:00:01 Returning block of 4004247 for bucket 21 bucket 40: 10% Getting block 52 of 209 Reserving size (6957365) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 42: 10% bucket 22: 100% Sorting block of length 6303748 for bucket 22 (Using difference cover) bucket 28: 20% Sorting block time: 00:00:02 Returning block of 5412894 for bucket 26 Getting block 53 of 209 Reserving size (6957365) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 45: 10% bucket 46: 10% bucket 30: 20% bucket 29: 10% bucket 47: 10% bucket 35: 10% bucket 39: 10% bucket 32: 10% bucket 34: 20% bucket 33: 10% bucket 48: 10% bucket 49: 10% bucket 36: 10% bucket 31: 20% bucket 41: 10% bucket 37: 20% bucket 38: 20% Sorting block time: 00:00:02 Returning block of 6303749 for bucket 22 Getting block 54 of 209 Reserving size (6957365) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 51: 10% bucket 40: 20% bucket 42: 20% bucket 43: 10% bucket 44: 10% bucket 30: 30% bucket 45: 20% bucket 46: 20% bucket 39: 20% bucket 28: 30% bucket 34: 30% bucket 31: 30% bucket 50: 10% bucket 37: 30% bucket 38: 30% bucket 47: 20% bucket 29: 20% bucket 49: 20% bucket 48: 20% bucket 40: 30% bucket 52: 10% bucket 42: 30% bucket 30: 40% bucket 53: 10% bucket 35: 20% bucket 51: 20% bucket 32: 20% bucket 45: 30% bucket 46: 30% bucket 39: 30% bucket 41: 20% bucket 34: 40% bucket 33: 20% bucket 36: 20% bucket 31: 40% bucket 37: 40% bucket 38: 40% bucket 29: 30% bucket 47: 30% bucket 40: 40% bucket 49: 30% bucket 48: 30% bucket 42: 40% bucket 54: 10% bucket 30: 50% bucket 44: 20% bucket 43: 20% bucket 28: 40% bucket 39: 40% bucket 34: 50% bucket 37: 50% bucket 38: 50% bucket 31: 50% bucket 45: 40% bucket 46: 40% bucket 29: 40% bucket 50: 20% bucket 40: 50% bucket 47: 40% bucket 49: 40% bucket 48: 40% bucket 42: 50% bucket 30: 60% bucket 52: 20% bucket 35: 30% bucket 39: 50% bucket 37: 60% bucket 34: 60% bucket 38: 60% bucket 31: 60% bucket 29: 50% bucket 41: 30% bucket 45: 50% bucket 46: 50% bucket 32: 30% bucket 53: 20% bucket 36: 30% bucket 33: 30% bucket 51: 30% bucket 40: 60% bucket 47: 50% bucket 42: 60% bucket 49: 50% bucket 48: 50% bucket 30: 70% bucket 39: 60% bucket 38: 70% bucket 37: 70% bucket 34: 70% bucket 54: 20% bucket 31: 70% bucket 44: 30% bucket 29: 60% bucket 28: 50% bucket 43: 30% bucket 45: 60% bucket 46: 60% bucket 40: 70% bucket 50: 30% bucket 42: 70% bucket 30: 80% bucket 47: 60% bucket 49: 60% bucket 48: 60% bucket 35: 40% bucket 38: 80% bucket 37: 80% bucket 34: 80% bucket 39: 70% bucket 31: 80% bucket 29: 70% bucket 52: 30% bucket 41: 40% bucket 32: 40% bucket 36: 40% bucket 33: 40% bucket 40: 80% bucket 45: 70% bucket 46: 70% bucket 51: 40% bucket 30: 90% bucket 42: 80% bucket 53: 30% bucket 47: 70% bucket 49: 70% bucket 38: 90% bucket 37: 90% bucket 48: 70% bucket 34: 90% bucket 39: 80% bucket 31: 90% bucket 29: 80% bucket 28: 60% bucket 44: 40% bucket 40: 90% bucket 54: 30% bucket 45: 80% bucket 30: 100% Sorting block of length 6446052 for bucket 30 (Using difference cover) bucket 46: 80% bucket 42: 90% bucket 43: 40% bucket 50: 40% bucket 35: 50% bucket 47: 80% bucket 38: 100% Sorting block of length 4685226 for bucket 38 (Using difference cover) bucket 37: 100% Sorting block of length 5239655 for bucket 37 (Using difference cover) bucket 34: 100% Sorting block of length 5622848 for bucket 34 (Using difference cover) bucket 39: 90% bucket 49: 80% bucket 29: 90% bucket 31: 100% Sorting block of length 6747718 for bucket 31 (Using difference cover) bucket 48: 80% Sorting block time: 00:00:02 Returning block of 6446053 for bucket 30 bucket 41: 50% Getting block 55 of 209 Reserving size (6957365) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 40: 100% Sorting block of length 5654874 for bucket 40 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4685227 for bucket 38 bucket 32: 50% bucket 45: 90% bucket 36: 50% bucket 33: 50% bucket 46: 90% Sorting block time: 00:00:02 Returning block of 5239656 for bucket 37 bucket 42: 100% Sorting block of length 5151566 for bucket 42 (Using difference cover) Getting block 56 of 209 Reserving size (6957365) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: Getting block 57 of 209 Reserving size (6957365) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 52: 40% Sorting block time: 00:00:02 Returning block of 5622849 for bucket 34 Getting block 58 of 209 Reserving size (6957365) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: bucket 39: 100% Sorting block of length 5190545 for bucket 39 (Using difference cover) Sorting block time: 00:00:03 bucket 51: 50% Returning block of 6747719 for bucket 31 bucket 29: 100% Sorting block of length 6103341 for bucket 29 (Using difference cover) bucket 47: 90% Getting block 59 of 209 Reserving size (6957365) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 49: 90% Sorting block time: 00:00:02 Returning block of 5654875 for bucket 40 Getting block 60 of 209 Reserving size (6957365) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 48: 90% Sorting block time: 00:00:02 Returning block of 5151567 for bucket 42 Getting block 61 of 209 Reserving size (6957365) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: bucket 28: 70% bucket 53: 40% bucket 44: 50% bucket 55: 10% Sorting block time: 00:00:02 Returning block of 5190546 for bucket 39 Getting block 62 of 209 Reserving size (6957365) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 45: 100% Sorting block of length 5247488 for bucket 45 (Using difference cover) bucket 46: 100% Sorting block of length 6520272 for bucket 46 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6103342 for bucket 29 Getting block 63 of 209 Reserving size (6957365) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 56: 10% bucket 57: 10% bucket 54: 40% bucket 35: 60% bucket 58: 10% bucket 47: 100% Sorting block of length 6251902 for bucket 47 (Using difference cover) bucket 49: 100% Sorting block of length 5053286 for bucket 49 (Using difference cover) bucket 43: 50% bucket 50: 50% bucket 59: 10% bucket 33: 60% bucket 48: 100% Sorting block of length 2085583 for bucket 48 (Using difference cover) Sorting block time: 00:00:02 Returning block of 5247489 for bucket 45 Getting block 64 of 209 Reserving size (6957365) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 60: 10% bucket 61: 10% Sorting block time: 00:00:02 Returning block of 6520273 for bucket 46 bucket 41: 60% Sorting block time: 00:00:00 Returning block of 2085584 for bucket 48 Getting block 65 of 209 Reserving size (6957365) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: Getting block 66 of 209 Reserving size (6957365) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: bucket 32: 60% bucket 55: 20% bucket 51: 60% bucket 36: 60% Sorting block time: 00:00:02 Returning block of 5053287 for bucket 49 Sorting block time: 00:00:02 Returning block of 6251903 for bucket 47 bucket 62: 10% Getting block 67 of 209 Reserving size (6957365) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: Getting block 68 of 209 Reserving size (6957365) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 56: 20% bucket 63: 10% bucket 58: 20% bucket 52: 50% bucket 33: 70% bucket 28: 80% bucket 64: 10% bucket 59: 20% bucket 60: 20% bucket 66: 10% bucket 65: 10% bucket 44: 60% bucket 53: 50% bucket 61: 20% bucket 51: 70% bucket 67: 10% bucket 35: 70% bucket 68: 10% bucket 56: 30% bucket 62: 20% bucket 63: 20% bucket 33: 80% bucket 58: 30% bucket 64: 20% bucket 57: 20% bucket 54: 50% bucket 50: 60% bucket 43: 60% bucket 41: 70% bucket 66: 20% bucket 65: 20% bucket 32: 70% bucket 59: 30% bucket 36: 70% bucket 60: 30% bucket 51: 80% bucket 67: 20% bucket 68: 20% bucket 61: 30% bucket 28: 90% bucket 56: 40% bucket 55: 30% bucket 33: 90% bucket 64: 30% bucket 63: 30% bucket 62: 30% bucket 52: 60% bucket 58: 40% bucket 66: 30% bucket 65: 30% bucket 44: 70% bucket 35: 80% bucket 67: 30% bucket 68: 30% bucket 51: 90% bucket 59: 40% bucket 60: 40% bucket 53: 60% bucket 61: 40% bucket 56: 50% bucket 33: 100% Sorting block of length 6212934 for bucket 33 (Using difference cover) bucket 64: 40% bucket 63: 40% bucket 41: 80% bucket 50: 70% bucket 62: 40% bucket 58: 50% bucket 66: 40% bucket 65: 40% bucket 57: 30% bucket 54: 60% bucket 43: 70% bucket 68: 40% bucket 67: 40% bucket 32: 80% bucket 36: 80% bucket 51: 100% Sorting block of length 6104995 for bucket 51 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6212935 for bucket 33 bucket 28: 100% Sorting block of length 4067270 for bucket 28 (Using difference cover) Getting block 69 of 209 Reserving size (6957365) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: bucket 59: 50% bucket 64: 50% bucket 60: 50% bucket 61: 50% bucket 56: 60% Sorting block time: 00:00:01 Returning block of 4067271 for bucket 28 bucket 55: 40% Getting block 70 of 209 Reserving size (6957365) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: bucket 66: 50% bucket 63: 50% Sorting block time: 00:00:02 Returning block of 6104996 for bucket 51 bucket 52: 70% Getting block 71 of 209 Reserving size (6957365) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: bucket 35: 90% bucket 68: 50% bucket 58: 60% bucket 62: 50% bucket 67: 50% bucket 44: 80% bucket 65: 50% bucket 69: 10% bucket 64: 60% bucket 59: 60% bucket 56: 70% bucket 60: 60% bucket 61: 60% bucket 41: 90% bucket 53: 70% bucket 70: 10% bucket 50: 80% bucket 66: 60% bucket 71: 10% bucket 68: 60% bucket 63: 60% bucket 67: 60% bucket 32: 90% bucket 36: 90% bucket 58: 70% bucket 62: 60% bucket 69: 20% bucket 43: 80% bucket 54: 70% bucket 64: 70% bucket 57: 40% bucket 59: 70% bucket 56: 80% bucket 70: 20% bucket 66: 70% bucket 61: 70% bucket 60: 70% bucket 71: 20% bucket 35: 100% Sorting block of length 3432102 for bucket 35 (Using difference cover) bucket 65: 60% bucket 68: 70% bucket 67: 70% bucket 63: 70% bucket 44: 90% bucket 69: 30% bucket 52: 80% bucket 55: 50% Sorting block time: 00:00:01 Returning block of 3432103 for bucket 35 Getting block 72 of 209 Reserving size (6957365) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 58: 80% bucket 64: 80% bucket 62: 70% bucket 41: 100% Sorting block of length 5703004 for bucket 41 (Using difference cover) bucket 66: 80% bucket 59: 80% bucket 56: 90% bucket 65: 70% bucket 68: 80% bucket 71: 30% bucket 67: 80% bucket 50: 90% bucket 61: 80% bucket 53: 80% bucket 60: 80% bucket 32: 100% Sorting block of length 5809140 for bucket 32 (Using difference cover) bucket 69: 40% bucket 36: 100% Sorting block of length 5326189 for bucket 36 (Using difference cover) Sorting block time: 00:00:01 Returning block of 5703005 for bucket 41 bucket 64: 90% bucket 63: 80% Getting block 73 of 209 Reserving size (6957365) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: bucket 58: 90% bucket 43: 90% bucket 54: 80% bucket 62: 80% Sorting block time: 00:00:02 Returning block of 5326190 for bucket 36 Sorting block time: 00:00:02 Returning block of 5809141 for bucket 32 Getting block 74 of 209 Reserving size (6957365) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: Getting block 75 of 209 Reserving size (6957365) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 66: 90% bucket 70: 30% bucket 65: 80% bucket 57: 50% bucket 71: 40% bucket 56: 100% Sorting block of length 3443572 for bucket 56 (Using difference cover) bucket 67: 90% bucket 59: 90% bucket 69: 50% bucket 61: 90% bucket 64: 100% Sorting block of length 5991150 for bucket 64 (Using difference cover) bucket 60: 90% bucket 44: 100% Sorting block of length 6753142 for bucket 44 (Using difference cover) bucket 73: 10% bucket 72: 10% Sorting block time: 00:00:01 Returning block of 3443573 for bucket 56 Getting block 76 of 209 Reserving size (6957365) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 68: 90% bucket 52: 90% bucket 63: 90% bucket 55: 60% bucket 58: 100% Sorting block of length 4992676 for bucket 58 (Using difference cover) bucket 75: 10% bucket 65: 90% bucket 62: 90% Sorting block time: 00:00:02 Returning block of 5991151 for bucket 64 bucket 71: 50% bucket 67: 100% Sorting block of length 4194320 for bucket 67 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6753143 for bucket 44 Getting block 77 of 209 Reserving size (6957365) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: Getting block 78 of 209 Reserving size (6957365) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 50: 100% Sorting block of length 3300868 for bucket 50 (Using difference cover) bucket 69: 60% bucket 59: 100% Sorting block of length 5490016 for bucket 59 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4992677 for bucket 58 Getting block 79 of 209 Reserving size (6957365) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 76: 10% bucket 61: 100% Sorting block of length 5572801 for bucket 61 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4194321 for bucket 67 Sorting block time: 00:00:01 Returning block of 3300869 for bucket 50 bucket 60: 100% Sorting block of length 6401714 for bucket 60 (Using difference cover) Getting block 80 of 209 Reserving size (6957365) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: Getting block 81 of 209 Reserving size (6957365) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 53: 90% bucket 63: 100% Sorting block of length 3111817 for bucket 63 (Using difference cover) bucket 43: 100% Sorting block of length 4403266 for bucket 43 (Using difference cover) bucket 68: 100% Sorting block of length 5857918 for bucket 68 (Using difference cover) bucket 65: 100% Sorting block of length 4000922 for bucket 65 (Using difference cover) bucket 75: 20% bucket 66: 100% Sorting block of length 3685935 for bucket 66 (Using difference cover) Sorting block time: 00:00:02 Returning block of 5490017 for bucket 59 Getting block 82 of 209 Reserving size (6957365) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 73: 20% bucket 70: 40% bucket 74: 10% bucket 71: 60% bucket 54: 90% bucket 77: 10% bucket 72: 20% Sorting block time: 00:00:01 Returning block of 3111818 for bucket 63 Getting block 83 of 209 Reserving size (6957365) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 62: 100% Sorting block of length 3958744 for bucket 62 (Using difference cover) bucket 69: 70% Sorting block time: 00:00:02 Returning block of 5572802 for bucket 61 bucket 57: 60% Sorting block time: 00:00:02 Returning block of 4000923 for bucket 65 Sorting block time: 00:00:02 Returning block of 4403267 for bucket 43 Sorting block time: 00:00:02 Returning block of 3685936 for bucket 66 Sorting block time: 00:00:03 Returning block of 6401715 for bucket 60 Sorting block time: 00:00:02 Returning block of 5857919 for bucket 68 bucket 79: 10% bucket 76: 20% bucket 52: 100% Sorting block of length 6929998 for bucket 52 (Using difference cover) bucket 80: 10% bucket 55: 70% bucket 81: 10% Sorting block time: 00:00:02 Returning block of 3958745 for bucket 62 bucket 78: 10% Getting block 84 of 209 Reserving size (6957365) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: Getting block 85 of 209 Reserving size (6957365) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: Getting block 86 of 209 Reserving size (6957365) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 75: 30% Getting block 87 of 209 Reserving size (6957365) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: Getting block 88 of 209 Reserving size (6957365) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: Getting block 89 of 209 Reserving size (6957365) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: Getting block 90 of 209 Reserving size (6957365) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 77: 20% bucket 71: 70% bucket 82: 10% bucket 70: 50% bucket 72: 30% bucket 53: 100% Sorting block of length 4254917 for bucket 53 (Using difference cover) bucket 69: 80% bucket 83: 10% Sorting block time: 00:00:03 Returning block of 6929999 for bucket 52 bucket 76: 30% bucket 73: 30% bucket 74: 20% Getting block 91 of 209 Reserving size (6957365) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 79: 20% bucket 80: 20% Sorting block time: 00:00:01 Returning block of 4254918 for bucket 53 Getting block 92 of 209 Reserving size (6957365) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: bucket 54: 100% Sorting block of length 3664845 for bucket 54 (Using difference cover) bucket 90: 10% bucket 87: 10% bucket 86: 10% bucket 88: 10% bucket 77: 30% bucket 71: 80% Sorting block time: 00:00:02 Returning block of 3664846 for bucket 54 bucket 57: 70% Getting block 93 of 209 Reserving size (6957365) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 70: 60% bucket 82: 20% bucket 72: 40% bucket 69: 90% bucket 83: 20% bucket 76: 40% bucket 79: 30% bucket 80: 30% bucket 81: 20% bucket 78: 20% bucket 55: 80% bucket 75: 40% bucket 77: 40% bucket 87: 20% bucket 90: 20% bucket 84: 10% bucket 86: 20% bucket 71: 90% bucket 85: 10% bucket 88: 20% bucket 70: 70% bucket 69: 100% Sorting block of length 2463011 for bucket 69 (Using difference cover) bucket 89: 10% bucket 72: 50% bucket 82: 30% bucket 76: 50% Sorting block time: 00:00:01 Returning block of 2463012 for bucket 69 bucket 83: 30% Getting block 94 of 209 Reserving size (6957365) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: bucket 79: 40% bucket 80: 40% bucket 73: 40% bucket 74: 30% bucket 91: 10% bucket 77: 50% bucket 92: 10% bucket 87: 30% bucket 84: 20% bucket 71: 100% Sorting block of length 2922396 for bucket 71 (Using difference cover) bucket 86: 30% bucket 70: 80% bucket 88: 30% bucket 72: 60% bucket 82: 40% bucket 76: 60% Sorting block time: 00:00:01 Returning block of 2922397 for bucket 71 Getting block 95 of 209 Reserving size (6957365) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 93: 10% bucket 83: 40% bucket 80: 50% bucket 79: 50% bucket 94: 10% bucket 57: 80% bucket 81: 30% bucket 78: 30% bucket 77: 60% bucket 75: 50% bucket 84: 30% bucket 87: 40% bucket 86: 40% bucket 70: 90% bucket 55: 90% bucket 88: 40% bucket 76: 70% bucket 72: 70% bucket 90: 30% bucket 82: 50% bucket 85: 20% bucket 80: 60% bucket 79: 60% bucket 95: 10% bucket 89: 20% bucket 83: 50% bucket 94: 20% bucket 73: 50% bucket 74: 40% bucket 77: 70% bucket 91: 20% bucket 84: 40% bucket 70: 100% Sorting block of length 6629044 for bucket 70 (Using difference cover) bucket 87: 50% bucket 86: 50% bucket 76: 80% bucket 92: 20% bucket 72: 80% bucket 88: 50% bucket 82: 60% bucket 80: 70% bucket 79: 70% bucket 93: 20% bucket 83: 60% bucket 95: 20% bucket 94: 30% bucket 81: 40% bucket 78: 40% bucket 77: 80% Sorting block time: 00:00:03 Returning block of 6629045 for bucket 70 Getting block 96 of 209 Reserving size (6957365) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 57: 90% bucket 84: 50% bucket 75: 60% bucket 76: 90% bucket 87: 60% bucket 86: 60% bucket 72: 90% bucket 80: 80% bucket 88: 60% bucket 79: 80% bucket 82: 70% bucket 90: 40% bucket 55: 100% Sorting block of length 6858965 for bucket 55 (Using difference cover) bucket 83: 70% bucket 85: 30% bucket 95: 30% bucket 89: 30% bucket 77: 90% bucket 94: 40% bucket 73: 60% bucket 74: 50% bucket 91: 30% bucket 96: 10% bucket 76: 100% Sorting block of length 5668132 for bucket 76 (Using difference cover) bucket 84: 60% bucket 87: 70% bucket 86: 70% bucket 80: 90% bucket 72: 100% Sorting block of length 4865363 for bucket 72 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6858966 for bucket 55 Getting block 97 of 209 Reserving size (6957365) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: bucket 79: 90% bucket 88: 70% bucket 92: 30% Sorting block time: 00:00:02 Returning block of 5668133 for bucket 76 Getting block 98 of 209 Reserving size (6957365) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 83: 80% bucket 82: 80% bucket 77: 100% Sorting block of length 2393060 for bucket 77 (Using difference cover) bucket 78: 50% bucket 95: 40% bucket 81: 50% bucket 93: 30% Sorting block time: 00:00:02 Returning block of 4865364 for bucket 72 Getting block 99 of 209 Reserving size (6957365) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: bucket 94: 50% Sorting block time: 00:00:01 Returning block of 2393061 for bucket 77 Getting block 100 of 209 Reserving size (6957365) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: bucket 96: 20% bucket 84: 70% bucket 75: 70% bucket 80: 100% Sorting block of length 979613 for bucket 80 (Using difference cover) bucket 87: 80% bucket 86: 80% bucket 79: 100% Sorting block of length 6189597 for bucket 79 (Using difference cover) Sorting block time: 00:00:00 Returning block of 979614 for bucket 80 Getting block 101 of 209 Reserving size (6957365) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 57: 100% Sorting block of length 6945407 for bucket 57 (Using difference cover) bucket 97: 10% bucket 88: 80% bucket 90: 50% bucket 85: 40% bucket 83: 90% bucket 98: 10% bucket 95: 50% bucket 73: 70% bucket 89: 40% bucket 94: 60% bucket 99: 10% Sorting block time: 00:00:02 Returning block of 6189598 for bucket 79 bucket 74: 60% Getting block 102 of 209 Reserving size (6957365) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: Sorting block time: 00:00:02 Returning block of 6945408 for bucket 57 Getting block 103 of 209 Reserving size (6957365) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: bucket 100: 10% bucket 84: 80% bucket 96: 30% bucket 91: 40% bucket 87: 90% bucket 86: 90% bucket 97: 20% bucket 88: 90% bucket 83: 100% Sorting block of length 2612189 for bucket 83 (Using difference cover) bucket 78: 60% bucket 92: 40% bucket 82: 90% bucket 81: 60% bucket 95: 60% bucket 98: 20% bucket 93: 40% bucket 94: 70% bucket 101: 10% bucket 99: 20% Sorting block time: 00:00:01 Returning block of 2612190 for bucket 83 bucket 75: 80% Getting block 104 of 209 Reserving size (6957365) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: bucket 84: 90% bucket 102: 10% bucket 100: 20% bucket 96: 40% bucket 103: 10% bucket 87: 100% Sorting block of length 1438812 for bucket 87 (Using difference cover) bucket 86: 100% Sorting block of length 5827853 for bucket 86 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1438813 for bucket 87 Getting block 105 of 209 Reserving size (6957365) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 97: 30% bucket 90: 60% bucket 73: 80% bucket 85: 50% bucket 95: 70% Sorting block time: 00:00:02 Returning block of 5827854 for bucket 86 Getting block 106 of 209 Reserving size (6957365) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 98: 30% bucket 94: 80% bucket 74: 70% bucket 89: 50% bucket 84: 100% Sorting block of length 4712046 for bucket 84 (Using difference cover) bucket 99: 30% bucket 104: 10% bucket 102: 20% bucket 96: 50% bucket 101: 20% bucket 100: 30% bucket 88: 100% Sorting block of length 5544645 for bucket 88 (Using difference cover) bucket 103: 20% bucket 91: 50% bucket 105: 10% bucket 97: 40% Sorting block time: 00:00:02 Returning block of 4712047 for bucket 84 bucket 78: 70% bucket 81: 70% Getting block 107 of 209 Reserving size (6957365) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 82: 100% Sorting block of length 6908749 for bucket 82 (Using difference cover) bucket 92: 50% bucket 95: 80% Sorting block time: 00:00:02 Returning block of 5544646 for bucket 88 Getting block 108 of 209 Reserving size (6957365) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 93: 50% bucket 75: 90% bucket 94: 90% bucket 98: 40% bucket 106: 10% bucket 99: 40% bucket 104: 20% bucket 96: 60% bucket 102: 30% bucket 100: 40% Sorting block time: 00:00:02 Returning block of 6908750 for bucket 82 Getting block 109 of 209 Reserving size (6957365) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 103: 30% bucket 101: 30% bucket 97: 50% bucket 73: 90% bucket 90: 70% bucket 105: 20% bucket 107: 10% bucket 85: 60% bucket 74: 80% bucket 95: 90% bucket 89: 60% bucket 94: 100% Sorting block of length 6647236 for bucket 94 (Using difference cover) bucket 106: 20% bucket 91: 60% bucket 99: 50% bucket 96: 70% bucket 104: 30% bucket 102: 40% bucket 100: 50% bucket 78: 80% bucket 109: 10% bucket 108: 10% bucket 103: 40% bucket 81: 80% bucket 97: 60% Sorting block time: 00:00:02 Returning block of 6647237 for bucket 94 Getting block 110 of 209 Reserving size (6957365) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 101: 40% bucket 98: 50% bucket 107: 20% bucket 75: 100% Sorting block of length 5302916 for bucket 75 (Using difference cover) bucket 92: 60% bucket 95: 100% Sorting block of length 5248886 for bucket 95 (Using difference cover) bucket 93: 60% bucket 106: 30% bucket 99: 60% bucket 96: 80% Sorting block time: 00:00:02 Returning block of 5302917 for bucket 75 Getting block 111 of 209 Reserving size (6957365) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: Sorting block time: 00:00:01 Returning block of 5248887 for bucket 95 bucket 102: 50% bucket 104: 40% Getting block 112 of 209 Reserving size (6957365) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 100: 60% bucket 109: 20% bucket 105: 30% bucket 73: 100% Sorting block of length 6360815 for bucket 73 (Using difference cover) bucket 108: 20% bucket 97: 70% bucket 103: 50% bucket 90: 80% bucket 110: 10% bucket 85: 70% bucket 78: 90% bucket 74: 90% bucket 107: 30% bucket 89: 70% bucket 91: 70% Sorting block time: 00:00:02 Returning block of 6360816 for bucket 73 Getting block 113 of 209 Reserving size (6957365) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 101: 50% bucket 106: 40% bucket 99: 70% bucket 81: 90% bucket 111: 10% bucket 102: 60% bucket 112: 10% bucket 109: 30% bucket 108: 30% bucket 97: 80% bucket 104: 50% bucket 96: 90% bucket 103: 60% bucket 110: 20% bucket 92: 70% bucket 98: 60% bucket 93: 70% bucket 100: 70% bucket 107: 40% bucket 99: 80% bucket 113: 10% bucket 106: 50% bucket 101: 60% bucket 111: 20% bucket 102: 70% bucket 97: 90% bucket 78: 100% Sorting block of length 6910421 for bucket 78 (Using difference cover) bucket 108: 40% bucket 109: 40% bucket 90: 90% bucket 112: 20% bucket 85: 80% bucket 74: 100% Sorting block of length 5028258 for bucket 74 (Using difference cover) bucket 104: 60% bucket 105: 40% bucket 103: 70% bucket 110: 30% bucket 107: 50% bucket 89: 80% bucket 91: 80% Sorting block time: 00:00:02 Returning block of 5028259 for bucket 74 Sorting block time: 00:00:02 Returning block of 6910422 for bucket 78 Getting block 114 of 209 Reserving size (6957365) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: Getting block 115 of 209 Reserving size (6957365) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 81: 100% Sorting block of length 6838601 for bucket 81 (Using difference cover) bucket 99: 90% bucket 106: 60% bucket 113: 20% bucket 101: 70% bucket 102: 80% bucket 111: 30% bucket 97: 100% Sorting block of length 6233086 for bucket 97 (Using difference cover) bucket 108: 50% bucket 109: 50% bucket 96: 100% Sorting block of length 5470391 for bucket 96 (Using difference cover) bucket 112: 30% bucket 104: 70% Sorting block time: 00:00:02 Returning block of 6838602 for bucket 81 bucket 93: 80% bucket 92: 80% bucket 110: 40% bucket 103: 80% bucket 107: 60% bucket 98: 70% Sorting block time: 00:00:01 Returning block of 5470392 for bucket 96 bucket 100: 80% Getting block 116 of 209 Reserving size (6957365) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: Getting block 117 of 209 Reserving size (6957365) 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 6233087 for bucket 97 Getting block 118 of 209 Reserving size (6957365) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: bucket 99: 100% Sorting block of length 2987567 for bucket 99 (Using difference cover) bucket 106: 70% bucket 113: 30% Sorting block time: 00:00:01 Returning block of 2987568 for bucket 99 bucket 102: 90% Getting block 119 of 209 Reserving size (6957365) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: bucket 109: 60% bucket 85: 90% bucket 111: 40% bucket 90: 100% Sorting block of length 6591385 for bucket 90 (Using difference cover) bucket 101: 80% bucket 104: 80% bucket 112: 40% bucket 105: 50% bucket 89: 90% bucket 110: 50% bucket 91: 90% bucket 103: 90% bucket 107: 70% bucket 108: 60% Sorting block time: 00:00:01 Returning block of 6591386 for bucket 90 Getting block 120 of 209 Reserving size (6957365) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 116: 10% bucket 118: 10% bucket 106: 80% bucket 115: 10% bucket 114: 10% bucket 100: 90% bucket 113: 40% bucket 119: 10% bucket 102: 100% Sorting block of length 5414275 for bucket 102 (Using difference cover) bucket 109: 70% bucket 104: 90% bucket 112: 50% bucket 93: 90% bucket 110: 60% bucket 92: 90% bucket 108: 70% bucket 107: 80% bucket 103: 100% Sorting block of length 5411074 for bucket 103 (Using difference cover) Sorting block time: 00:00:02 Returning block of 5414276 for bucket 102 Getting block 121 of 209 Reserving size (6957365) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 116: 20% bucket 118: 20% bucket 98: 80% bucket 106: 90% bucket 117: 10% bucket 100: 100% Sorting block of length 5153285 for bucket 100 (Using difference cover) bucket 113: 50% bucket 85: 100% Sorting block of length 6728329 for bucket 85 (Using difference cover) bucket 119: 20% Sorting block time: 00:00:02 Returning block of 5411075 for bucket 103 bucket 109: 80% Getting block 122 of 209 Reserving size (6957365) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 104: 100% Sorting block of length 6628859 for bucket 104 (Using difference cover) bucket 105: 60% bucket 111: 50% Sorting block time: 00:00:02 Returning block of 5153286 for bucket 100 bucket 112: 60% Getting block 123 of 209 Reserving size (6957365) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 110: 70% Sorting block time: 00:00:02 Returning block of 6728330 for bucket 85 bucket 108: 80% bucket 91: 100% Sorting block of length 3284890 for bucket 91 (Using difference cover) bucket 107: 90% bucket 89: 100% Sorting block of length 4343985 for bucket 89 (Using difference cover) Getting block 124 of 209 Reserving size (6957365) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 101: 90% bucket 120: 10% bucket 118: 30% bucket 106: 100% Sorting block of length 5433010 for bucket 106 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3284891 for bucket 91 bucket 115: 20% bucket 116: 30% Getting block 125 of 209 Reserving size (6957365) 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 6628860 for bucket 104 bucket 114: 20% Getting block 126 of 209 Reserving size (6957365) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: Sorting block time: 00:00:02 Returning block of 4343986 for bucket 89 Getting block 127 of 209 Reserving size (6957365) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 121: 10% bucket 119: 30% bucket 113: 60% bucket 109: 90% bucket 122: 10% bucket 105: 70% Sorting block time: 00:00:02 Returning block of 5433011 for bucket 106 Getting block 128 of 209 Reserving size (6957365) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: bucket 93: 100% Sorting block of length 5580037 for bucket 93 (Using difference cover) bucket 123: 10% bucket 92: 100% Sorting block of length 6575064 for bucket 92 (Using difference cover) bucket 112: 70% bucket 110: 80% bucket 108: 90% bucket 107: 100% Sorting block of length 4281547 for bucket 107 (Using difference cover) bucket 98: 90% bucket 117: 20% Sorting block time: 00:00:02 Returning block of 5580038 for bucket 93 Sorting block time: 00:00:01 Returning block of 4281548 for bucket 107 Getting block 129 of 209 Reserving size (6957365) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: Getting block 130 of 209 Reserving size (6957365) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: bucket 124: 10% bucket 121: 20% bucket 119: 40% Sorting block time: 00:00:02 Returning block of 6575065 for bucket 92 bucket 127: 10% Getting block 131 of 209 Reserving size (6957365) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 113: 70% bucket 109: 100% Sorting block of length 4697988 for bucket 109 (Using difference cover) bucket 122: 20% bucket 101: 100% Sorting block of length 6592145 for bucket 101 (Using difference cover) bucket 111: 60% bucket 105: 80% bucket 126: 10% bucket 128: 10% bucket 123: 20% bucket 118: 40% bucket 108: 100% Sorting block of length 2692905 for bucket 108 (Using difference cover) bucket 110: 90% Sorting block time: 00:00:02 Returning block of 4697989 for bucket 109 Getting block 132 of 209 Reserving size (6957365) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: Sorting block time: 00:00:01 Returning block of 2692906 for bucket 108 Getting block 133 of 209 Reserving size (6957365) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 120: 20% bucket 115: 30% Sorting block time: 00:00:03 Returning block of 6592146 for bucket 101 Getting block 134 of 209 Reserving size (6957365) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 121: 30% bucket 119: 50% bucket 116: 40% bucket 124: 20% bucket 114: 30% bucket 125: 10% bucket 127: 20% bucket 113: 80% bucket 122: 30% bucket 105: 90% bucket 126: 20% bucket 112: 80% bucket 128: 20% bucket 123: 30% bucket 110: 100% Sorting block of length 5874524 for bucket 110 (Using difference cover) bucket 98: 100% Sorting block of length 6458577 for bucket 98 (Using difference cover) bucket 132: 10% bucket 130: 10% bucket 133: 10% bucket 117: 30% bucket 121: 40% bucket 119: 60% bucket 129: 10% bucket 134: 10% bucket 131: 10% bucket 124: 30% Sorting block time: 00:00:02 Returning block of 5874525 for bucket 110 Getting block 135 of 209 Reserving size (6957365) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 127: 30% bucket 122: 40% bucket 113: 90% Sorting block time: 00:00:02 Returning block of 6458578 for bucket 98 Getting block 136 of 209 Reserving size (6957365) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 126: 30% bucket 105: 100% Sorting block of length 2107484 for bucket 105 (Using difference cover) bucket 111: 70% bucket 128: 30% bucket 123: 40% bucket 118: 50% Sorting block time: 00:00:01 Returning block of 2107485 for bucket 105 Getting block 137 of 209 Reserving size (6957365) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 120: 30% bucket 133: 20% bucket 115: 40% bucket 121: 50% bucket 119: 70% bucket 116: 50% bucket 114: 40% bucket 125: 20% bucket 132: 20% bucket 124: 40% bucket 134: 20% bucket 135: 10% bucket 127: 40% bucket 122: 50% bucket 113: 100% Sorting block of length 6077514 for bucket 113 (Using difference cover) bucket 112: 90% bucket 136: 10% bucket 130: 20% bucket 126: 40% bucket 117: 40% bucket 129: 20% bucket 123: 50% bucket 131: 20% bucket 128: 40% Sorting block time: 00:00:02 Returning block of 6077515 for bucket 113 Getting block 138 of 209 Reserving size (6957365) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 111: 80% bucket 137: 10% bucket 118: 60% bucket 120: 40% bucket 115: 50% bucket 116: 60% bucket 114: 50% bucket 125: 30% bucket 132: 30% bucket 121: 60% bucket 133: 30% bucket 119: 80% bucket 112: 100% Sorting block of length 1320458 for bucket 112 (Using difference cover) bucket 127: 50% bucket 124: 50% bucket 134: 30% bucket 122: 60% Sorting block time: 00:00:01 Returning block of 1320459 for bucket 112 Getting block 139 of 209 Reserving size (6957365) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 130: 30% bucket 117: 50% bucket 135: 20% bucket 129: 30% bucket 131: 30% bucket 126: 50% bucket 136: 20% bucket 111: 90% bucket 123: 60% bucket 118: 70% bucket 128: 50% bucket 120: 50% bucket 115: 60% bucket 138: 10% bucket 116: 70% bucket 137: 20% bucket 114: 60% bucket 125: 40% bucket 132: 40% bucket 127: 60% bucket 121: 70% bucket 119: 90% bucket 133: 40% bucket 139: 10% bucket 117: 60% bucket 130: 40% bucket 129: 40% bucket 131: 40% bucket 124: 60% bucket 122: 70% bucket 134: 40% bucket 135: 30% bucket 111: 100% Sorting block of length 5665386 for bucket 111 (Using difference cover) bucket 118: 80% bucket 120: 60% bucket 126: 60% bucket 115: 70% bucket 123: 70% bucket 116: 80% bucket 136: 30% bucket 114: 70% bucket 125: 50% bucket 128: 60% bucket 132: 50% bucket 138: 20% Sorting block time: 00:00:01 Returning block of 5665387 for bucket 111 Getting block 140 of 209 Reserving size (6957365) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: bucket 137: 30% bucket 127: 70% bucket 117: 70% bucket 139: 20% bucket 130: 50% bucket 119: 100% Sorting block of length 1455646 for bucket 119 (Using difference cover) bucket 121: 80% bucket 129: 50% bucket 131: 50% Sorting block time: 00:00:00 Returning block of 1455647 for bucket 119 Getting block 141 of 209 Reserving size (6957365) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 133: 50% bucket 120: 70% bucket 122: 80% bucket 118: 90% bucket 124: 70% bucket 115: 80% bucket 134: 50% bucket 135: 40% bucket 116: 90% bucket 114: 80% bucket 126: 70% bucket 125: 60% bucket 132: 60% bucket 123: 80% bucket 140: 10% bucket 128: 70% bucket 136: 40% bucket 127: 80% bucket 117: 80% bucket 138: 30% bucket 139: 30% bucket 130: 60% bucket 137: 40% bucket 129: 60% bucket 131: 60% bucket 121: 90% bucket 120: 80% bucket 118: 100% Sorting block of length 6911504 for bucket 118 (Using difference cover) bucket 141: 10% bucket 133: 60% bucket 115: 90% bucket 122: 90% bucket 124: 80% bucket 116: 100% Sorting block of length 6446061 for bucket 116 (Using difference cover) bucket 114: 90% bucket 134: 60% bucket 125: 70% bucket 135: 50% bucket 126: 80% bucket 132: 70% bucket 123: 90% bucket 140: 20% bucket 117: 90% Sorting block time: 00:00:02 Returning block of 6911505 for bucket 118 bucket 127: 90% bucket 128: 80% Getting block 142 of 209 Reserving size (6957365) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 136: 50% bucket 139: 40% bucket 138: 40% bucket 130: 70% bucket 129: 70% bucket 131: 70% bucket 137: 50% Sorting block time: 00:00:02 Returning block of 6446062 for bucket 116 Getting block 143 of 209 Reserving size (6957365) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 120: 90% bucket 121: 100% Sorting block of length 2382298 for bucket 121 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2382299 for bucket 121 bucket 115: 100% Sorting block of length 6825143 for bucket 115 (Using difference cover) Getting block 144 of 209 Reserving size (6957365) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 122: 100% Sorting block of length 6858190 for bucket 122 (Using difference cover) bucket 141: 20% bucket 114: 100% Sorting block of length 5199503 for bucket 114 (Using difference cover) bucket 133: 70% bucket 124: 90% bucket 125: 80% bucket 132: 80% bucket 140: 30% bucket 117: 100% Sorting block of length 594120 for bucket 117 (Using difference cover) bucket 127: 100% Sorting block of length 6060863 for bucket 127 (Using difference cover) Sorting block time: 00:00:00 Returning block of 594121 for bucket 117 Getting block 145 of 209 Reserving size (6957365) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 134: 70% bucket 126: 90% bucket 135: 60% bucket 123: 100% Sorting block of length 5969235 for bucket 123 (Using difference cover) bucket 139: 50% Sorting block time: 00:00:02 Returning block of 5199504 for bucket 114 Getting block 146 of 209 Reserving size (6957365) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: bucket 129: 80% bucket 131: 80% bucket 130: 80% Sorting block time: 00:00:02 Returning block of 6825144 for bucket 115 bucket 136: 60% Sorting block time: 00:00:02 Returning block of 6858191 for bucket 122 Getting block 147 of 209 Reserving size (6957365) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 128: 90% bucket 143: 10% bucket 142: 10% Getting block 148 of 209 Reserving size (6957365) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 120: 100% Sorting block of length 6485084 for bucket 120 (Using difference cover) bucket 138: 50% bucket 137: 60% Sorting block time: 00:00:02 Returning block of 6060864 for bucket 127 Getting block 149 of 209 Reserving size (6957365) 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 5969236 for bucket 123 Getting block 150 of 209 Reserving size (6957365) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 125: 90% Sorting block time: 00:00:02 Returning block of 6485085 for bucket 120 bucket 132: 90% Getting block 151 of 209 Reserving size (6957365) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 144: 10% bucket 140: 40% bucket 141: 30% bucket 124: 100% Sorting block of length 4900666 for bucket 124 (Using difference cover) bucket 133: 80% bucket 145: 10% bucket 129: 90% bucket 139: 60% bucket 131: 90% bucket 146: 10% bucket 130: 90% bucket 147: 10% bucket 134: 80% bucket 143: 20% bucket 126: 100% Sorting block of length 1710277 for bucket 126 (Using difference cover) bucket 135: 70% bucket 136: 70% Sorting block time: 00:00:02 Returning block of 4900667 for bucket 124 Getting block 152 of 209 Reserving size (6957365) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: Sorting block time: 00:00:01 Returning block of 1710278 for bucket 126 Getting block 153 of 209 Reserving size (6957365) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 128: 100% Sorting block of length 6335043 for bucket 128 (Using difference cover) bucket 148: 10% bucket 142: 20% bucket 149: 10% bucket 138: 60% bucket 137: 70% bucket 125: 100% Sorting block of length 6184417 for bucket 125 (Using difference cover) bucket 151: 10% bucket 132: 100% Sorting block of length 5752157 for bucket 132 (Using difference cover) bucket 140: 50% bucket 150: 10% bucket 145: 20% Sorting block time: 00:00:02 Returning block of 6335044 for bucket 128 Getting block 154 of 209 Reserving size (6957365) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 144: 20% bucket 129: 100% Sorting block of length 2433665 for bucket 129 (Using difference cover) bucket 131: 100% Sorting block of length 1343817 for bucket 131 (Using difference cover) bucket 139: 70% bucket 146: 20% Sorting block time: 00:00:02 Returning block of 6184418 for bucket 125 bucket 130: 100% Sorting block of length 6492974 for bucket 130 (Using difference cover) bucket 147: 20% bucket 143: 30% bucket 141: 40% bucket 134: 90% bucket 133: 90% Getting block 155 of 209 Reserving size (6957365) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: Sorting block time: 00:00:00 Returning block of 1343818 for bucket 131 Getting block 156 of 209 Reserving size (6957365) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: Sorting block time: 00:00:02 Returning block of 5752158 for bucket 132 Getting block 157 of 209 Reserving size (6957365) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: Sorting block time: 00:00:01 Returning block of 2433666 for bucket 129 Getting block 158 of 209 Reserving size (6957365) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: bucket 135: 80% bucket 136: 80% bucket 152: 10% bucket 153: 10% bucket 148: 20% bucket 149: 20% bucket 142: 30% bucket 138: 70% Sorting block time: 00:00:02 Returning block of 6492975 for bucket 130 bucket 137: 80% Getting block 159 of 209 Reserving size (6957365) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 140: 60% bucket 150: 20% bucket 151: 20% bucket 154: 10% bucket 144: 30% bucket 145: 30% bucket 141: 50% bucket 133: 100% Sorting block of length 3777428 for bucket 133 (Using difference cover) bucket 139: 80% bucket 146: 30% bucket 143: 40% bucket 147: 30% bucket 156: 10% bucket 134: 100% Sorting block of length 5399377 for bucket 134 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3777429 for bucket 133 bucket 155: 10% Getting block 160 of 209 Reserving size (6957365) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 157: 10% bucket 158: 10% bucket 135: 90% bucket 153: 20% bucket 152: 20% bucket 140: 70% bucket 149: 30% bucket 136: 90% bucket 148: 30% bucket 159: 10% bucket 142: 40% bucket 138: 80% bucket 137: 90% Sorting block time: 00:00:01 Returning block of 5399378 for bucket 134 Getting block 161 of 209 Reserving size (6957365) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 151: 30% bucket 145: 40% bucket 150: 30% bucket 154: 20% bucket 139: 90% bucket 146: 40% bucket 143: 50% bucket 144: 40% bucket 147: 40% bucket 156: 20% bucket 141: 60% bucket 158: 20% bucket 157: 20% bucket 140: 80% bucket 149: 40% bucket 159: 20% bucket 160: 10% bucket 155: 20% bucket 135: 100% Sorting block of length 2680009 for bucket 135 (Using difference cover) bucket 153: 30% bucket 152: 30% bucket 161: 10% bucket 148: 40% bucket 151: 40% bucket 142: 50% bucket 136: 100% Sorting block of length 6883328 for bucket 136 (Using difference cover) bucket 138: 90% Sorting block time: 00:00:01 Returning block of 2680010 for bucket 135 bucket 137: 100% Sorting block of length 6827345 for bucket 137 (Using difference cover) Getting block 162 of 209 Reserving size (6957365) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 150: 40% bucket 143: 60% bucket 145: 50% bucket 144: 50% bucket 141: 70% bucket 154: 30% Sorting block time: 00:00:02 Returning block of 6883329 for bucket 136 bucket 139: 100% Sorting block of length 6319812 for bucket 139 (Using difference cover) Getting block 163 of 209 Reserving size (6957365) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: Sorting block time: 00:00:03 Returning block of 6827346 for bucket 137 bucket 146: 50% Getting block 164 of 209 Reserving size (6957365) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 147: 50% bucket 156: 30% bucket 160: 20% bucket 158: 30% bucket 157: 30% bucket 155: 30% bucket 140: 90% bucket 149: 50% bucket 153: 40% bucket 148: 50% bucket 152: 40% bucket 142: 60% bucket 138: 100% Sorting block of length 4052929 for bucket 138 (Using difference cover) bucket 159: 30% Sorting block time: 00:00:01 Returning block of 6319813 for bucket 139 Getting block 165 of 209 Reserving size (6957365) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 162: 10% bucket 161: 20% bucket 151: 50% bucket 143: 70% Sorting block time: 00:00:02 Returning block of 4052930 for bucket 138 Getting block 166 of 209 Reserving size (6957365) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 145: 60% bucket 150: 50% bucket 154: 40% bucket 146: 60% bucket 156: 40% bucket 147: 60% bucket 144: 60% bucket 141: 80% bucket 158: 40% bucket 157: 40% bucket 163: 10% bucket 164: 10% bucket 140: 100% Sorting block of length 1707163 for bucket 140 (Using difference cover) bucket 149: 60% bucket 160: 30% bucket 159: 40% Sorting block time: 00:00:00 Returning block of 1707164 for bucket 140 Getting block 167 of 209 Reserving size (6957365) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: bucket 165: 10% bucket 161: 30% bucket 151: 60% bucket 143: 80% bucket 155: 40% bucket 148: 60% bucket 153: 50% bucket 152: 50% bucket 142: 70% bucket 145: 70% bucket 162: 20% bucket 154: 50% bucket 156: 50% bucket 166: 10% bucket 150: 60% bucket 146: 70% bucket 147: 70% bucket 158: 50% bucket 157: 50% bucket 149: 70% bucket 144: 70% bucket 141: 90% bucket 159: 50% bucket 163: 20% bucket 165: 20% bucket 164: 20% bucket 160: 40% bucket 167: 10% bucket 151: 70% bucket 161: 40% bucket 143: 90% bucket 148: 70% bucket 153: 60% bucket 142: 80% bucket 155: 50% bucket 152: 60% bucket 162: 30% bucket 150: 70% bucket 145: 80% bucket 166: 20% bucket 144: 80% bucket 141: 100% Sorting block of length 6387124 for bucket 141 (Using difference cover) bucket 156: 60% bucket 163: 30% bucket 164: 30% bucket 160: 50% bucket 154: 60% bucket 147: 80% bucket 146: 80% bucket 167: 20% bucket 148: 80% bucket 153: 70% bucket 142: 90% bucket 152: 70% bucket 162: 40% bucket 155: 60% Sorting block time: 00:00:02 Returning block of 6387125 for bucket 141 bucket 158: 60% bucket 150: 80% Getting block 168 of 209 Reserving size (6957365) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 157: 60% bucket 149: 80% bucket 159: 60% bucket 166: 30% bucket 165: 30% bucket 151: 80% bucket 161: 50% bucket 143: 100% Sorting block of length 3330410 for bucket 143 (Using difference cover) bucket 144: 90% bucket 145: 90% Sorting block time: 00:00:01 Returning block of 3330411 for bucket 143 Getting block 169 of 209 Reserving size (6957365) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 156: 70% bucket 163: 40% bucket 164: 40% bucket 160: 60% bucket 147: 90% bucket 146: 90% bucket 154: 70% bucket 158: 70% bucket 167: 30% bucket 162: 50% bucket 157: 70% bucket 148: 90% bucket 142: 100% Sorting block of length 5882410 for bucket 142 (Using difference cover) bucket 149: 90% bucket 153: 80% bucket 152: 80% bucket 159: 70% bucket 150: 90% bucket 155: 70% bucket 165: 40% bucket 168: 10% bucket 151: 90% bucket 161: 60% Sorting block time: 00:00:02 Returning block of 5882411 for bucket 142 bucket 166: 40% Getting block 170 of 209 Reserving size (6957365) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 145: 100% Sorting block of length 1649691 for bucket 145 (Using difference cover) bucket 169: 10% bucket 156: 80% Sorting block time: 00:00:01 Returning block of 1649692 for bucket 145 Getting block 171 of 209 Reserving size (6957365) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 146: 100% Sorting block of length 2053489 for bucket 146 (Using difference cover) bucket 147: 100% Sorting block of length 5313993 for bucket 147 (Using difference cover) bucket 144: 100% Sorting block of length 6590323 for bucket 144 (Using difference cover) bucket 158: 80% bucket 154: 80% bucket 160: 70% bucket 162: 60% Sorting block time: 00:00:00 Returning block of 2053490 for bucket 146 Getting block 172 of 209 Reserving size (6957365) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: bucket 164: 50% bucket 163: 50% bucket 157: 80% bucket 149: 100% Sorting block of length 5355112 for bucket 149 (Using difference cover) bucket 167: 40% bucket 159: 80% Sorting block time: 00:00:02 Returning block of 5313994 for bucket 147 Getting block 173 of 209 Reserving size (6957365) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: bucket 148: 100% Sorting block of length 1811454 for bucket 148 (Using difference cover) bucket 153: 90% Sorting block time: 00:00:02 Returning block of 6590324 for bucket 144 bucket 152: 90% Getting block 174 of 209 Reserving size (6957365) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 150: 100% Sorting block of length 6567116 for bucket 150 (Using difference cover) bucket 165: 50% Sorting block time: 00:00:00 Returning block of 1811455 for bucket 148 Getting block 175 of 209 Reserving size (6957365) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: Sorting block time: 00:00:02 Returning block of 5355113 for bucket 149 bucket 168: 20% bucket 155: 80% Getting block 176 of 209 Reserving size (6957365) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: bucket 151: 100% Sorting block of length 6405845 for bucket 151 (Using difference cover) bucket 161: 70% bucket 166: 50% bucket 170: 10% bucket 162: 70% Sorting block time: 00:00:02 Returning block of 6567117 for bucket 150 bucket 154: 90% Getting block 177 of 209 Reserving size (6957365) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 164: 60% bucket 163: 60% Sorting block time: 00:00:02 Returning block of 6405846 for bucket 151 Getting block 178 of 209 Reserving size (6957365) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: bucket 167: 50% bucket 156: 90% bucket 169: 20% bucket 171: 10% bucket 153: 100% Sorting block of length 2647345 for bucket 153 (Using difference cover) bucket 174: 10% bucket 152: 100% Sorting block of length 5833695 for bucket 152 (Using difference cover) bucket 158: 90% bucket 160: 80% bucket 172: 10% Sorting block time: 00:00:01 Returning block of 2647346 for bucket 153 bucket 175: 10% Getting block 179 of 209 Reserving size (6957365) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 168: 30% bucket 157: 90% bucket 155: 90% bucket 159: 90% bucket 166: 60% bucket 170: 20% Sorting block time: 00:00:02 Returning block of 5833696 for bucket 152 bucket 173: 10% Getting block 180 of 209 Reserving size (6957365) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 165: 60% bucket 176: 10% bucket 161: 80% bucket 177: 10% bucket 162: 80% bucket 156: 100% Sorting block of length 6652533 for bucket 156 (Using difference cover) bucket 178: 10% bucket 169: 30% bucket 154: 100% Sorting block of length 5697009 for bucket 154 (Using difference cover) bucket 164: 70% bucket 163: 70% bucket 171: 20% bucket 158: 100% Sorting block of length 5786915 for bucket 158 (Using difference cover) bucket 160: 90% bucket 167: 60% bucket 172: 20% bucket 157: 100% Sorting block of length 2753444 for bucket 157 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6652534 for bucket 156 Getting block 181 of 209 Reserving size (6957365) 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 5697010 for bucket 154 Getting block 182 of 209 Reserving size (6957365) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 159: 100% Sorting block of length 4734846 for bucket 159 (Using difference cover) bucket 174: 20% Sorting block time: 00:00:01 Returning block of 2753445 for bucket 157 Getting block 183 of 209 Reserving size (6957365) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: bucket 165: 70% bucket 173: 20% bucket 176: 20% Sorting block time: 00:00:02 Returning block of 5786916 for bucket 158 bucket 168: 40% Getting block 184 of 209 Reserving size (6957365) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 161: 90% bucket 175: 20% bucket 179: 10% bucket 177: 20% Sorting block time: 00:00:02 Returning block of 4734847 for bucket 159 bucket 155: 100% Sorting block of length 1880613 for bucket 155 (Using difference cover) bucket 170: 30% bucket 166: 70% Getting block 185 of 209 Reserving size (6957365) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 178: 20% bucket 180: 10% bucket 169: 40% Sorting block time: 00:00:00 Returning block of 1880614 for bucket 155 Getting block 186 of 209 Reserving size (6957365) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: bucket 171: 30% bucket 160: 100% Sorting block of length 2530278 for bucket 160 (Using difference cover) bucket 162: 90% bucket 172: 30% Sorting block time: 00:00:01 Returning block of 2530279 for bucket 160 Getting block 187 of 209 Reserving size (6957365) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: bucket 164: 80% bucket 163: 80% bucket 181: 10% bucket 167: 70% bucket 165: 80% bucket 183: 10% bucket 176: 30% bucket 173: 30% bucket 184: 10% bucket 161: 100% Sorting block of length 5399806 for bucket 161 (Using difference cover) bucket 182: 10% bucket 174: 30% bucket 177: 30% bucket 185: 10% bucket 178: 30% bucket 168: 50% bucket 169: 50% bucket 175: 30% bucket 179: 20% bucket 166: 80% bucket 180: 20% bucket 170: 40% bucket 171: 40% bucket 186: 10% bucket 172: 40% bucket 162: 100% Sorting block of length 6197394 for bucket 162 (Using difference cover) Sorting block time: 00:00:02 Returning block of 5399807 for bucket 161 bucket 187: 10% bucket 181: 20% Getting block 188 of 209 Reserving size (6957365) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 165: 90% bucket 164: 90% bucket 183: 20% bucket 163: 90% bucket 184: 20% bucket 176: 40% bucket 167: 80% bucket 173: 40% Sorting block time: 00:00:02 Returning block of 6197395 for bucket 162 Getting block 189 of 209 Reserving size (6957365) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 185: 20% bucket 169: 60% bucket 178: 40% bucket 182: 20% bucket 174: 40% bucket 177: 40% bucket 170: 50% bucket 168: 60% bucket 175: 40% bucket 179: 30% bucket 171: 50% bucket 172: 50% bucket 180: 30% bucket 166: 90% bucket 181: 30% bucket 187: 20% bucket 188: 10% bucket 186: 20% bucket 165: 100% Sorting block of length 2571285 for bucket 165 (Using difference cover) bucket 183: 30% bucket 184: 30% bucket 176: 50% Sorting block time: 00:00:01 Returning block of 2571286 for bucket 165 bucket 173: 50% Getting block 190 of 209 Reserving size (6957365) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 185: 30% bucket 169: 70% bucket 164: 100% Sorting block of length 6360654 for bucket 164 (Using difference cover) bucket 167: 90% bucket 178: 50% bucket 163: 100% Sorting block of length 6023837 for bucket 163 (Using difference cover) bucket 189: 10% bucket 170: 60% bucket 182: 30% bucket 174: 50% bucket 171: 60% bucket 181: 40% bucket 177: 50% Sorting block time: 00:00:02 Returning block of 6360655 for bucket 164 bucket 172: 60% Sorting block time: 00:00:02 Returning block of 6023838 for bucket 163 Getting block 191 of 209 Reserving size (6957365) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: Getting block 192 of 209 Reserving size (6957365) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 187: 30% bucket 168: 70% bucket 175: 50% bucket 179: 40% bucket 184: 40% bucket 183: 40% bucket 180: 40% bucket 188: 20% bucket 176: 60% bucket 166: 100% Sorting block of length 5034342 for bucket 166 (Using difference cover) bucket 173: 60% bucket 169: 80% bucket 185: 40% bucket 190: 10% bucket 186: 30% bucket 178: 60% bucket 167: 100% Sorting block of length 4231823 for bucket 167 (Using difference cover) Sorting block time: 00:00:01 Returning block of 5034343 for bucket 166 Getting block 193 of 209 Reserving size (6957365) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: bucket 170: 70% Sorting block time: 00:00:01 Returning block of 4231824 for bucket 167 Getting block 194 of 209 Reserving size (6957365) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 181: 50% bucket 191: 10% bucket 172: 70% bucket 189: 20% bucket 187: 40% bucket 171: 70% bucket 182: 40% bucket 174: 60% bucket 184: 50% bucket 177: 60% bucket 183: 50% bucket 176: 70% bucket 192: 10% bucket 168: 80% bucket 173: 70% bucket 175: 60% bucket 169: 90% bucket 185: 50% bucket 179: 50% bucket 178: 70% bucket 180: 50% bucket 188: 30% bucket 170: 80% bucket 190: 20% bucket 186: 40% bucket 194: 10% bucket 181: 60% bucket 191: 20% bucket 193: 10% bucket 172: 80% bucket 187: 50% bucket 171: 80% bucket 184: 60% bucket 189: 30% bucket 183: 60% bucket 176: 80% bucket 182: 50% bucket 174: 70% bucket 173: 80% bucket 177: 70% bucket 169: 100% Sorting block of length 4810201 for bucket 169 (Using difference cover) bucket 185: 60% bucket 192: 20% bucket 178: 80% bucket 168: 90% bucket 175: 70% bucket 179: 60% bucket 180: 60% bucket 188: 40% bucket 170: 90% bucket 194: 20% bucket 190: 30% bucket 186: 50% bucket 181: 70% bucket 191: 30% bucket 172: 90% bucket 187: 60% bucket 193: 20% bucket 171: 90% bucket 184: 70% bucket 183: 70% bucket 176: 90% bucket 182: 60% bucket 189: 40% bucket 174: 80% bucket 177: 80% bucket 185: 70% bucket 173: 90% bucket 192: 30% bucket 178: 90% bucket 168: 100% Sorting block of length 6865946 for bucket 168 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4810202 for bucket 169 bucket 175: 80% bucket 180: 70% bucket 179: 70% Getting block 195 of 209 Reserving size (6957365) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 188: 50% bucket 170: 100% Sorting block of length 5400510 for bucket 170 (Using difference cover) bucket 181: 80% bucket 194: 30% bucket 186: 60% bucket 190: 40% bucket 191: 40% bucket 172: 100% Sorting block of length 6182008 for bucket 172 (Using difference cover) bucket 187: 70% bucket 193: 30% bucket 171: 100% Sorting block of length 3500102 for bucket 171 (Using difference cover) bucket 184: 80% bucket 183: 80% bucket 176: 100% Sorting block of length 6287261 for bucket 176 (Using difference cover) bucket 182: 70% bucket 174: 90% bucket 189: 50% bucket 185: 80% bucket 177: 90% bucket 173: 100% Sorting block of length 6430042 for bucket 173 (Using difference cover) bucket 192: 40% bucket 178: 100% Sorting block of length 6410267 for bucket 178 (Using difference cover) bucket 175: 90% bucket 180: 80% bucket 195: 10% bucket 179: 80% bucket 188: 60% bucket 181: 90% bucket 194: 40% bucket 186: 70% bucket 191: 50% Sorting block time: 00:00:02 Returning block of 6865947 for bucket 168 bucket 190: 50% Getting block 196 of 209 Reserving size (6957365) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 187: 80% bucket 193: 40% Sorting block time: 00:00:02 Returning block of 5400511 for bucket 170 Sorting block time: 00:00:02 Returning block of 3500103 for bucket 171 Getting block 197 of 209 Reserving size (6957365) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: Getting block 198 of 209 Reserving size (6957365) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 184: 90% Sorting block time: 00:00:02 Returning block of 6182009 for bucket 172 Getting block 199 of 209 Reserving size (6957365) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: bucket 182: 80% bucket 174: 100% Sorting block of length 3094265 for bucket 174 (Using difference cover) Sorting block time: 00:00:02 Returning block of 6287262 for bucket 176 bucket 189: 60% Getting block 200 of 209 Reserving size (6957365) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 177: 100% Sorting block of length 5386012 for bucket 177 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6430043 for bucket 173 Sorting block time: 00:00:02 Returning block of 6410268 for bucket 178 Getting block 201 of 209 Reserving size (6957365) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: Getting block 202 of 209 Reserving size (6957365) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 183: 90% bucket 192: 50% Sorting block time: 00:00:01 Returning block of 3094266 for bucket 174 Getting block 203 of 209 Reserving size (6957365) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: bucket 175: 100% Sorting block of length 6709966 for bucket 175 (Using difference cover) bucket 180: 90% bucket 179: 90% bucket 188: 70% bucket 185: 90% bucket 191: 60% bucket 186: 80% Sorting block time: 00:00:01 Returning block of 5386013 for bucket 177 bucket 195: 20% bucket 190: 60% bucket 196: 10% Getting block 204 of 209 Reserving size (6957365) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: bucket 193: 50% Sorting block time: 00:00:02 Returning block of 6709967 for bucket 175 Getting block 205 of 209 Reserving size (6957365) for bucket 205 Calculating Z arrays for bucket 205 Entering block accumulator loop for bucket 205: bucket 182: 90% bucket 189: 70% bucket 181: 100% Sorting block of length 3999598 for bucket 181 (Using difference cover) bucket 192: 60% bucket 194: 50% bucket 203: 10% bucket 180: 100% Sorting block of length 6823622 for bucket 180 (Using difference cover) bucket 188: 80% bucket 179: 100% Sorting block of length 4311011 for bucket 179 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3999599 for bucket 181 bucket 191: 70% Getting block 206 of 209 Reserving size (6957365) for bucket 206 Calculating Z arrays for bucket 206 Entering block accumulator loop for bucket 206: bucket 187: 90% bucket 186: 90% bucket 197: 10% bucket 184: 100% Sorting block of length 4362499 for bucket 184 (Using difference cover) bucket 198: 10% bucket 190: 70% bucket 204: 10% bucket 196: 20% bucket 199: 10% bucket 193: 60% Sorting block time: 00:00:02 Returning block of 4311012 for bucket 179 Getting block 207 of 209 Reserving size (6957365) for bucket 207 Calculating Z arrays for bucket 207 Entering block accumulator loop for bucket 207: bucket 200: 10% Sorting block time: 00:00:02 Returning block of 6823623 for bucket 180 bucket 202: 10% bucket 205: 10% Getting block 208 of 209 Reserving size (6957365) for bucket 208 Calculating Z arrays for bucket 208 Entering block accumulator loop for bucket 208: bucket 201: 10% bucket 182: 100% Sorting block of length 3799671 for bucket 182 (Using difference cover) bucket 183: 100% Sorting block of length 5969586 for bucket 183 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4362500 for bucket 184 Getting block 209 of 209 Reserving size (6957365) for bucket 209 Calculating Z arrays for bucket 209 Entering block accumulator loop for bucket 209: bucket 189: 80% bucket 185: 100% Sorting block of length 3135180 for bucket 185 (Using difference cover) bucket 192: 70% bucket 203: 20% bucket 188: 90% Sorting block time: 00:00:01 Returning block of 3135181 for bucket 185 bucket 191: 80% Sorting block time: 00:00:02 Returning block of 3799672 for bucket 182 bucket 195: 30% bucket 186: 100% Sorting block of length 4726967 for bucket 186 (Using difference cover) Sorting block time: 00:00:02 Returning block of 5969587 for bucket 183 bucket 190: 80% bucket 194: 60% bucket 204: 20% bucket 196: 30% bucket 193: 70% bucket 207: 10% Sorting block time: 00:00:02 Returning block of 4726968 for bucket 186 bucket 208: 10% bucket 209: 10% bucket 206: 10% bucket 187: 100% Sorting block of length 4799816 for bucket 187 (Using difference cover) bucket 205: 20% bucket 197: 20% bucket 198: 20% bucket 199: 20% bucket 189: 90% bucket 200: 20% bucket 192: 80% bucket 202: 20% bucket 201: 20% bucket 203: 30% Sorting block time: 00:00:02 Returning block of 4799817 for bucket 187 bucket 188: 100% Sorting block of length 4606490 for bucket 188 (Using difference cover) bucket 195: 40% bucket 191: 90% bucket 196: 40% bucket 204: 30% bucket 193: 80% Sorting block time: 00:00:02 Returning block of 4606491 for bucket 188 bucket 207: 20% bucket 205: 30% bucket 189: 100% Sorting block of length 5177582 for bucket 189 (Using difference cover) bucket 192: 90% bucket 209: 20% bucket 206: 20% bucket 203: 40% bucket 195: 50% bucket 190: 90% bucket 191: 100% Sorting block of length 1658375 for bucket 191 (Using difference cover) bucket 194: 70% Sorting block time: 00:00:01 Returning block of 5177583 for bucket 189 Sorting block time: 00:00:01 Returning block of 1658376 for bucket 191 bucket 196: 50% bucket 204: 40% bucket 208: 20% bucket 193: 90% bucket 207: 30% bucket 199: 30% bucket 205: 40% bucket 200: 30% bucket 197: 30% bucket 198: 30% bucket 201: 30% bucket 192: 100% Sorting block of length 5390340 for bucket 192 (Using difference cover) bucket 206: 30% bucket 202: 30% bucket 203: 50% bucket 195: 60% Sorting block time: 00:00:01 Returning block of 5390341 for bucket 192 bucket 196: 60% bucket 209: 30% bucket 204: 50% bucket 193: 100% Sorting block of length 5344923 for bucket 193 (Using difference cover) bucket 207: 40% bucket 205: 50% bucket 201: 40% bucket 203: 60% bucket 206: 40% bucket 195: 70% Sorting block time: 00:00:02 Returning block of 5344924 for bucket 193 bucket 197: 40% bucket 190: 100% Sorting block of length 5862242 for bucket 190 (Using difference cover) bucket 194: 80% bucket 196: 70% bucket 204: 60% bucket 207: 50% bucket 208: 30% bucket 205: 60% bucket 199: 40% bucket 200: 40% Sorting block time: 00:00:02 Returning block of 5862243 for bucket 190 bucket 209: 40% bucket 198: 40% bucket 203: 70% bucket 206: 50% bucket 195: 80% bucket 202: 40% bucket 197: 50% bucket 196: 80% bucket 204: 70% bucket 207: 60% bucket 201: 50% bucket 205: 70% bucket 208: 40% bucket 206: 60% bucket 203: 80% bucket 209: 50% bucket 195: 90% bucket 194: 90% bucket 196: 90% bucket 204: 80% bucket 198: 50% bucket 199: 50% bucket 207: 70% bucket 205: 80% bucket 200: 50% bucket 197: 60% bucket 202: 50% bucket 206: 70% bucket 208: 50% bucket 203: 90% bucket 201: 60% bucket 195: 100% Sorting block of length 1603204 for bucket 195 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1603205 for bucket 195 bucket 196: 100% Sorting block of length 6264504 for bucket 196 (Using difference cover) bucket 204: 90% bucket 207: 80% bucket 205: 90% bucket 209: 60% bucket 197: 70% bucket 206: 80% bucket 203: 100% Sorting block of length 4931696 for bucket 203 (Using difference cover) bucket 208: 60% bucket 194: 100% Sorting block of length 5687711 for bucket 194 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6264505 for bucket 196 bucket 198: 60% bucket 199: 60% bucket 204: 100% Sorting block of length 6645427 for bucket 204 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4931697 for bucket 203 bucket 207: 90% bucket 205: 100% Sorting block of length 6774400 for bucket 205 (Using difference cover) Sorting block time: 00:00:02 Returning block of 5687712 for bucket 194 bucket 200: 60% bucket 206: 90% bucket 197: 80% bucket 208: 70% bucket 209: 70% bucket 202: 60% Sorting block time: 00:00:02 Returning block of 6645428 for bucket 204 bucket 201: 70% Sorting block time: 00:00:02 Returning block of 6774401 for bucket 205 bucket 207: 100% Sorting block of length 5214851 for bucket 207 (Using difference cover) bucket 199: 70% bucket 206: 100% Sorting block of length 4135542 for bucket 206 (Using difference cover) bucket 209: 80% bucket 208: 80% bucket 198: 70% Sorting block time: 00:00:02 Returning block of 5214852 for bucket 207 bucket 197: 90% bucket 200: 70% bucket 202: 70% Sorting block time: 00:00:02 Returning block of 4135543 for bucket 206 bucket 201: 80% bucket 209: 90% bucket 199: 80% bucket 198: 80% bucket 208: 90% bucket 200: 80% bucket 202: 80% bucket 197: 100% Sorting block of length 2815947 for bucket 197 (Using difference cover) bucket 201: 90% bucket 209: 100% Sorting block of length 4274639 for bucket 209 (Using difference cover) bucket 199: 90% Sorting block time: 00:00:01 Returning block of 2815948 for bucket 197 bucket 198: 90% bucket 208: 100% Sorting block of length 4611639 for bucket 208 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4274640 for bucket 209 bucket 200: 90% bucket 202: 90% bucket 201: 100% Sorting block of length 3679407 for bucket 201 (Using difference cover) bucket 199: 100% Sorting block of length 1563451 for bucket 199 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4611640 for bucket 208 bucket 198: 100% Sorting block of length 6832184 for bucket 198 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1563452 for bucket 199 bucket 200: 100% Sorting block of length 5558901 for bucket 200 (Using difference cover) bucket 202: 100% Sorting block of length 6337037 for bucket 202 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3679408 for bucket 201 Sorting block time: 00:00:02 Returning block of 5558902 for bucket 200 Sorting block time: 00:00:02 Returning block of 6832185 for bucket 198 Sorting block time: 00:00:03 Returning block of 6337038 for bucket 202 Exited Ebwt loop fchr[A]: 0 fchr[C]: 329461670 fchr[G]: 329461670 fchr[T]: 519415916 fchr[$]: 1038966499 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 356457280 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 259741632 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 1038966499 bwtLen: 1038966500 sz: 259741625 bwtSz: 259741625 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 64935407 offsSz: 259741628 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 5411284 numLines: 5411284 ebwtTotLen: 346322176 ebwtTotSz: 346322176 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:07:01 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_10_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_10_s456_trimmed.fq to zr1394_10_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_10_s456_trimmed.fq to zr1394_10_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_10_s456_trimmed.fq (78221457 sequences in total) Input files are zr1394_10_s456_trimmed.fq_C_to_T.fastq and zr1394_10_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_10_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1108:2120_1:Y:0:TATCTT 4 * 0 0 * * 0 0 ATTAATGAGAATGATTTTTTTTTTA B//FF>> Writing bisulfite mapping results to zr1394_10_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_10_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far Processed 65000000 sequences so far Processed 66000000 sequences so far Processed 67000000 sequences so far Processed 68000000 sequences so far Processed 69000000 sequences so far Processed 70000000 sequences so far Processed 71000000 sequences so far Processed 72000000 sequences so far Processed 73000000 sequences so far Processed 74000000 sequences so far Processed 75000000 sequences so far Processed 76000000 sequences so far Processed 77000000 sequences so far Processed 78000000 sequences so far 78221457 reads; of these: 78221457 (100.00%) were unpaired; of these: 52563922 (67.20%) aligned 0 times 9871870 (12.62%) aligned exactly 1 time 15785665 (20.18%) aligned >1 times 32.80% overall alignment rate 78221457 reads; of these: 78221457 (100.00%) were unpaired; of these: 52432262 (67.03%) aligned 0 times 9817369 (12.55%) aligned exactly 1 time 15971826 (20.42%) aligned >1 times 32.97% overall alignment rate 78221457 reads; of these: 78221457 (100.00%) were unpaired; of these: 53214979 (68.03%) aligned 0 times 9440803 (12.07%) aligned exactly 1 time 15565675 (19.90%) aligned >1 times 31.97% overall alignment rate 78221457 reads; of these: 78221457 (100.00%) were unpaired; of these: 53297202 (68.14%) aligned 0 times 9468736 (12.11%) aligned exactly 1 time 15455519 (19.76%) aligned >1 times 31.86% overall alignment rate Processed 78221457 sequences in total Successfully deleted the temporary files zr1394_10_s456_trimmed.fq_C_to_T.fastq and zr1394_10_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 78221457 Number of alignments with a unique best hit from the different alignments: 25374001 Mapping efficiency: 32.4% Sequences with no alignments under any condition: 21899233 Sequences did not map uniquely: 30948223 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 6511929 ((converted) top strand) CT/GA: 6446118 ((converted) bottom strand) GA/CT: 6239306 (complementary to (converted) top strand) GA/GA: 6176648 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 159318003 Total methylated C's in CpG context: 24571414 Total methylated C's in CHG context: 738291 Total methylated C's in CHH context: 8532254 Total methylated C's in Unknown context: 7636 Total unmethylated C's in CpG context: 4429949 Total unmethylated C's in CHG context: 33811864 Total unmethylated C's in CHH context: 87234231 Total unmethylated C's in Unknown context: 52101 C methylated in CpG context: 84.7% C methylated in CHG context: 2.1% C methylated in CHH context: 8.9% C methylated in Unknown context (CN or CHN): 12.8% Bismark completed in 0d 1h 45m 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_11_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_11_s456_trimmed.fq to zr1394_11_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_11_s456_trimmed.fq to zr1394_11_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_11_s456_trimmed.fq (54458572 sequences in total) Input files are zr1394_11_s456_trimmed.fq_C_to_T.fastq and zr1394_11_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_11_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1243:2134_1:N:0:GGCTAC 4 * 0 0 * * 0 0 TATTGATATTATAATTATTTTTTTTTATAT >> Writing bisulfite mapping results to zr1394_11_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_11_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far 54458572 reads; of these: 54458572 (100.00%) were unpaired; of these: 38185466 (70.12%) aligned 0 times 5695447 (10.46%) aligned exactly 1 time 10577659 (19.42%) aligned >1 times 29.88% overall alignment rate 54458572 reads; of these: 54458572 (100.00%) were unpaired; of these: 38186441 (70.12%) aligned 0 times 5729407 (10.52%) aligned exactly 1 time 10542724 (19.36%) aligned >1 times 29.88% overall alignment rate 54458572 reads; of these: 54458572 (100.00%) were unpaired; of these: 35682783 (65.52%) aligned 0 times 6190440 (11.37%) aligned exactly 1 time 12585349 (23.11%) aligned >1 times 34.48% overall alignment rate 54458572 reads; of these: 54458572 (100.00%) were unpaired; of these: 35655180 (65.47%) aligned 0 times 6140747 (11.28%) aligned exactly 1 time 12662645 (23.25%) aligned >1 times 34.53% overall alignment rate Processed 54458572 sequences in total Successfully deleted the temporary files zr1394_11_s456_trimmed.fq_C_to_T.fastq and zr1394_11_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 54458572 Number of alignments with a unique best hit from the different alignments: 15624995 Mapping efficiency: 28.7% Sequences with no alignments under any condition: 16588302 Sequences did not map uniquely: 22245275 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3520857 ((converted) top strand) CT/GA: 3490103 ((converted) bottom strand) GA/CT: 4325599 (complementary to (converted) top strand) GA/GA: 4288436 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 100017389 Total methylated C's in CpG context: 17631307 Total methylated C's in CHG context: 489793 Total methylated C's in CHH context: 5187559 Total methylated C's in Unknown context: 4922 Total unmethylated C's in CpG context: 2899970 Total unmethylated C's in CHG context: 19768605 Total unmethylated C's in CHH context: 54040155 Total unmethylated C's in Unknown context: 34485 C methylated in CpG context: 85.9% C methylated in CHG context: 2.4% C methylated in CHH context: 8.8% C methylated in Unknown context (CN or CHN): 12.5% Bismark completed in 0d 1h 8m 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_12_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_12_s456_trimmed.fq to zr1394_12_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_12_s456_trimmed.fq to zr1394_12_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_12_s456_trimmed.fq (59459431 sequences in total) Input files are zr1394_12_s456_trimmed.fq_C_to_T.fastq and zr1394_12_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_12_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1130:2172_1:N:0:CTTGTA 4 * 0 0 * * 0 0 TTTTTTGGTTGGATGTAATAGATTATGATTG BFB/FF//FF////7/>> Writing bisulfite mapping results to zr1394_12_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_12_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:8728:78906_1:N:0:CTTGTA Contig6 90850008 Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far 59459431 reads; of these: 59459431 (100.00%) were unpaired; of these: 41773412 (70.26%) aligned 0 times 7284867 (12.25%) aligned exactly 1 time 10401152 (17.49%) aligned >1 times 29.74% overall alignment rate 59459431 reads; of these: 59459431 (100.00%) were unpaired; of these: 38972688 (65.55%) aligned 0 times 7870016 (13.24%) aligned exactly 1 time 12616727 (21.22%) aligned >1 times 34.45% overall alignment rate 59459431 reads; of these: 59459431 (100.00%) were unpaired; of these: 41857706 (70.40%) aligned 0 times 7253441 (12.20%) aligned exactly 1 time 10348284 (17.40%) aligned >1 times 29.60% overall alignment rate 59459431 reads; of these: 59459431 (100.00%) were unpaired; of these: 39026504 (65.64%) aligned 0 times 7846267 (13.20%) aligned exactly 1 time 12586660 (21.17%) aligned >1 times 34.36% overall alignment rate Processed 59459431 sequences in total Successfully deleted the temporary files zr1394_12_s456_trimmed.fq_C_to_T.fastq and zr1394_12_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 59459431 Number of alignments with a unique best hit from the different alignments: 20027644 Mapping efficiency: 33.7% Sequences with no alignments under any condition: 17427831 Sequences did not map uniquely: 22003956 Sequences which were discarded because genomic sequence could not be extracted: 1 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 4488497 ((converted) top strand) CT/GA: 4455831 ((converted) bottom strand) GA/CT: 5561933 (complementary to (converted) top strand) GA/GA: 5521382 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 119680665 Total methylated C's in CpG context: 13746910 Total methylated C's in CHG context: 459821 Total methylated C's in CHH context: 6669855 Total methylated C's in Unknown context: 4804 Total unmethylated C's in CpG context: 3405203 Total unmethylated C's in CHG context: 23855059 Total unmethylated C's in CHH context: 71543817 Total unmethylated C's in Unknown context: 33356 C methylated in CpG context: 80.1% C methylated in CHG context: 1.9% C methylated in CHH context: 8.5% C methylated in Unknown context (CN or CHN): 12.6% 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_13_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_13_s456_trimmed.fq to zr1394_13_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_13_s456_trimmed.fq to zr1394_13_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_13_s456_trimmed.fq (64352550 sequences in total) Input files are zr1394_13_s456_trimmed.fq_C_to_T.fastq and zr1394_13_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_13_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1235:2169_1:N:0:AGTCAA 0 Contig3_CT_converted 68077324 0 31M * 0 0 GGTAAGTTTTGTTTTATTAATATGTTGTTGT FBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:8A22 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from zr1394_13_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1235:2169_1:N:0:AGTCAA 16 Contig4_GA_converted 136330822 1 31M * 0 0 ACAACAACATATTAATAAAACAAAACTTACC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFBF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:31 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from zr1394_13_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1235:2169_1:N:0:AGTCAA 4 * 0 0 * * 0 0 AATAAATTTTATTTTATTAATATATCATCAC FBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from zr1394_13_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1235:2169_1:N:0:AGTCAA 4 * 0 0 * * 0 0 AATAAATTTTATTTTATTAATATATCATCAC FBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to zr1394_13_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_13_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far 6435255064352550 reads; of these: reads; of these: 6435255064352550 ( (100.00100.00%%) were unpaired; of these:) were unpaired; of these: 4492455741743877 ( (69.8164.87%%) aligned 0 times) aligned 0 times 71590307778385 ( (11.1212.09%%) aligned exactly 1 time) aligned exactly 1 time 1226896314830288 ( (19.07%) aligned >1 times 30.19% overall alignment rate 23.05%) aligned >1 times 35.13% overall alignment rate 64352550 reads; of these: 64352550 (100.00%) were unpaired; of these: 41679847 (64.77%) aligned 0 times 7759060 (12.06%) aligned exactly 1 time 14913643 (23.17%) aligned >1 times 35.23% overall alignment rate 64352550 reads; of these: 64352550 (100.00%) were unpaired; of these: 45011249 (69.94%) aligned 0 times 7167691 (11.14%) aligned exactly 1 time 12173610 (18.92%) aligned >1 times 30.06% overall alignment rate Processed 64352550 sequences in total Successfully deleted the temporary files zr1394_13_s456_trimmed.fq_C_to_T.fastq and zr1394_13_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 64352550 Number of alignments with a unique best hit from the different alignments: 19626793 Mapping efficiency: 30.5% Sequences with no alignments under any condition: 18775282 Sequences did not map uniquely: 25950475 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 4395883 ((converted) top strand) CT/GA: 4355123 ((converted) bottom strand) GA/CT: 5461739 (complementary to (converted) top strand) GA/GA: 5414048 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 123096958 Total methylated C's in CpG context: 19042523 Total methylated C's in CHG context: 554503 Total methylated C's in CHH context: 6406969 Total methylated C's in Unknown context: 5721 Total unmethylated C's in CpG context: 3213173 Total unmethylated C's in CHG context: 24745143 Total unmethylated C's in CHH context: 69134647 Total unmethylated C's in Unknown context: 38192 C methylated in CpG context: 85.6% C methylated in CHG context: 2.2% C methylated in CHH context: 8.5% C methylated in Unknown context (CN or CHN): 13.0% Bismark completed in 0d 1h 25m 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_14_s456_trimmed.fq to zr1394_14_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_14_s456_trimmed.fq to zr1394_14_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_14_s456_trimmed.fq (87834637 sequences in total) Input files are zr1394_14_s456_trimmed.fq_C_to_T.fastq and zr1394_14_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_14_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1225:2220_1:N:0:AGTTCC 4 * 0 0 * * 0 0 TTATTTTTAAATTAAATTTATTTATTTTA FF>> Writing bisulfite mapping results to zr1394_14_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far Processed 65000000 sequences so far Processed 66000000 sequences so far Processed 67000000 sequences so far Processed 68000000 sequences so far Processed 69000000 sequences so far Processed 70000000 sequences so far Processed 71000000 sequences so far Processed 72000000 sequences so far Processed 73000000 sequences so far Processed 74000000 sequences so far Processed 75000000 sequences so far Processed 76000000 sequences so far Processed 77000000 sequences so far Processed 78000000 sequences so far Processed 79000000 sequences so far Processed 80000000 sequences so far Processed 81000000 sequences so far Processed 82000000 sequences so far Processed 83000000 sequences so far Processed 84000000 sequences so far Processed 85000000 sequences so far Processed 86000000 sequences so far Processed 87000000 sequences so far 87834637 reads; of these: 87834637 (100.00%) were unpaired; of these: 61287482 (69.78%) aligned 0 times 9359757 (10.66%) aligned exactly 1 time 17187398 (19.57%) aligned >1 times 30.22% overall alignment rate 87834637 reads; of these: 87834637 (100.00%) were unpaired; of these: 61219299 (69.70%) aligned 0 times 9333582 (10.63%) aligned exactly 1 time 17281756 (19.68%) aligned >1 times 30.30% overall alignment rate 87834637 reads; of these: 87834637 (100.00%) were unpaired; of these: 57199309 (65.12%) aligned 0 times 10057749 (11.45%) aligned exactly 1 time 20577579 (23.43%) aligned >1 times 34.88% overall alignment rate 87834637 reads; of these: 87834637 (100.00%) were unpaired; of these: 57257594 (65.19%) aligned 0 times 10094865 (11.49%) aligned exactly 1 time 20482178 (23.32%) aligned >1 times 34.81% overall alignment rate Processed 87834637 sequences in total Successfully deleted the temporary files zr1394_14_s456_trimmed.fq_C_to_T.fastq and zr1394_14_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 87834637 Number of alignments with a unique best hit from the different alignments: 25416779 Mapping efficiency: 28.9% Sequences with no alignments under any condition: 26593175 Sequences did not map uniquely: 35824683 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 5706998 ((converted) top strand) CT/GA: 5681196 ((converted) bottom strand) GA/CT: 7036812 (complementary to (converted) top strand) GA/GA: 6991773 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 157858861 Total methylated C's in CpG context: 24048953 Total methylated C's in CHG context: 699575 Total methylated C's in CHH context: 8140563 Total methylated C's in Unknown context: 7073 Total unmethylated C's in CpG context: 4179384 Total unmethylated C's in CHG context: 29973809 Total unmethylated C's in CHH context: 90816577 Total unmethylated C's in Unknown context: 50756 C methylated in CpG context: 85.2% C methylated in CHG context: 2.3% C methylated in CHH context: 8.2% C methylated in Unknown context (CN or CHN): 12.2% Bismark completed in 0d 1h 56m 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_15_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_15_s456_trimmed.fq to zr1394_15_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_15_s456_trimmed.fq to zr1394_15_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_15_s456_trimmed.fq (67984205 sequences in total) Input files are zr1394_15_s456_trimmed.fq_C_to_T.fastq and zr1394_15_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_15_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1117:2111_1:Y:0:ATGNCA 0 Contig6_CT_converted 13712092 0 31M * 0 0 TAATGGAGTGTAATTTTATTTTTAATTTTGT />> Writing bisulfite mapping results to zr1394_15_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_15_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far Processed 65000000 sequences so far Processed 66000000 sequences so far Processed 67000000 sequences so far 67984205 reads; of these: 67984205 (100.00%) were unpaired; of these: 44501965 (65.46%) aligned 0 times 7825498 (11.51%) aligned exactly 1 time 15656742 (23.03%) aligned >1 times 34.54% overall alignment rate 67984205 reads; of these: 67984205 (100.00%) were unpaired; of these: 44545641 (65.52%) aligned 0 times 7876884 (11.59%) aligned exactly 1 time 15561680 (22.89%) aligned >1 times 34.48% overall alignment rate 67984205 reads; of these: 67984205 (100.00%) were unpaired; of these: 47610413 (70.03%) aligned 0 times 7309126 (10.75%) aligned exactly 1 time 13064666 (19.22%) aligned >1 times 29.97% overall alignment rate 67984205 reads; of these: 67984205 (100.00%) were unpaired; of these: 47554676 (69.95%) aligned 0 times 7281314 (10.71%) aligned exactly 1 time 13148215 (19.34%) aligned >1 times 30.05% overall alignment rate Processed 67984205 sequences in total Successfully deleted the temporary files zr1394_15_s456_trimmed.fq_C_to_T.fastq and zr1394_15_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 67984205 Number of alignments with a unique best hit from the different alignments: 19910397 Mapping efficiency: 29.3% Sequences with no alignments under any condition: 20663417 Sequences did not map uniquely: 27410391 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 4492226 ((converted) top strand) CT/GA: 4462783 ((converted) bottom strand) GA/CT: 5501159 (complementary to (converted) top strand) GA/GA: 5454229 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 126130939 Total methylated C's in CpG context: 21339729 Total methylated C's in CHG context: 602762 Total methylated C's in CHH context: 6674685 Total methylated C's in Unknown context: 6246 Total unmethylated C's in CpG context: 3060010 Total unmethylated C's in CHG context: 25313525 Total unmethylated C's in CHH context: 69140228 Total unmethylated C's in Unknown context: 42456 C methylated in CpG context: 87.5% C methylated in CHG context: 2.3% C methylated in CHH context: 8.8% C methylated in Unknown context (CN or CHN): 12.8% 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_16_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_16_s456_trimmed.fq to zr1394_16_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_16_s456_trimmed.fq to zr1394_16_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_16_s456_trimmed.fq (74531056 sequences in total) Input files are zr1394_16_s456_trimmed.fq_C_to_T.fastq and zr1394_16_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_16_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1095:2123_1:Y:0:NCGTCC 4 * 0 0 * * 0 0 TATATTAAAAATTAATTTTTAATATTTGTGT FFBBFFFFFFFF/FFFF/FFB/FFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from zr1394_16_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1095:2123_1:Y:0:NCGTCC 4 * 0 0 * * 0 0 TATATTAAAAATTAATTTTTAATATTTGTGT FFBBFFFFFFFF/FFFF/FFB/FFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from zr1394_16_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1095:2123_1:Y:0:NCGTCC 4 * 0 0 * * 0 0 TACATTAAAAATCAATTCCCAATACTCACAC FFBBFFFFFFFF/FFFF/FFB/FFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from zr1394_16_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1095:2123_1:Y:0:NCGTCC 4 * 0 0 * * 0 0 TACATTAAAAATCAATTCCCAATACTCACAC FFBBFFFFFFFF/FFFF/FFB/FFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to zr1394_16_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_16_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2103:17898:79304_1:N:0:CCGTCC Contig10 50401263 Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far Processed 65000000 sequences so far Processed 66000000 sequences so far Processed 67000000 sequences so far Processed 68000000 sequences so far Processed 69000000 sequences so far Processed 70000000 sequences so far Processed 71000000 sequences so far Processed 72000000 sequences so far Processed 73000000 sequences so far Processed 74000000 sequences so far 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 49144714 (65.94%) aligned 0 times 8389685 (11.26%) aligned exactly 1 time 16996657 (22.80%) aligned >1 times 34.06% overall alignment rate 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 49123429 (65.91%) aligned 0 times 8346763 (11.20%) aligned exactly 1 time 17060864 (22.89%) aligned >1 times 34.09% overall alignment rate 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 51775113 (69.47%) aligned 0 times 7887497 (10.58%) aligned exactly 1 time 14868446 (19.95%) aligned >1 times 30.53% overall alignment rate 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 51814374 (69.52%) aligned 0 times 7915732 (10.62%) aligned exactly 1 time 14800950 (19.86%) aligned >1 times 30.48% overall alignment rate Processed 74531056 sequences in total Successfully deleted the temporary files zr1394_16_s456_trimmed.fq_C_to_T.fastq and zr1394_16_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 74531056 Number of alignments with a unique best hit from the different alignments: 21286993 Mapping efficiency: 28.6% Sequences with no alignments under any condition: 22899250 Sequences did not map uniquely: 30344813 Sequences which were discarded because genomic sequence could not be extracted: 1 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 4885328 ((converted) top strand) CT/GA: 4850825 ((converted) bottom strand) GA/CT: 5798212 (complementary to (converted) top strand) GA/GA: 5752627 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 133884872 Total methylated C's in CpG context: 22055874 Total methylated C's in CHG context: 631312 Total methylated C's in CHH context: 7117972 Total methylated C's in Unknown context: 6682 Total unmethylated C's in CpG context: 3714505 Total unmethylated C's in CHG context: 25955078 Total unmethylated C's in CHH context: 74410131 Total unmethylated C's in Unknown context: 43671 C methylated in CpG context: 85.6% C methylated in CHG context: 2.4% C methylated in CHH context: 8.7% C methylated in Unknown context (CN or CHN): 13.3% Bismark completed in 0d 1h 35m 44s ==================== 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_17_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_17_s456_trimmed.fq to zr1394_17_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_17_s456_trimmed.fq to zr1394_17_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_17_s456_trimmed.fq (42070546 sequences in total) Input files are zr1394_17_s456_trimmed.fq_C_to_T.fastq and zr1394_17_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_17_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1337:2117_1:Y:0:GTCCGC 4 * 0 0 * * 0 0 AATAATTAAATATTTTTTATTAATTAATTA >> Writing bisulfite mapping results to zr1394_17_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_17_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 29363576 (69.80%) aligned 0 times 4787305 (11.38%) aligned exactly 1 time 7919665 (18.82%) aligned >1 times 30.20% overall alignment rate 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 27432316 (65.21%) aligned 0 times 5050709 (12.01%) aligned exactly 1 time 9587521 (22.79%) aligned >1 times 34.79% overall alignment rate 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 29313070 (69.68%) aligned 0 times 4761957 (11.32%) aligned exactly 1 time 7995519 (19.01%) aligned >1 times 30.32% overall alignment rate 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 27477447 (65.31%) aligned 0 times 5088716 (12.10%) aligned exactly 1 time 9504383 (22.59%) aligned >1 times 34.69% overall alignment rate Processed 42070546 sequences in total Successfully deleted the temporary files zr1394_17_s456_trimmed.fq_C_to_T.fastq and zr1394_17_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 42070546 Number of alignments with a unique best hit from the different alignments: 12831686 Mapping efficiency: 30.5% Sequences with no alignments under any condition: 12357075 Sequences did not map uniquely: 16881785 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2921720 ((converted) top strand) CT/GA: 2901018 ((converted) bottom strand) GA/CT: 3516819 (complementary to (converted) top strand) GA/GA: 3492129 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 79974402 Total methylated C's in CpG context: 12811467 Total methylated C's in CHG context: 384407 Total methylated C's in CHH context: 4482631 Total methylated C's in Unknown context: 3769 Total unmethylated C's in CpG context: 2034144 Total unmethylated C's in CHG context: 16655326 Total unmethylated C's in CHH context: 43606427 Total unmethylated C's in Unknown context: 25194 C methylated in CpG context: 86.3% C methylated in CHG context: 2.3% C methylated in CHH context: 9.3% C methylated in Unknown context (CN or CHN): 13.0% Bismark completed in 0d 0h 53m 39s ==================== 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_18_s456_trimmed.fq to zr1394_18_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_18_s456_trimmed.fq to zr1394_18_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_18_s456_trimmed.fq (55048106 sequences in total) Input files are zr1394_18_s456_trimmed.fq_C_to_T.fastq and zr1394_18_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_18_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1154:2201_1:N:0:GTGAAA 4 * 0 0 * * 0 0 ATAGTAGGTTAGTTAGTTGAGTTATGTT FFFBFFB/<>> Writing bisulfite mapping results to zr1394_18_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far 55048106 reads; of these: 55048106 (100.00%) were unpaired; of these: 35394899 (64.30%) aligned 0 times 7158644 (13.00%) aligned exactly 1 time 12494563 (22.70%) aligned >1 times 35.70% overall alignment rate 55048106 reads; of these: 55048106 (100.00%) were unpaired; of these: 38713165 (70.33%) aligned 0 times 6531301 (11.86%) aligned exactly 1 time 9803640 (17.81%) aligned >1 times 29.67% overall alignment rate 55048106 reads; of these: 55048106 (100.00%) were unpaired; of these: 38786188 (70.46%) aligned 0 times 6528553 (11.86%) aligned exactly 1 time 9733365 (17.68%) aligned >1 times 29.54% overall alignment rate 55048106 reads; of these: 55048106 (100.00%) were unpaired; of these: 35447712 (64.39%) aligned 0 times 7161164 (13.01%) aligned exactly 1 time 12439230 (22.60%) aligned >1 times 35.61% overall alignment rate Processed 55048106 sequences in total Successfully deleted the temporary files zr1394_18_s456_trimmed.fq_C_to_T.fastq and zr1394_18_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 55048106 Number of alignments with a unique best hit from the different alignments: 18068736 Mapping efficiency: 32.8% Sequences with no alignments under any condition: 15701339 Sequences did not map uniquely: 21278031 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3964570 ((converted) top strand) CT/GA: 3939560 ((converted) bottom strand) GA/CT: 5099608 (complementary to (converted) top strand) GA/GA: 5064998 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 109172180 Total methylated C's in CpG context: 13950028 Total methylated C's in CHG context: 447236 Total methylated C's in CHH context: 5912338 Total methylated C's in Unknown context: 4134 Total unmethylated C's in CpG context: 2826959 Total unmethylated C's in CHG context: 22196207 Total unmethylated C's in CHH context: 63839412 Total unmethylated C's in Unknown context: 30681 C methylated in CpG context: 83.1% C methylated in CHG context: 2.0% C methylated in CHH context: 8.5% C methylated in Unknown context (CN or CHN): 11.9% Bismark completed in 0d 1h 12m 53s ==================== 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_1_s456_trimmed.fq to zr1394_1_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_1_s456_trimmed.fq to zr1394_1_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_1_s456_trimmed.fq (46792286 sequences in total) Input files are zr1394_1_s456_trimmed.fq_C_to_T.fastq and zr1394_1_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_1_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1447:2175_1:N:0:ATCACG 0 Contig13_CT_converted 22707643 1 31M * 0 0 TAAAAAGATTAAAGTTTAAGATAGATAGATT FFFFFFFFFFFFFFFFFFFFBFFFFFFFB>> Writing bisulfite mapping results to zr1394_1_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:1329:15641_1:N:0:ATCACG Contig6 2 Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far 46792286 reads; of these: 46792286 (100.00%) were unpaired; of these: 32847683 (70.20%) aligned 0 times 5370414 (11.48%) aligned exactly 1 time 8574189 (18.32%) aligned >1 times 29.80% overall alignment rate 46792286 reads; of these: 46792286 (100.00%) were unpaired; of these: 30700767 (65.61%) aligned 0 times 5730092 (12.25%) aligned exactly 1 time 10361427 (22.14%) aligned >1 times 34.39% overall alignment rate 46792286 reads; of these: 46792286 (100.00%) were unpaired; of these: 32784387 (70.06%) aligned 0 times 5378622 (11.49%) aligned exactly 1 time 8629277 (18.44%) aligned >1 times 29.94% overall alignment rate 46792286 reads; of these: 46792286 (100.00%) were unpaired; of these: 30739055 (65.69%) aligned 0 times 5733184 (12.25%) aligned exactly 1 time 10320047 (22.06%) aligned >1 times 34.31% overall alignment rate Processed 46792286 sequences in total Successfully deleted the temporary files zr1394_1_s456_trimmed.fq_C_to_T.fastq and zr1394_1_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 46792286 Number of alignments with a unique best hit from the different alignments: 14534760 Mapping efficiency: 31.1% Sequences with no alignments under any condition: 14155170 Sequences did not map uniquely: 18102356 Sequences which were discarded because genomic sequence could not be extracted: 1 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3291229 ((converted) top strand) CT/GA: 3266810 ((converted) bottom strand) GA/CT: 4005984 (complementary to (converted) top strand) GA/GA: 3970736 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 88484060 Total methylated C's in CpG context: 11703467 Total methylated C's in CHG context: 417556 Total methylated C's in CHH context: 5009940 Total methylated C's in Unknown context: 3647 Total unmethylated C's in CpG context: 2470410 Total unmethylated C's in CHG context: 17414271 Total unmethylated C's in CHH context: 51468416 Total unmethylated C's in Unknown context: 25966 C methylated in CpG context: 82.6% C methylated in CHG context: 2.3% C methylated in CHH context: 8.9% C methylated in Unknown context (CN or CHN): 12.3% Bismark completed in 0d 1h 3m 28s ==================== 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_2_s456_trimmed.fq to zr1394_2_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_2_s456_trimmed.fq to zr1394_2_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_2_s456_trimmed.fq (46105140 sequences in total) Input files are zr1394_2_s456_trimmed.fq_C_to_T.fastq and zr1394_2_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_2_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1359:2236_1:N:0:CGATGT 4 * 0 0 * * 0 0 AATGTAATGATGTTAAATATGTATTAGAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from zr1394_2_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1359:2236_1:N:0:CGATGT 16 Contig6_GA_converted 53569013 0 31M * 0 0 ATTTCTAATACATATTTAACATCATTACATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:23T7 YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from zr1394_2_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1359:2236_1:N:0:CGATGT 4 * 0 0 * * 0 0 AATATAATAATATTAAATACATATTAAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from zr1394_2_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1359:2236_1:N:0:CGATGT 4 * 0 0 * * 0 0 AATATAATAATATTAAATACATATTAAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to zr1394_2_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far 46105140 reads; of these: 46105140 (100.00%) were unpaired; of these: 32691426 (70.91%) aligned 0 times 5400491 (11.71%) aligned exactly 1 time 8013223 (17.38%) aligned >1 times 29.09% overall alignment rate 46105140 reads; of these: 46105140 (100.00%) were unpaired; of these: 30410371 (65.96%) aligned 0 times 5831099 (12.65%) aligned exactly 1 time 9863670 (21.39%) aligned >1 times 34.04% overall alignment rate 46105140 reads; of these: 46105140 (100.00%) were unpaired; of these: 32646165 (70.81%) aligned 0 times 5405460 (11.72%) aligned exactly 1 time 8053515 (17.47%) aligned >1 times 29.19% overall alignment rate 46105140 reads; of these: 46105140 (100.00%) were unpaired; of these: 30369007 (65.87%) aligned 0 times 5827876 (12.64%) aligned exactly 1 time 9908257 (21.49%) aligned >1 times 34.13% overall alignment rate Processed 46105140 sequences in total Successfully deleted the temporary files zr1394_2_s456_trimmed.fq_C_to_T.fastq and zr1394_2_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 46105140 Number of alignments with a unique best hit from the different alignments: 14822810 Mapping efficiency: 32.2% Sequences with no alignments under any condition: 14100920 Sequences did not map uniquely: 17181410 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3308195 ((converted) top strand) CT/GA: 3289743 ((converted) bottom strand) GA/CT: 4126694 (complementary to (converted) top strand) GA/GA: 4098178 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 89520561 Total methylated C's in CpG context: 11404907 Total methylated C's in CHG context: 408791 Total methylated C's in CHH context: 5222368 Total methylated C's in Unknown context: 3817 Total unmethylated C's in CpG context: 2330389 Total unmethylated C's in CHG context: 17926332 Total unmethylated C's in CHH context: 52227774 Total unmethylated C's in Unknown context: 25383 C methylated in CpG context: 83.0% C methylated in CHG context: 2.2% C methylated in CHH context: 9.1% C methylated in Unknown context (CN or CHN): 13.1% Bismark completed in 0d 1h 2m 15s ==================== 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_3_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_3_s456_trimmed.fq to zr1394_3_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_3_s456_trimmed.fq to zr1394_3_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_3_s456_trimmed.fq (48376729 sequences in total) Input files are zr1394_3_s456_trimmed.fq_C_to_T.fastq and zr1394_3_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_3_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1217:2194_1:N:0:TTAGGC 4 * 0 0 * * 0 0 TTAATTTTTTTAAAATATTTTATTTTATTTA FFF>> Writing bisulfite mapping results to zr1394_3_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_3_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 31835721 (65.81%) aligned 0 times 5861396 (12.12%) aligned exactly 1 time 10679612 (22.08%) aligned >1 times 34.19% overall alignment rate 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 31795035 (65.72%) aligned 0 times 5858036 (12.11%) aligned exactly 1 time 10723658 (22.17%) aligned >1 times 34.28% overall alignment rate 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 34150844 (70.59%) aligned 0 times 5461471 (11.29%) aligned exactly 1 time 8764414 (18.12%) aligned >1 times 29.41% overall alignment rate 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 34107279 (70.50%) aligned 0 times 5462811 (11.29%) aligned exactly 1 time 8806639 (18.20%) aligned >1 times 29.50% overall alignment rate Processed 48376729 sequences in total Successfully deleted the temporary files zr1394_3_s456_trimmed.fq_C_to_T.fastq and zr1394_3_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 48376729 Number of alignments with a unique best hit from the different alignments: 14759690 Mapping efficiency: 30.5% Sequences with no alignments under any condition: 14949228 Sequences did not map uniquely: 18667811 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3305606 ((converted) top strand) CT/GA: 3281671 ((converted) bottom strand) GA/CT: 4103783 (complementary to (converted) top strand) GA/GA: 4068630 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 89218342 Total methylated C's in CpG context: 11414576 Total methylated C's in CHG context: 405883 Total methylated C's in CHH context: 5151062 Total methylated C's in Unknown context: 3929 Total unmethylated C's in CpG context: 2383288 Total unmethylated C's in CHG context: 17125947 Total unmethylated C's in CHH context: 52737586 Total unmethylated C's in Unknown context: 27879 C methylated in CpG context: 82.7% C methylated in CHG context: 2.3% C methylated in CHH context: 8.9% C methylated in Unknown context (CN or CHN): 12.4% Bismark completed in 0d 1h 5m 25s ==================== 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_4_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_4_s456_trimmed.fq to zr1394_4_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_4_s456_trimmed.fq to zr1394_4_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_4_s456_trimmed.fq (44905078 sequences in total) Input files are zr1394_4_s456_trimmed.fq_C_to_T.fastq and zr1394_4_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_4_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1202:2117_1:N:0:TGACCA 4 * 0 0 * * 0 0 AAATATTATTTTTGTTTTTTTGATTGAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFB>> Writing bisulfite mapping results to zr1394_4_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_4_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far 44905078 reads; of these: 44905078 (100.00%) were unpaired; of these: 29455538 (65.60%) aligned 0 times 5473122 (12.19%) aligned exactly 1 time 9976418 (22.22%) aligned >1 times 34.40% overall alignment rate 44905078 reads; of these: 44905078 (100.00%) were unpaired; of these: 29495664 (65.68%) aligned 0 times 5494780 (12.24%) aligned exactly 1 time 9914634 (22.08%) aligned >1 times 34.32% overall alignment rate 44905078 reads; of these: 44905078 (100.00%) were unpaired; of these: 31717089 (70.63%) aligned 0 times 5076460 (11.30%) aligned exactly 1 time 8111529 (18.06%) aligned >1 times 29.37% overall alignment rate 44905078 reads; of these: 44905078 (100.00%) were unpaired; of these: 31765607 (70.74%) aligned 0 times 5076670 (11.31%) aligned exactly 1 time 8062801 (17.96%) aligned >1 times 29.26% overall alignment rate Processed 44905078 sequences in total Successfully deleted the temporary files zr1394_4_s456_trimmed.fq_C_to_T.fastq and zr1394_4_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 44905078 Number of alignments with a unique best hit from the different alignments: 13872301 Mapping efficiency: 30.9% Sequences with no alignments under any condition: 13715942 Sequences did not map uniquely: 17316835 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3093739 ((converted) top strand) CT/GA: 3070130 ((converted) bottom strand) GA/CT: 3864472 (complementary to (converted) top strand) GA/GA: 3843960 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 85006558 Total methylated C's in CpG context: 11729361 Total methylated C's in CHG context: 405370 Total methylated C's in CHH context: 4793316 Total methylated C's in Unknown context: 3754 Total unmethylated C's in CpG context: 1940399 Total unmethylated C's in CHG context: 16871129 Total unmethylated C's in CHH context: 49266983 Total unmethylated C's in Unknown context: 25310 C methylated in CpG context: 85.8% C methylated in CHG context: 2.3% C methylated in CHH context: 8.9% C methylated in Unknown context (CN or CHN): 12.9% Bismark completed in 0d 0h 59m 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_5_s456_trimmed.fq to zr1394_5_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_5_s456_trimmed.fq to zr1394_5_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_5_s456_trimmed.fq (47401736 sequences in total) Input files are zr1394_5_s456_trimmed.fq_C_to_T.fastq and zr1394_5_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_5_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1173:2158_1:N:0:ACAGTG 4 * 0 0 * * 0 0 ATATTAAATATTATAAATTTATTATATATT B/FF/FFFFFFFF>> Writing bisulfite mapping results to zr1394_5_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 31216522 (65.86%) aligned 0 times 6203562 (13.09%) aligned exactly 1 time 9981652 (21.06%) aligned >1 times 34.14% overall alignment rate 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 33284737 (70.22%) aligned 0 times 5845859 (12.33%) aligned exactly 1 time 8271140 (17.45%) aligned >1 times 29.78% overall alignment rate 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 33237319 (70.12%) aligned 0 times 5861390 (12.37%) aligned exactly 1 time 8303027 (17.52%) aligned >1 times 29.88% overall alignment rate 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 31261639 (65.95%) aligned 0 times 6186188 (13.05%) aligned exactly 1 time 9953909 (21.00%) aligned >1 times 34.05% overall alignment rate Processed 47401736 sequences in total Successfully deleted the temporary files zr1394_5_s456_trimmed.fq_C_to_T.fastq and zr1394_5_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 47401736 Number of alignments with a unique best hit from the different alignments: 15747029 Mapping efficiency: 33.2% Sequences with no alignments under any condition: 14134741 Sequences did not map uniquely: 17519966 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3575045 ((converted) top strand) CT/GA: 3556303 ((converted) bottom strand) GA/CT: 4329383 (complementary to (converted) top strand) GA/GA: 4286298 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 93113950 Total methylated C's in CpG context: 9933157 Total methylated C's in CHG context: 400913 Total methylated C's in CHH context: 5646633 Total methylated C's in Unknown context: 3851 Total unmethylated C's in CpG context: 3086035 Total unmethylated C's in CHG context: 18513739 Total unmethylated C's in CHH context: 55533473 Total unmethylated C's in Unknown context: 25960 C methylated in CpG context: 76.3% C methylated in CHG context: 2.1% C methylated in CHH context: 9.2% C methylated in Unknown context (CN or CHN): 12.9% Bismark completed in 0d 1h 4m 42s ==================== 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_6_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_6_s456_trimmed.fq to zr1394_6_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_6_s456_trimmed.fq to zr1394_6_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_6_s456_trimmed.fq (46455148 sequences in total) Input files are zr1394_6_s456_trimmed.fq_C_to_T.fastq and zr1394_6_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_6_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1223:2248_1:N:0:GCCAAT 4 * 0 0 * * 0 0 AATTAATAAATAAATAATAAAATATGATAAA FFFFFFFFFFFFFFFFFFFFFFFBF/>> Writing bisulfite mapping results to zr1394_6_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_6_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far 46455148 reads; of these: 46455148 (100.00%) were unpaired; of these: 32837091 (70.69%) aligned 0 times 5702338 (12.27%) aligned exactly 1 time 7915719 (17.04%) aligned >1 times 29.31% overall alignment rate 46455148 reads; of these: 46455148 (100.00%) were unpaired; of these: 32895373 (70.81%) aligned 0 times 5689744 (12.25%) aligned exactly 1 time 787003146455148 reads; of these: ( 16.94 %46455148) aligned >1 times ( 29.19% overall alignment rate 100.00%) were unpaired; of these: 30586557 (65.84%) aligned 0 times 6111875 (13.16%) aligned exactly 1 time 9756716 (21.00%) aligned >1 times 34.16% overall alignment rate 46455148 reads; of these: 46455148 (100.00%) were unpaired; of these: 30620745 (65.91%) aligned 0 times 6106862 (13.15%) aligned exactly 1 time 9727541 (20.94%) aligned >1 times 34.09% overall alignment rate Processed 46455148 sequences in total Successfully deleted the temporary files zr1394_6_s456_trimmed.fq_C_to_T.fastq and zr1394_6_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 46455148 Number of alignments with a unique best hit from the different alignments: 15528129 Mapping efficiency: 33.4% Sequences with no alignments under any condition: 14024669 Sequences did not map uniquely: 16902350 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3458972 ((converted) top strand) CT/GA: 3443377 ((converted) bottom strand) GA/CT: 4328400 (complementary to (converted) top strand) GA/GA: 4297380 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 90762894 Total methylated C's in CpG context: 9013613 Total methylated C's in CHG context: 404127 Total methylated C's in CHH context: 5399151 Total methylated C's in Unknown context: 3111 Total unmethylated C's in CpG context: 2337404 Total unmethylated C's in CHG context: 17531974 Total unmethylated C's in CHH context: 56076625 Total unmethylated C's in Unknown context: 24469 C methylated in CpG context: 79.4% C methylated in CHG context: 2.3% C methylated in CHH context: 8.8% C methylated in Unknown context (CN or CHN): 11.3% Bismark completed in 0d 1h 5m 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_7_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_7_s456_trimmed.fq to zr1394_7_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_7_s456_trimmed.fq to zr1394_7_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_7_s456_trimmed.fq (49730113 sequences in total) Input files are zr1394_7_s456_trimmed.fq_C_to_T.fastq and zr1394_7_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_7_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1323:2170_1:N:0:CAGATC 0 Contig3_CT_converted 66858544 42 31M * 0 0 GTTGTATTATGTATTTTTAAAATATAGTGTT FFFFFFFFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to zr1394_7_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_7_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 34883238 (70.15%) aligned 0 times 5691018 (11.44%) aligned exactly 1 time 9155857 (18.41%) aligned >1 times 29.85% overall alignment rate 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 32818065 (65.99%) aligned 0 times 6025152 (12.12%) aligned exactly 1 time 10886896 (21.89%) aligned >1 times 34.01% overall alignment rate 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 34838493 (70.06%) aligned 0 times 5694643 (11.45%) aligned exactly 1 time 9196977 (18.49%) aligned >1 times 29.94% overall alignment rate 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 32849965 (66.06%) aligned 0 times 6031207 (12.13%) aligned exactly 1 time 10848941 (21.82%) aligned >1 times 33.94% overall alignment rate Processed 49730113 sequences in total Successfully deleted the temporary files zr1394_7_s456_trimmed.fq_C_to_T.fastq and zr1394_7_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 49730113 Number of alignments with a unique best hit from the different alignments: 15378146 Mapping efficiency: 30.9% Sequences with no alignments under any condition: 15119845 Sequences did not map uniquely: 19232122 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3512207 ((converted) top strand) CT/GA: 3490392 ((converted) bottom strand) GA/CT: 4205558 (complementary to (converted) top strand) GA/GA: 4169989 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 94177787 Total methylated C's in CpG context: 12731776 Total methylated C's in CHG context: 439419 Total methylated C's in CHH context: 5211666 Total methylated C's in Unknown context: 4444 Total unmethylated C's in CpG context: 2510434 Total unmethylated C's in CHG context: 18674935 Total unmethylated C's in CHH context: 54609557 Total unmethylated C's in Unknown context: 29264 C methylated in CpG context: 83.5% C methylated in CHG context: 2.3% C methylated in CHH context: 8.7% C methylated in Unknown context (CN or CHN): 13.2% Bismark completed in 0d 1h 6m 37s ==================== 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_8_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_8_s456_trimmed.fq to zr1394_8_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_8_s456_trimmed.fq to zr1394_8_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_8_s456_trimmed.fq (38697189 sequences in total) Input files are zr1394_8_s456_trimmed.fq_C_to_T.fastq and zr1394_8_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_8_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1180:2121_1:Y:0:ACTTGA 4 * 0 0 * * 0 0 GTTTTATAATATATGTATTATGAGTTTTT FFFBF/B/>> Writing bisulfite mapping results to zr1394_8_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_8_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far 38697189 reads; of these: 38697189 (100.00%) were unpaired; of these: 25174699 (65.06%) aligned 0 times 4757172 (12.29%) aligned exactly 1 time 8765318 (22.65%) aligned >1 times 34.94% overall alignment rate 38697189 reads; of these: 38697189 (100.00%) were unpaired; of these: 25204201 (65.13%) aligned 0 times 4772232 (12.33%) aligned exactly 1 time 8720756 (22.54%) aligned >1 times 34.87% overall alignment rate 38697189 reads; of these: 38697189 (100.00%) were unpaired; of these: 27215203 (70.33%) aligned 0 times 4382814 (11.33%) aligned exactly 1 time 7099172 (18.35%) aligned >1 times 29.67% overall alignment rate 38697189 reads; of these: 38697189 (100.00%) were unpaired; of these: 27262712 (70.45%) aligned 0 times 4386791 (11.34%) aligned exactly 1 time 7047686 (18.21%) aligned >1 times 29.55% overall alignment rate Processed 38697189 sequences in total Successfully deleted the temporary files zr1394_8_s456_trimmed.fq_C_to_T.fastq and zr1394_8_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 38697189 Number of alignments with a unique best hit from the different alignments: 12035925 Mapping efficiency: 31.1% Sequences with no alignments under any condition: 11580098 Sequences did not map uniquely: 15081166 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2668893 ((converted) top strand) CT/GA: 2655377 ((converted) bottom strand) GA/CT: 3365800 (complementary to (converted) top strand) GA/GA: 3345855 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 73932964 Total methylated C's in CpG context: 10514623 Total methylated C's in CHG context: 336033 Total methylated C's in CHH context: 4067854 Total methylated C's in Unknown context: 3281 Total unmethylated C's in CpG context: 1610852 Total unmethylated C's in CHG context: 14707547 Total unmethylated C's in CHH context: 42696055 Total unmethylated C's in Unknown context: 21955 C methylated in CpG context: 86.7% C methylated in CHG context: 2.2% C methylated in CHH context: 8.7% C methylated in Unknown context (CN or CHN): 13.0% Bismark completed in 0d 0h 51m 15s ==================== 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_9_s456_trimmed.fq to zr1394_9_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_9_s456_trimmed.fq to zr1394_9_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_9_s456_trimmed.fq (77350922 sequences in total) Input files are zr1394_9_s456_trimmed.fq_C_to_T.fastq and zr1394_9_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_9_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1382:2160_1:N:0:GATCAG 4 * 0 0 * * 0 0 TATTTAAAAAATTTTTATTATTTTAATATTA B>> Writing bisulfite mapping results to zr1394_9_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1115:2690:69865_1:N:0:GATCAG Contig6 2 Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far Processed 65000000 sequences so far Processed 66000000 sequences so far Processed 67000000 sequences so far Processed 68000000 sequences so far Processed 69000000 sequences so far Processed 70000000 sequences so far Processed 71000000 sequences so far Processed 72000000 sequences so far Processed 73000000 sequences so far Processed 74000000 sequences so far Processed 75000000 sequences so far Processed 76000000 sequences so far Processed 77000000 sequences so far 77350922 reads; of these: 77350922 (100.00%) were unpaired; of these: 53668765 (69.38%) aligned 0 times 9302713 (12.03%) aligned exactly 1 time 14379444 (18.59%) aligned >1 times 30.62% overall alignment rate 77350922 reads; of these: 77350922 (77350922100.00 reads; of these:% ) were unpaired; of these: 77350922 (53779959 (69.53%) aligned 0 times 100.00 %9293137) were unpaired; of these: ( 12.01 %50178090) aligned exactly 1 time ( 64.87 %14277826) aligned 0 times ( 18.46 %10003373) aligned >1 times ( 12.9330.47%%) aligned exactly 1 time overall alignment rate 17169459 (22.20%) aligned >1 times 35.13% overall alignment rate 77350922 reads; of these: 77350922 (100.00%) were unpaired; of these: 50118793 (64.79%) aligned 0 times 9995788 (12.92%) aligned exactly 1 time 17236341 (22.28%) aligned >1 times 35.21% overall alignment rate Processed 77350922 sequences in total Successfully deleted the temporary files zr1394_9_s456_trimmed.fq_C_to_T.fastq and zr1394_9_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 77350922 Number of alignments with a unique best hit from the different alignments: 25240310 Mapping efficiency: 32.6% Sequences with no alignments under any condition: 22010659 Sequences did not map uniquely: 30099953 Sequences which were discarded because genomic sequence could not be extracted: 1 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 5674291 ((converted) top strand) CT/GA: 5647087 ((converted) bottom strand) GA/CT: 6980377 (complementary to (converted) top strand) GA/GA: 6938554 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 150063744 Total methylated C's in CpG context: 16646053 Total methylated C's in CHG context: 573090 Total methylated C's in CHH context: 8128400 Total methylated C's in Unknown context: 5241 Total unmethylated C's in CpG context: 4057189 Total unmethylated C's in CHG context: 28845101 Total unmethylated C's in CHH context: 91813911 Total unmethylated C's in Unknown context: 42803 C methylated in CpG context: 80.4% C methylated in CHG context: 1.9% C methylated in CHH context: 8.1% C methylated in Unknown context (CN or CHN): 10.9% Bismark completed in 0d 1h 47m 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/olurida-bs/v98/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v98/)' 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/sr320/070322-olymerge-snp'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_all_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/070322-olymerge-snp Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v98/ chr Contig1 (138455862 bp) chr Contig2 (162977795 bp) chr Contig3 (162888229 bp) chr Contig4 (138666776 bp) chr Contig5 (115454673 bp) chr Contig6 (90850039 bp) chr Contig7 (78741030 bp) chr Contig8 (63405826 bp) chr Contig9 (60272286 bp) chr Contig10 (50401293 bp) chr Contig11 (49394880 bp) chr Contig12 (48053427 bp) chr Contig13 (45952961 bp) chr Contig14 (45463667 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_all_s456_trimmed.fq to zr1394_all_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_all_s456_trimmed.fq to zr1394_all_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_all_s456_trimmed.fq (605809374 sequences in total) Input files are zr1394_all_s456_trimmed.fq_C_to_T.fastq and zr1394_all_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_all_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/olurida-bs/v98/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1108:2120_1:Y:0:TATCTT 4 * 0 0 * * 0 0 ATTAATGAGAATGATTTTTTTTTTA B//FF>> Writing bisulfite mapping results to zr1394_all_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_all_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 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Processed 71000000 sequences so far Processed 72000000 sequences so far Processed 73000000 sequences so far Processed 74000000 sequences so far Processed 75000000 sequences so far Processed 76000000 sequences so far Processed 77000000 sequences so far Processed 78000000 sequences so far Processed 79000000 sequences so far Processed 80000000 sequences so far Processed 81000000 sequences so far Processed 82000000 sequences so far Processed 83000000 sequences so far Processed 84000000 sequences so far Processed 85000000 sequences so far Processed 86000000 sequences so far Processed 87000000 sequences so far Processed 88000000 sequences so far Processed 89000000 sequences so far Processed 90000000 sequences so far Processed 91000000 sequences so far Processed 92000000 sequences so far Processed 93000000 sequences so far Processed 94000000 sequences so far Processed 95000000 sequences so far Processed 96000000 sequences so far Processed 97000000 sequences so far Processed 98000000 sequences so far Processed 99000000 sequences so far Processed 100000000 sequences so far Processed 101000000 sequences so far Processed 102000000 sequences so far Processed 103000000 sequences so far Processed 104000000 sequences so far Processed 105000000 sequences so far Processed 106000000 sequences so far Processed 107000000 sequences so far Processed 108000000 sequences so far Processed 109000000 sequences so far Processed 110000000 sequences so far Processed 111000000 sequences so far Processed 112000000 sequences so far Processed 113000000 sequences so far Processed 114000000 sequences so far Processed 115000000 sequences so far Processed 116000000 sequences so far Processed 117000000 sequences so far Processed 118000000 sequences so far Processed 119000000 sequences so far Processed 120000000 sequences so far Processed 121000000 sequences so far Processed 122000000 sequences so far Processed 123000000 sequences so far Processed 124000000 sequences so far Processed 125000000 sequences so far Processed 126000000 sequences so far Processed 127000000 sequences so far Processed 128000000 sequences so far Processed 129000000 sequences so far Processed 130000000 sequences so far Processed 131000000 sequences so far Processed 132000000 sequences so far Processed 133000000 sequences so far Processed 134000000 sequences so far Processed 135000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:8728:78906_1:N:0:CTTGTA Contig6 90850008 Processed 136000000 sequences so far Processed 137000000 sequences so far Processed 138000000 sequences so far Processed 139000000 sequences so far Processed 140000000 sequences so far Processed 141000000 sequences so far Processed 142000000 sequences so far Processed 143000000 sequences so far Processed 144000000 sequences so far Processed 145000000 sequences so far Processed 146000000 sequences so far Processed 147000000 sequences so far Processed 148000000 sequences so far Processed 149000000 sequences so far Processed 150000000 sequences so far Processed 151000000 sequences so far Processed 152000000 sequences so far Processed 153000000 sequences so far Processed 154000000 sequences so far Processed 155000000 sequences so far Processed 156000000 sequences so far Processed 157000000 sequences so far Processed 158000000 sequences so far Processed 159000000 sequences so far Processed 160000000 sequences so far Processed 161000000 sequences so far Processed 162000000 sequences so far Processed 163000000 sequences so far Processed 164000000 sequences so far Processed 165000000 sequences so far Processed 166000000 sequences so far Processed 167000000 sequences so far Processed 168000000 sequences so far Processed 169000000 sequences so far Processed 170000000 sequences so far Processed 171000000 sequences so far Processed 172000000 sequences so far Processed 173000000 sequences so far Processed 174000000 sequences so far Processed 175000000 sequences so far Processed 176000000 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sequences so far Processed 285000000 sequences so far Processed 286000000 sequences so far Processed 287000000 sequences so far Processed 288000000 sequences so far Processed 289000000 sequences so far Processed 290000000 sequences so far Processed 291000000 sequences so far Processed 292000000 sequences so far Processed 293000000 sequences so far Processed 294000000 sequences so far Processed 295000000 sequences so far Processed 296000000 sequences so far Processed 297000000 sequences so far Processed 298000000 sequences so far Processed 299000000 sequences so far Processed 300000000 sequences so far Processed 301000000 sequences so far Processed 302000000 sequences so far Processed 303000000 sequences so far Processed 304000000 sequences so far Processed 305000000 sequences so far Processed 306000000 sequences so far Processed 307000000 sequences so far Processed 308000000 sequences so far Processed 309000000 sequences so far Processed 310000000 sequences so far Processed 311000000 sequences so far Processed 312000000 sequences so far Processed 313000000 sequences so far Processed 314000000 sequences so far Processed 315000000 sequences so far Processed 316000000 sequences so far Processed 317000000 sequences so far Processed 318000000 sequences so far Processed 319000000 sequences so far Processed 320000000 sequences so far Processed 321000000 sequences so far Processed 322000000 sequences so far Processed 323000000 sequences so far Processed 324000000 sequences so far Processed 325000000 sequences so far Processed 326000000 sequences so far Processed 327000000 sequences so far Processed 328000000 sequences so far Processed 329000000 sequences so far Processed 330000000 sequences so far Processed 331000000 sequences so far Processed 332000000 sequences so far Processed 333000000 sequences so far Processed 334000000 sequences so far Processed 335000000 sequences so far Processed 336000000 sequences so far Processed 337000000 sequences so far Processed 338000000 sequences so far Processed 339000000 sequences so far Processed 340000000 sequences so far Processed 341000000 sequences so far Processed 342000000 sequences so far Processed 343000000 sequences so far Processed 344000000 sequences so far Processed 345000000 sequences so far Processed 346000000 sequences so far Processed 347000000 sequences so far Processed 348000000 sequences so far Processed 349000000 sequences so far Processed 350000000 sequences so far Processed 351000000 sequences so far Processed 352000000 sequences so far Processed 353000000 sequences so far Processed 354000000 sequences so far Processed 355000000 sequences so far Processed 356000000 sequences so far Processed 357000000 sequences so far Processed 358000000 sequences so far Processed 359000000 sequences so far Processed 360000000 sequences so far Processed 361000000 sequences so far Processed 362000000 sequences so far Processed 363000000 sequences so far Processed 364000000 sequences so far Processed 365000000 sequences so far Processed 366000000 sequences so far Processed 367000000 sequences so far Processed 368000000 sequences so far Processed 369000000 sequences so far Processed 370000000 sequences so far Processed 371000000 sequences so far Processed 372000000 sequences so far Processed 373000000 sequences so far Processed 374000000 sequences so far Processed 375000000 sequences so far Processed 376000000 sequences so far Processed 377000000 sequences so far Processed 378000000 sequences so far Processed 379000000 sequences so far Processed 380000000 sequences so far Processed 381000000 sequences so far Processed 382000000 sequences so far Processed 383000000 sequences so far Processed 384000000 sequences so far Processed 385000000 sequences so far Processed 386000000 sequences so far Processed 387000000 sequences so far Processed 388000000 sequences so far Processed 389000000 sequences so far Processed 390000000 sequences so far Processed 391000000 sequences so far Processed 392000000 sequences so far Processed 393000000 sequences so far Processed 394000000 sequences so far Processed 395000000 sequences so far Processed 396000000 sequences so far Processed 397000000 sequences so far Processed 398000000 sequences so far Processed 399000000 sequences so far Processed 400000000 sequences so far Processed 401000000 sequences so far Processed 402000000 sequences so far Processed 403000000 sequences so far Processed 404000000 sequences so far Processed 405000000 sequences so far Processed 406000000 sequences so far Processed 407000000 sequences so far Processed 408000000 sequences so far Processed 409000000 sequences so far Processed 410000000 sequences so far Processed 411000000 sequences so far Processed 412000000 sequences so far Processed 413000000 sequences so far Processed 414000000 sequences so far Processed 415000000 sequences so far Processed 416000000 sequences so far Processed 417000000 sequences so far Processed 418000000 sequences so far Processed 419000000 sequences so far Processed 420000000 sequences so far Processed 421000000 sequences so far Processed 422000000 sequences so far Processed 423000000 sequences so far Processed 424000000 sequences so far Processed 425000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2103:17898:79304_1:N:0:CCGTCC Contig10 50401263 Processed 426000000 sequences so far Processed 427000000 sequences so far Processed 428000000 sequences so far Processed 429000000 sequences so far Processed 430000000 sequences so far Processed 431000000 sequences so far Processed 432000000 sequences so far Processed 433000000 sequences so far Processed 434000000 sequences so far Processed 435000000 sequences so far Processed 436000000 sequences so far Processed 437000000 sequences so far Processed 438000000 sequences so far Processed 439000000 sequences so far Processed 440000000 sequences so far Processed 441000000 sequences so far Processed 442000000 sequences so far Processed 443000000 sequences so far Processed 444000000 sequences so far Processed 445000000 sequences so far Processed 446000000 sequences so far Processed 447000000 sequences so far Processed 448000000 sequences so far Processed 449000000 sequences so far Processed 450000000 sequences so far Processed 451000000 sequences so far Processed 452000000 sequences so far Processed 453000000 sequences so far Processed 454000000 sequences so far Processed 455000000 sequences so far Processed 456000000 sequences so far Processed 457000000 sequences so far Processed 458000000 sequences so far Processed 459000000 sequences so far Processed 460000000 sequences so far Processed 461000000 sequences so far Processed 462000000 sequences so far Processed 463000000 sequences so far Processed 464000000 sequences so far Processed 465000000 sequences so far Processed 466000000 sequences so far Processed 467000000 sequences so far Processed 468000000 sequences so far Processed 469000000 sequences so far Processed 470000000 sequences so far Processed 471000000 sequences so far Processed 472000000 sequences so far Processed 473000000 sequences so far Processed 474000000 sequences so far Processed 475000000 sequences so far Processed 476000000 sequences so far Processed 477000000 sequences so far Processed 478000000 sequences so far Processed 479000000 sequences so far Processed 480000000 sequences so far Processed 481000000 sequences so far Processed 482000000 sequences so far Processed 483000000 sequences so far Processed 484000000 sequences so far Processed 485000000 sequences so far Processed 486000000 sequences so far Processed 487000000 sequences so far Processed 488000000 sequences so far Processed 489000000 sequences so far Processed 490000000 sequences so far Processed 491000000 sequences so far Processed 492000000 sequences so far Processed 493000000 sequences so far Processed 494000000 sequences so far Processed 495000000 sequences so far Processed 496000000 sequences so far Processed 497000000 sequences so far Processed 498000000 sequences so far Processed 499000000 sequences so far Processed 500000000 sequences so far Processed 501000000 sequences so far Processed 502000000 sequences so far Processed 503000000 sequences so far Processed 504000000 sequences so far Processed 505000000 sequences so far Processed 506000000 sequences so far Processed 507000000 sequences so far Processed 508000000 sequences so far Processed 509000000 sequences so far Processed 510000000 sequences so far Processed 511000000 sequences so far Processed 512000000 sequences so far Processed 513000000 sequences so far Processed 514000000 sequences so far Processed 515000000 sequences so far Processed 516000000 sequences so far Processed 517000000 sequences so far Processed 518000000 sequences so far Processed 519000000 sequences so far Processed 520000000 sequences so far Processed 521000000 sequences so far Processed 522000000 sequences so far Processed 523000000 sequences so far Processed 524000000 sequences so far Processed 525000000 sequences so far Processed 526000000 sequences so far Processed 527000000 sequences so far Processed 528000000 sequences so far Processed 529000000 sequences so far Processed 530000000 sequences so far Processed 531000000 sequences so far Processed 532000000 sequences so far Processed 533000000 sequences so far Processed 534000000 sequences so far Processed 535000000 sequences so far Processed 536000000 sequences so far Processed 537000000 sequences so far Processed 538000000 sequences so far Processed 539000000 sequences so far Processed 540000000 sequences so far Processed 541000000 sequences so far Processed 542000000 sequences so far Processed 543000000 sequences so far Processed 544000000 sequences so far Processed 545000000 sequences so far Processed 546000000 sequences so far Processed 547000000 sequences so far Processed 548000000 sequences so far Processed 549000000 sequences so far Processed 550000000 sequences so far Processed 551000000 sequences so far Processed 552000000 sequences so far Processed 553000000 sequences so far Processed 554000000 sequences so far Processed 555000000 sequences so far Processed 556000000 sequences so far Processed 557000000 sequences so far Processed 558000000 sequences so far Processed 559000000 sequences so far Processed 560000000 sequences so far Processed 561000000 sequences so far Processed 562000000 sequences so far Processed 563000000 sequences so far Processed 564000000 sequences so far Processed 565000000 sequences so far Processed 566000000 sequences so far Processed 567000000 sequences so far Processed 568000000 sequences so far Processed 569000000 sequences so far Processed 570000000 sequences so far Processed 571000000 sequences so far Processed 572000000 sequences so far Processed 573000000 sequences so far Processed 574000000 sequences so far Processed 575000000 sequences so far Processed 576000000 sequences so far Processed 577000000 sequences so far Processed 578000000 sequences so far Processed 579000000 sequences so far Processed 580000000 sequences so far Processed 581000000 sequences so far Processed 582000000 sequences so far Processed 583000000 sequences so far Processed 584000000 sequences so far Processed 585000000 sequences so far Processed 586000000 sequences so far Processed 587000000 sequences so far Processed 588000000 sequences so far Processed 589000000 sequences so far Processed 590000000 sequences so far Processed 591000000 sequences so far Processed 592000000 sequences so far Processed 593000000 sequences so far Processed 594000000 sequences so far Processed 595000000 sequences so far Processed 596000000 sequences so far Processed 597000000 sequences so far Processed 598000000 sequences so far Processed 599000000 sequences so far Processed 600000000 sequences so far Processed 601000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:1329:15641_1:N:0:ATCACG Contig6 2 Processed 602000000 sequences so far Processed 603000000 sequences so far Processed 604000000 sequences so far Processed 605000000 sequences so far 605809374 reads; of these: 605809374 (605809374 reads; of these:100.00 % ) were unpaired; of these:605809374 ( 421780474 (69.62%) aligned 0 times 100.00 %68443298) were unpaired; of these: ( 11.30 %397941310) aligned exactly 1 time ( 65.69 %115585602) aligned 0 times ( 19.08 %72581976) aligned >1 times ( 60580937411.9830.38 reads; of these:%% ) aligned exactly 1 time overall alignment rate 605809374 (135286088 (22.33100.00%%) aligned >1 times) were unpaired; of these: 34.31 %397474336 overall alignment rate ( 65.61%) aligned 0 times 72335444 (11.94%) aligned exactly 1 time 135999594 (22.45%) aligned >1 times 34.39% overall alignment rate 605809374 reads; of these: 605809374 (100.00%) were unpaired; of these: 421161100 (69.52%) aligned 0 times 68276156 (11.27%) aligned exactly 1 time 116372118 (19.21%) aligned >1 times 30.48% overall alignment rate Processed 605809374 sequences in total Successfully deleted the temporary files zr1394_all_s456_trimmed.fq_C_to_T.fastq and zr1394_all_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 605809374 Number of alignments with a unique best hit from the different alignments: 184983541 Mapping efficiency: 30.5% Sequences with no alignments under any condition: 179447426 Sequences did not map uniquely: 241378407 Sequences which were discarded because genomic sequence could not be extracted: 3 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 42432699 ((converted) top strand) CT/GA: 42116194 ((converted) bottom strand) GA/CT: 50418251 (complementary to (converted) top strand) GA/GA: 50016394 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1150617798 Total methylated C's in CpG context: 174688062 Total methylated C's in CHG context: 5203372 Total methylated C's in CHH context: 61461946 Total methylated C's in Unknown context: 52708 Total unmethylated C's in CpG context: 30920274 Total unmethylated C's in CHG context: 230451229 Total unmethylated C's in CHH context: 647892915 Total unmethylated C's in Unknown context: 362895 C methylated in CpG context: 85.0% C methylated in CHG context: 2.2% C methylated in CHH context: 8.7% C methylated in Unknown context (CN or CHN): 12.7% Bismark completed in 0d 13h 17m 12s ==================== Bismark run complete ==================== Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_10_s456_trimmed_bismark_bt2.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 >>zr1394_10_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_10_s456_trimmed_bismark_bt2.bam: 25374001 Total number duplicated alignments removed: 16495646 (65.01%) Duplicated alignments were found at: 3861835 different position(s) Total count of deduplicated leftover sequences: 8878355 (34.99% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_10_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_11_s456_trimmed_bismark_bt2.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 >>zr1394_11_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_11_s456_trimmed_bismark_bt2.bam: 15624995 Total number duplicated alignments removed: 7497739 (47.99%) Duplicated alignments were found at: 1897754 different position(s) Total count of deduplicated leftover sequences: 8127256 (52.01% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_11_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_12_s456_trimmed_bismark_bt2.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 >>zr1394_12_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_12_s456_trimmed_bismark_bt2.bam: 20027643 Total number duplicated alignments removed: 6465802 (32.28%) Duplicated alignments were found at: 2597927 different position(s) Total count of deduplicated leftover sequences: 13561841 (67.72% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_12_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_13_s456_trimmed_bismark_bt2.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 >>zr1394_13_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_13_s456_trimmed_bismark_bt2.bam: 19626793 Total number duplicated alignments removed: 8468769 (43.15%) Duplicated alignments were found at: 2605304 different position(s) Total count of deduplicated leftover sequences: 11158024 (56.85% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_13_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_14_s456_trimmed_bismark_bt2.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 >>zr1394_14_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_14_s456_trimmed_bismark_bt2.bam: 25416779 Total number duplicated alignments removed: 11087897 (43.62%) Duplicated alignments were found at: 3309421 different position(s) Total count of deduplicated leftover sequences: 14328882 (56.38% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_15_s456_trimmed_bismark_bt2.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 >>zr1394_15_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_15_s456_trimmed_bismark_bt2.bam: 19910397 Total number duplicated alignments removed: 9181609 (46.11%) Duplicated alignments were found at: 2576549 different position(s) Total count of deduplicated leftover sequences: 10728788 (53.89% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_15_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_16_s456_trimmed_bismark_bt2.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 >>zr1394_16_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_16_s456_trimmed_bismark_bt2.bam: 21286992 Total number duplicated alignments removed: 9440963 (44.35%) Duplicated alignments were found at: 2727031 different position(s) Total count of deduplicated leftover sequences: 11846029 (55.65% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_16_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_17_s456_trimmed_bismark_bt2.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 >>zr1394_17_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_17_s456_trimmed_bismark_bt2.bam: 12831686 Total number duplicated alignments removed: 5035157 (39.24%) Duplicated alignments were found at: 1717392 different position(s) Total count of deduplicated leftover sequences: 7796529 (60.76% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_17_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_18_s456_trimmed_bismark_bt2.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 >>zr1394_18_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_18_s456_trimmed_bismark_bt2.bam: 18068736 Total number duplicated alignments removed: 6050893 (33.49%) Duplicated alignments were found at: 2424460 different position(s) Total count of deduplicated leftover sequences: 12017843 (66.51% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_1_s456_trimmed_bismark_bt2.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 >>zr1394_1_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_1_s456_trimmed_bismark_bt2.bam: 14534759 Total number duplicated alignments removed: 4339435 (29.86%) Duplicated alignments were found at: 1752249 different position(s) Total count of deduplicated leftover sequences: 10195324 (70.14% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_2_s456_trimmed_bismark_bt2.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 >>zr1394_2_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_2_s456_trimmed_bismark_bt2.bam: 14822810 Total number duplicated alignments removed: 4550192 (30.70%) Duplicated alignments were found at: 1967952 different position(s) Total count of deduplicated leftover sequences: 10272618 (69.30% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_3_s456_trimmed_bismark_bt2.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 >>zr1394_3_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_3_s456_trimmed_bismark_bt2.bam: 14759690 Total number duplicated alignments removed: 4327491 (29.32%) Duplicated alignments were found at: 1731966 different position(s) Total count of deduplicated leftover sequences: 10432199 (70.68% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_3_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_4_s456_trimmed_bismark_bt2.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 >>zr1394_4_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_4_s456_trimmed_bismark_bt2.bam: 13872301 Total number duplicated alignments removed: 4357575 (31.41%) Duplicated alignments were found at: 1707009 different position(s) Total count of deduplicated leftover sequences: 9514726 (68.59% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_4_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_5_s456_trimmed_bismark_bt2.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 >>zr1394_5_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_5_s456_trimmed_bismark_bt2.bam: 15747029 Total number duplicated alignments removed: 3970742 (25.22%) Duplicated alignments were found at: 1836778 different position(s) Total count of deduplicated leftover sequences: 11776287 (74.78% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_6_s456_trimmed_bismark_bt2.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 >>zr1394_6_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_6_s456_trimmed_bismark_bt2.bam: 15528129 Total number duplicated alignments removed: 3714960 (23.92%) Duplicated alignments were found at: 1783653 different position(s) Total count of deduplicated leftover sequences: 11813169 (76.08% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_6_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_7_s456_trimmed_bismark_bt2.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 >>zr1394_7_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_7_s456_trimmed_bismark_bt2.bam: 15378146 Total number duplicated alignments removed: 4686910 (30.48%) Duplicated alignments were found at: 1882201 different position(s) Total count of deduplicated leftover sequences: 10691236 (69.52% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_7_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_8_s456_trimmed_bismark_bt2.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 >>zr1394_8_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_8_s456_trimmed_bismark_bt2.bam: 12035925 Total number duplicated alignments removed: 3555064 (29.54%) Duplicated alignments were found at: 1451198 different position(s) Total count of deduplicated leftover sequences: 8480861 (70.46% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_8_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_9_s456_trimmed_bismark_bt2.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 >>zr1394_9_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_9_s456_trimmed_bismark_bt2.bam: 25240309 Total number duplicated alignments removed: 8683054 (34.40%) Duplicated alignments were found at: 3224875 different position(s) Total count of deduplicated leftover sequences: 16557255 (65.60% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_all_s456_trimmed_bismark_bt2.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 >>zr1394_all_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_all_s456_trimmed_bismark_bt2.bam: 184983538 Total number duplicated alignments removed: 124135383 (67.11%) Duplicated alignments were found at: 20776616 different position(s) Total count of deduplicated leftover sequences: 60848155 (32.89% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig1 LN:138455862 skipping header line: @SQ SN:Contig2 LN:162977795 skipping header line: @SQ SN:Contig3 LN:162888229 skipping header line: @SQ SN:Contig4 LN:138666776 skipping header line: @SQ SN:Contig5 LN:115454673 skipping header line: @SQ SN:Contig6 LN:90850039 skipping header line: @SQ SN:Contig7 LN:78741030 skipping header line: @SQ SN:Contig8 LN:63405826 skipping header line: @SQ SN:Contig9 LN:60272286 skipping header line: @SQ SN:Contig10 LN:50401293 skipping header line: @SQ SN:Contig11 LN:49394880 skipping header line: @SQ SN:Contig12 LN:48053427 skipping header line: @SQ SN:Contig13 LN:45952961 skipping header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_all_s456_trimmed.fq" *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Treating file(s) as single-end data (as extracted from @PG line) Summarising Bismark methylation extractor parameters: =============================================================== Bismark single-end SAM format specified (default) Number of cores to be used: 14 Output will be written to the current directory ('/gscratch/scrubbed/sr320/070322-olymerge-snp') 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 >>zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_10_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Merging individual splitting reports into overall report: 'zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 8878355 lines in total Total number of methylation call strings processed: 8878355 Final Cytosine Methylation Report ================================= Total number of C's analysed: 54346071 Total methylated C's in CpG context: 6587591 Total methylated C's in CHG context: 290156 Total methylated C's in CHH context: 4259112 Total C to T conversions in CpG context: 1552509 Total C to T conversions in CHG context: 10190620 Total C to T conversions in CHH context: 31466083 C methylated in CpG context: 80.9% C methylated in CHG context: 2.8% C methylated in CHH context: 11.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_10_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_10_s456_trimmed_bismark_bt2.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 zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_11_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Exiting.. Finished processing child process. Exiting.. Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Finished processing child process. Exiting.. Processed lines: 8000000 Finished processing child process. Exiting.. Processed lines: 8000000 Finished processing child process. Exiting.. Processed lines: 8000000 Finished processing child process. Exiting.. Processed lines: 8000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 8000000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Processed lines: 8000000 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: 'zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 8127256 lines in total Total number of methylation call strings processed: 8127256 Final Cytosine Methylation Report ================================= Total number of C's analysed: 50434695 Total methylated C's in CpG context: 7064178 Total methylated C's in CHG context: 278667 Total methylated C's in CHH context: 3575067 Total C to T conversions in CpG context: 1611371 Total C to T conversions in CHG context: 9128258 Total C to T conversions in CHH context: 28777154 C methylated in CpG context: 81.4% C methylated in CHG context: 3.0% C methylated in CHH context: 11.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_11_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_11_s456_trimmed_bismark_bt2.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 zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_12_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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lines: 12500000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13500000 Finished processing child process. Exiting.. Processed lines: 13000000 Finished processing child process. Exiting.. Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13000000 Processed lines: 13000000 Finished processing child process. Exiting.. Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13000000 Now waiting for all child processes to complete Processed lines: 13500000 Finished processing child process. Exiting.. Processed lines: 13500000 Processed lines: 13500000 Finished processing child process. Exiting.. Processed lines: 13500000 Processed lines: 13500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 13500000 Processed lines: 13500000 Finished processing child process. Exiting.. Processed lines: 13500000 Processed lines: 13500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 13500000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 13561841 lines in total Total number of methylation call strings processed: 13561841 Final Cytosine Methylation Report ================================= Total number of C's analysed: 80149813 Total methylated C's in CpG context: 8313907 Total methylated C's in CHG context: 333592 Total methylated C's in CHH context: 5271016 Total C to T conversions in CpG context: 2330165 Total C to T conversions in CHG context: 15191561 Total C to T conversions in CHH context: 48709572 C methylated in CpG context: 78.1% C methylated in CHG context: 2.1% C methylated in CHH context: 9.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_12_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_12_s456_trimmed_bismark_bt2.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 zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_13_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Exiting.. Finished processing child process. Exiting.. Processed lines: 11000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Finished processing child process. Exiting.. Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 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: 'zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 11158024 lines in total Total number of methylation call strings processed: 11158024 Final Cytosine Methylation Report ================================= Total number of C's analysed: 68398224 Total methylated C's in CpG context: 9042404 Total methylated C's in CHG context: 342660 Total methylated C's in CHH context: 4601823 Total C to T conversions in CpG context: 1816241 Total C to T conversions in CHG context: 12804713 Total C to T conversions in CHH context: 39790383 C methylated in CpG context: 83.3% C methylated in CHG context: 2.6% C methylated in CHH context: 10.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_13_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_13_s456_trimmed_bismark_bt2.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 zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Exiting.. Processed lines: 14000000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 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.. Merging individual splitting reports into overall report: 'zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 14328882 lines in total Total number of methylation call strings processed: 14328882 Final Cytosine Methylation Report ================================= Total number of C's analysed: 87103963 Total methylated C's in CpG context: 11148831 Total methylated C's in CHG context: 439594 Total methylated C's in CHH context: 5924738 Total C to T conversions in CpG context: 2386168 Total C to T conversions in CHG context: 15349838 Total C to T conversions in CHH context: 51854794 C methylated in CpG context: 82.4% C methylated in CHG context: 2.8% C methylated in CHH context: 10.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_14_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_14_s456_trimmed_bismark_bt2.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 zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_15_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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10000000 Processed lines: 9500000 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: 10500000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10000000 Processed lines: 10500000 Finished processing child process. Exiting.. Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10500000 Finished processing child process. Exiting.. Processed lines: 10500000 Finished processing child process. Exiting.. Finished 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: 10500000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 10728788 lines in total Total number of methylation call strings processed: 10728788 Final Cytosine Methylation Report ================================= Total number of C's analysed: 66291550 Total methylated C's in CpG context: 9369352 Total methylated C's in CHG context: 360980 Total methylated C's in CHH context: 4662164 Total C to T conversions in CpG context: 1667423 Total C to T conversions in CHG context: 12247476 Total C to T conversions in CHH context: 37984155 C methylated in CpG context: 84.9% C methylated in CHG context: 2.9% C methylated in CHH context: 10.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_15_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_15_s456_trimmed_bismark_bt2.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 zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_16_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Exiting.. Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Processed lines: 11500000 Processed lines: 11500000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 11846029 lines in total Total number of methylation call strings processed: 11846029 Final Cytosine Methylation Report ================================= Total number of C's analysed: 72753637 Total methylated C's in CpG context: 9949262 Total methylated C's in CHG context: 384933 Total methylated C's in CHH context: 5094149 Total C to T conversions in CpG context: 2085838 Total C to T conversions in CHG context: 13053209 Total C to T conversions in CHH context: 42186246 C methylated in CpG context: 82.7% C methylated in CHG context: 2.9% C methylated in CHH context: 10.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_16_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_16_s456_trimmed_bismark_bt2.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 zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_17_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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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 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. 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 Merging individual splitting reports into overall report: 'zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 7796529 lines in total Total number of methylation call strings processed: 7796529 Final Cytosine Methylation Report ================================= Total number of C's analysed: 47781647 Total methylated C's in CpG context: 6612578 Total methylated C's in CHG context: 249661 Total methylated C's in CHH context: 3301612 Total C to T conversions in CpG context: 1191663 Total C to T conversions in CHG context: 9371177 Total C to T conversions in CHH context: 27054956 C methylated in CpG context: 84.7% C methylated in CHG context: 2.6% C methylated in CHH context: 10.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_17_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_17_s456_trimmed_bismark_bt2.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 zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11500000 Processed lines: 12000000 Finished processing child process. Exiting.. Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 12000000 Finished processing child process. Exiting.. Processed lines: 12000000 Processed lines: 12000000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Processed lines: 12000000 Finished processing child process. Exiting.. Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12000000 Finished processing child process. Exiting.. Processed lines: 12000000 Finished processing child process. Exiting.. Processed lines: 12000000 Finished processing child process. Exiting.. Processed lines: 12000000 Processed lines: 12000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12000000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 12017843 lines in total Total number of methylation call strings processed: 12017843 Final Cytosine Methylation Report ================================= Total number of C's analysed: 71613889 Total methylated C's in CpG context: 8130684 Total methylated C's in CHG context: 313418 Total methylated C's in CHH context: 4538975 Total C to T conversions in CpG context: 1878504 Total C to T conversions in CHG context: 13868882 Total C to T conversions in CHH context: 42883426 C methylated in CpG context: 81.2% C methylated in CHG context: 2.2% C methylated in CHH context: 9.6% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_18_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_18_s456_trimmed_bismark_bt2.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 zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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10000000 Finished processing child process. Exiting.. Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Finished processing child process. Exiting.. Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10000000 Finished processing child process. Exiting.. Processed lines: 10000000 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: 'zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 10195324 lines in total Total number of methylation call strings processed: 10195324 Final Cytosine Methylation Report ================================= Total number of C's analysed: 61108365 Total methylated C's in CpG context: 7206035 Total methylated C's in CHG context: 301119 Total methylated C's in CHH context: 3975802 Total C to T conversions in CpG context: 1781863 Total C to T conversions in CHG context: 11485875 Total C to T conversions in CHH context: 36357671 C methylated in CpG context: 80.2% C methylated in CHG context: 2.6% C methylated in CHH context: 9.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_1_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_1_s456_trimmed_bismark_bt2.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 zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Exiting.. Processed lines: 10000000 Processed lines: 10000000 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.. 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: 'zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 10272618 lines in total Total number of methylation call strings processed: 10272618 Final Cytosine Methylation Report ================================= Total number of C's analysed: 61305714 Total methylated C's in CpG context: 7074055 Total methylated C's in CHG context: 296036 Total methylated C's in CHH context: 4093092 Total C to T conversions in CpG context: 1645137 Total C to T conversions in CHG context: 11724386 Total C to T conversions in CHH context: 36473008 C methylated in CpG context: 81.1% C methylated in CHG context: 2.5% C methylated in CHH context: 10.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_2_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_2_s456_trimmed_bismark_bt2.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 zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_3_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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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: 'zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 10432199 lines in total Total number of methylation call strings processed: 10432199 Final Cytosine Methylation Report ================================= Total number of C's analysed: 62129400 Total methylated C's in CpG context: 7053744 Total methylated C's in CHG context: 296595 Total methylated C's in CHH context: 4106276 Total C to T conversions in CpG context: 1706032 Total C to T conversions in CHG context: 11393779 Total C to T conversions in CHH context: 37572974 C methylated in CpG context: 80.5% C methylated in CHG context: 2.5% C methylated in CHH context: 9.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_3_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_3_s456_trimmed_bismark_bt2.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 zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_4_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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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: 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 Processed lines: 9000000 Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 9514726 lines in total Total number of methylation call strings processed: 9514726 Final Cytosine Methylation Report ================================= Total number of C's analysed: 57380051 Total methylated C's in CpG context: 7093417 Total methylated C's in CHG context: 290465 Total methylated C's in CHH context: 3757271 Total C to T conversions in CpG context: 1317260 Total C to T conversions in CHG context: 10875988 Total C to T conversions in CHH context: 34045650 C methylated in CpG context: 84.3% C methylated in CHG context: 2.6% C methylated in CHH context: 9.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_4_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_4_s456_trimmed_bismark_bt2.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 zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Exiting.. Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 11500000 Processed lines: 11500000 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.. 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: 'zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 11776287 lines in total Total number of methylation call strings processed: 11776287 Final Cytosine Methylation Report ================================= Total number of C's analysed: 68921607 Total methylated C's in CpG context: 6669103 Total methylated C's in CHG context: 306607 Total methylated C's in CHH context: 4610637 Total C to T conversions in CpG context: 2370609 Total C to T conversions in CHG context: 13169917 Total C to T conversions in CHH context: 41794734 C methylated in CpG context: 73.8% C methylated in CHG context: 2.3% C methylated in CHH context: 9.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_5_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_5_s456_trimmed_bismark_bt2.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 zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_6_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 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 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.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 11813169 lines in total Total number of methylation call strings processed: 11813169 Final Cytosine Methylation Report ================================= Total number of C's analysed: 68369911 Total methylated C's in CpG context: 6268748 Total methylated C's in CHG context: 306276 Total methylated C's in CHH context: 4421749 Total C to T conversions in CpG context: 1806827 Total C to T conversions in CHG context: 12801677 Total C to T conversions in CHH context: 42764634 C methylated in CpG context: 77.6% C methylated in CHG context: 2.3% C methylated in CHH context: 9.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_6_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_6_s456_trimmed_bismark_bt2.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 zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_7_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Exiting.. Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Processed lines: 10500000 Finished processing child process. Exiting.. Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Processed lines: 10500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 10691236 lines in total Total number of methylation call strings processed: 10691236 Final Cytosine Methylation Report ================================= Total number of C's analysed: 64455591 Total methylated C's in CpG context: 7807245 Total methylated C's in CHG context: 318516 Total methylated C's in CHH context: 4157485 Total C to T conversions in CpG context: 1756856 Total C to T conversions in CHG context: 12199183 Total C to T conversions in CHH context: 38216306 C methylated in CpG context: 81.6% C methylated in CHG context: 2.5% C methylated in CHH context: 9.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_7_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_7_s456_trimmed_bismark_bt2.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 zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_8_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Exiting.. Finished processing child process. Exiting.. 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.. 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: 'zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 8480861 lines in total Total number of methylation call strings processed: 8480861 Final Cytosine Methylation Report ================================= Total number of C's analysed: 51318369 Total methylated C's in CpG context: 6600233 Total methylated C's in CHG context: 246352 Total methylated C's in CHH context: 3250952 Total C to T conversions in CpG context: 1127010 Total C to T conversions in CHG context: 9781878 Total C to T conversions in CHH context: 30311944 C methylated in CpG context: 85.4% C methylated in CHG context: 2.5% C methylated in CHH context: 9.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_8_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_8_s456_trimmed_bismark_bt2.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 zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Processed lines: 15000000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 16000000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 16000000 Processed lines: 15500000 Processed lines: 16000000 Processed lines: 16000000 Processed lines: 16000000 Processed lines: 16000000 Processed lines: 16000000 Processed lines: 16000000 Processed lines: 16000000 Processed lines: 16000000 Processed lines: 16000000 Processed lines: 16500000 Processed lines: 16000000 Finished processing child process. Exiting.. Processed lines: 16000000 Processed lines: 16500000 Finished processing child process. Exiting.. Processed lines: 16500000 Processed lines: 16000000 Processed lines: 16500000 Finished processing child process. Exiting.. Processed lines: 16500000 Processed lines: 16500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 16500000 Finished processing child process. Exiting.. Processed lines: 16500000 Now waiting for all child processes to complete Processed lines: 16500000 Processed lines: 16500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 16500000 Processed lines: 16500000 Finished processing child process. Exiting.. Processed lines: 16500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 16500000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 16557255 lines in total Total number of methylation call strings processed: 16557255 Final Cytosine Methylation Report ================================= Total number of C's analysed: 96977575 Total methylated C's in CpG context: 9515451 Total methylated C's in CHG context: 403873 Total methylated C's in CHH context: 6284505 Total C to T conversions in CpG context: 2696345 Total C to T conversions in CHG context: 17686365 Total C to T conversions in CHH context: 60391036 C methylated in CpG context: 77.9% C methylated in CHG context: 2.2% C methylated in CHH context: 9.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_9_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_9_s456_trimmed_bismark_bt2.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 zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.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:Contig1 LN:138455862 skipping SAM header line: @SQ SN:Contig2 LN:162977795 skipping SAM header line: @SQ SN:Contig3 LN:162888229 skipping SAM header line: @SQ SN:Contig4 LN:138666776 skipping SAM header line: @SQ SN:Contig5 LN:115454673 skipping SAM header line: @SQ SN:Contig6 LN:90850039 skipping SAM header line: @SQ SN:Contig7 LN:78741030 skipping SAM header line: @SQ SN:Contig8 LN:63405826 skipping SAM header line: @SQ SN:Contig9 LN:60272286 skipping SAM header line: @SQ SN:Contig10 LN:50401293 skipping SAM header line: @SQ SN:Contig11 LN:49394880 skipping SAM header line: @SQ SN:Contig12 LN:48053427 skipping SAM header line: @SQ SN:Contig13 LN:45952961 skipping SAM header line: @SQ SN:Contig14 LN:45463667 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/olurida-bs/v98/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_all_s456_trimmed.fq" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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 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Exiting.. Processed lines: 56500000 Processed lines: 56500000 Processed lines: 57500000 Processed lines: 57500000 Processed lines: 57500000 Processed lines: 60000000 Processed lines: 56500000 Processed lines: 56500000 Processed lines: 58500000 Processed lines: 57000000 Processed lines: 57000000 Processed lines: 57000000 Processed lines: 56500000 Processed lines: 57000000 Processed lines: 57000000 Processed lines: 58000000 Processed lines: 58000000 Processed lines: 58000000 Processed lines: 60500000 Processed lines: 57000000 Processed lines: 57500000 Processed lines: 59000000 Processed lines: 57000000 Processed lines: 57500000 Processed lines: 57500000 Processed lines: 57000000 Finished processing child process. Exiting.. Processed lines: 57500000 Processed lines: 57500000 Processed lines: 58500000 Processed lines: 58500000 Processed lines: 58500000 Processed lines: 57500000 Processed lines: 59500000 Processed lines: 58000000 Processed lines: 57500000 Processed lines: 58000000 Processed lines: 58000000 Processed lines: 57500000 Processed lines: 58000000 Processed lines: 58000000 Processed lines: 59000000 Processed lines: 59000000 Processed lines: 59000000 Processed lines: 58000000 Processed lines: 60000000 Processed lines: 58500000 Processed lines: 58000000 Processed lines: 58500000 Processed lines: 58500000 Processed lines: 58000000 Processed lines: 58500000 Processed lines: 58500000 Processed lines: 59500000 Processed lines: 59500000 Processed lines: 59500000 Processed lines: 58500000 Processed lines: 60500000 Processed lines: 59000000 Processed lines: 59000000 Processed lines: 58500000 Processed lines: 59000000 Processed lines: 58500000 Processed lines: 59000000 Processed lines: 59000000 Processed lines: 60000000 Processed lines: 60000000 Finished processing child process. Exiting.. Processed lines: 60000000 Processed lines: 59000000 Processed lines: 59500000 Processed lines: 59500000 Processed lines: 59000000 Processed lines: 59500000 Processed lines: 59000000 Processed lines: 59500000 Processed lines: 60500000 Processed lines: 59500000 Processed lines: 60500000 Processed lines: 60500000 Processed lines: 59500000 Processed lines: 60000000 Processed lines: 60000000 Processed lines: 59500000 Finished processing child process. Exiting.. Processed lines: 60000000 Finished processing child process. Exiting.. Processed lines: 59500000 Processed lines: 60000000 Finished processing child process. Exiting.. Processed lines: 60000000 Processed lines: 60000000 Processed lines: 60500000 Processed lines: 60500000 Processed lines: 60000000 Processed lines: 60500000 Processed lines: 60000000 Processed lines: 60500000 Processed lines: 60500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 60500000 Now waiting for all child processes to complete Processed lines: 60500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 60500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 60848155 lines in total Total number of methylation call strings processed: 60848155 Final Cytosine Methylation Report ================================= Total number of C's analysed: 362887673 Total methylated C's in CpG context: 37503474 Total methylated C's in CHG context: 2098223 Total methylated C's in CHH context: 31599525 Total C to T conversions in CpG context: 11075480 Total C to T conversions in CHG context: 61396504 Total C to T conversions in CHH context: 219214467 C methylated in CpG context: 77.2% C methylated in CHG context: 3.3% C methylated in CHH context: 12.6% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 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_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_all_s456_trimmed_bismark_bt2.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/sr320/070322-olymerge-snp/CpG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/070322-olymerge-snp/CpG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_all_s456_trimmed_bismark_bt2.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 zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 19 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> zr1394_10_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_10_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_10_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_10_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_10_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_11_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_11_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_11_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_11_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_11_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_12_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_12_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_12_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_12_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_12_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_13_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_13_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_13_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_13_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_13_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_14_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_14_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_14_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_14_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_14_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_15_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_15_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_15_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_15_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_15_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_16_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_16_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_16_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_16_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_16_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_17_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_17_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_17_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_17_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_17_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_18_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_18_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_18_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_18_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_18_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_1_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_1_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_1_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_1_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_1_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_2_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_2_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_2_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_2_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_2_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_3_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_3_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_3_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_3_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_3_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_4_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_4_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_4_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_4_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_4_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_5_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_5_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_5_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_5_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_5_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_6_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_6_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_6_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_6_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_6_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_7_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_7_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_7_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_7_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_7_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_8_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_8_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_8_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_8_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_8_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_9_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_9_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_9_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_9_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_9_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_all_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_all_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_all_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_all_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_all_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_all_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_all_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Found Bismark/Bowtie2 single-end files No Bismark/Bowtie2 paired-end BAM files detected No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 19 Bismark BAM file(s)... >> Reading from Bismark report: zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_all_s456_trimmed_bismark_bt2_SE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html << [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_10snp.candidate.out. methCgFileName = zr1394_10meth.cg. methChgFileName = zr1394_10meth.chg. methChhFileName = zr1394_10meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_11snp.candidate.out. methCgFileName = zr1394_11meth.cg. methChgFileName = zr1394_11meth.chg. methChhFileName = zr1394_11meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_12snp.candidate.out. methCgFileName = zr1394_12meth.cg. methChgFileName = zr1394_12meth.chg. methChhFileName = zr1394_12meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_13snp.candidate.out. methCgFileName = zr1394_13meth.cg. methChgFileName = zr1394_13meth.chg. methChhFileName = zr1394_13meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_14snp.candidate.out. methCgFileName = zr1394_14meth.cg. methChgFileName = zr1394_14meth.chg. methChhFileName = zr1394_14meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_15snp.candidate.out. methCgFileName = zr1394_15meth.cg. methChgFileName = zr1394_15meth.chg. methChhFileName = zr1394_15meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_16snp.candidate.out. methCgFileName = zr1394_16meth.cg. methChgFileName = zr1394_16meth.chg. methChhFileName = zr1394_16meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_17snp.candidate.out. methCgFileName = zr1394_17meth.cg. methChgFileName = zr1394_17meth.chg. methChhFileName = zr1394_17meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_18snp.candidate.out. methCgFileName = zr1394_18meth.cg. methChgFileName = zr1394_18meth.chg. methChhFileName = zr1394_18meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_1snp.candidate.out. methCgFileName = zr1394_1meth.cg. methChgFileName = zr1394_1meth.chg. methChhFileName = zr1394_1meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_2snp.candidate.out. methCgFileName = zr1394_2meth.cg. methChgFileName = zr1394_2meth.chg. methChhFileName = zr1394_2meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_3snp.candidate.out. methCgFileName = zr1394_3meth.cg. methChgFileName = zr1394_3meth.chg. methChhFileName = zr1394_3meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_4snp.candidate.out. methCgFileName = zr1394_4meth.cg. methChgFileName = zr1394_4meth.chg. methChhFileName = zr1394_4meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_5snp.candidate.out. methCgFileName = zr1394_5meth.cg. methChgFileName = zr1394_5meth.chg. methChhFileName = zr1394_5meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_6snp.candidate.out. methCgFileName = zr1394_6meth.cg. methChgFileName = zr1394_6meth.chg. methChhFileName = zr1394_6meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_7snp.candidate.out. methCgFileName = zr1394_7meth.cg. methChgFileName = zr1394_7meth.chg. methChhFileName = zr1394_7meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_8snp.candidate.out. methCgFileName = zr1394_8meth.cg. methChgFileName = zr1394_8meth.chg. methChhFileName = zr1394_8meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_9snp.candidate.out. methCgFileName = zr1394_9meth.cg. methChgFileName = zr1394_9meth.chg. methChhFileName = zr1394_9meth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_all_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_allsnp.candidate.out. methCgFileName = zr1394_allmeth.cg. methChgFileName = zr1394_allmeth.chg. methChhFileName = zr1394_allmeth.chh. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_all_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_10_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_10_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_10_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_10_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_10_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_11_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_11_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_11_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_11_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_11_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_12_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_12_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_12_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_12_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_12_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_13_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_13_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_13_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_13_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_13_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_14_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_14_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_14_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_14_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_14_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_15_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_15_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_15_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_15_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_15_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_16_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_16_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_16_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_16_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_16_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_17_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_17_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_17_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_17_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_17_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_18_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_18_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_18_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_18_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_18_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_1_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_1_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_1_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_1_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_1_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_2_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_2_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_2_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_2_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_2_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_3_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_3_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_3_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_3_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_3_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_4_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_4_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_4_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_4_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_4_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_5_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_5_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_5_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_5_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_5_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_6_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_6_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_6_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_6_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_6_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_7_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_7_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_7_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_7_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_7_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_8_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_8_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_8_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_8_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_8_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_9_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_9_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_9_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_9_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_9_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110. zr1394_all_s456_trimmed_bismark_bt2 FLAG: 1 refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/v99/Olurida_v081-mergecat99.fa. bamFileName = zr1394_all_s456_trimmed_bismark_bt2.deduplicated.sorted.bam. snpFileName = zr1394_all_s456_trimmed_bismark_bt2.SNP-candidates.txt. methCgFileName = zr1394_all_s456_trimmed_bismark_bt2.CpG-meth-info.tab. methChgFileName = zr1394_all_s456_trimmed_bismark_bt2.CHG-meth-info.tab. methChhFileName = zr1394_all_s456_trimmed_bismark_bt2.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.