Path to genome folder specified as: /gscratch/srlab/sr320/data/olurida-bs/v082/ 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) A directory called /gscratch/srlab/sr320/data/olurida-bs/v082/Bisulfite_Genome/ already exists. Already existing converted sequences and/or already existing Bowtie 2 or HISAT2) indices will be overwritten! Step I - Prepare genome folders - completed Bismark Genome Preparation - Step II: Bisulfite converting reference genome conversions performed: chromosome C->T G->A Contig0 19690 21292 Contig2 23571 23595 Contig3 25186 27237 Contig5 23015 22905 Contig7 19570 20430 Contig9 19871 20719 Contig65 19060 17733 Contig84 17518 18418 Contig89 17329 17273 Contig468 18211 20941 Contig15326 18927 18446 Contig16524 21535 22100 Contig16668 17250 17528 Contig16915 19557 22573 Contig17050 20803 23816 Contig17624 20804 21380 Contig17876 23049 23114 Contig18024 19699 19064 Contig18052 20589 20701 Contig18174 18697 18986 Contig18571 19114 19373 Contig19267 21639 21348 Contig19330 19178 19189 Contig19646 34107 33002 Contig19826 18867 19710 Contig20140 23837 22387 Contig20625 19809 19324 Contig22814 24538 25089 Contig23978 19832 22048 Contig23979 22799 22846 Contig26138 18746 18999 Contig34578 26253 25187 Total number of conversions performed: C->T: 672650 G->A: 686753 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/v082/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 Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 33800 Using parameters --bmax 25350 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 25350 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 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 37, merged 129; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 14, merged 19; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 10, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 4, merged 8; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 4; iterating... Avg bucket size: 18739.8 (target: 25349) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 202 Getting block 2 of 202 Reserving size (25350) for bucket 1 Getting block 3 of 202 Getting block 4 of 202 Reserving size (25350) for bucket 2 Getting block 5 of 202 Getting block 6 of 202 Getting block 7 of 202 Getting block 8 of 202 Getting block 9 of 202 Getting block 10 of 202 Getting block 11 of 202 Getting block 12 of 202 Getting block 13 of 202 Getting block 14 of 202 Getting block 15 of 202 Getting block 16 of 202 Getting block 17 of 202 Getting block 18 of 202 Getting block 19 of 202 Getting block 20 of 202 Getting block 21 of 202 Getting block 22 of 202 Getting block 23 of 202 Getting block 24 of 202 Calculating Z arrays for bucket 1 Reserving size (25350) for bucket 3 Reserving size (25350) for bucket 4 Getting block 25 of 202 Getting block 26 of 202 Getting block 27 of 202 Calculating Z arrays for bucket 2 Reserving size (25350) for bucket 5 Reserving size (25350) for bucket 6 Reserving size (25350) for bucket 7 Reserving size (25350) for bucket 8 Reserving size (25350) for bucket 9 Reserving size (25350) for bucket 10 Reserving size (25350) for bucket 11 Reserving size (25350) for bucket 12 Reserving size (25350) for bucket 13 Reserving size (25350) for bucket 14 Reserving size (25350) for bucket 15 Reserving size (25350) for bucket 16 Reserving size (25350) for bucket 17 Reserving size (25350) for bucket 18 Reserving size (25350) for bucket 19 Reserving size (25350) for bucket 20 Reserving size (25350) for bucket 21 Reserving size (25350) for bucket 22 Reserving size (25350) for bucket 23 Reserving size (25350) for bucket 24 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 4 Reserving size (25350) for bucket 25 Reserving size (25350) for bucket 26 Reserving size (25350) for bucket 27 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 6 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 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 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: Calculating Z arrays for bucket 26 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 6: 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: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 27: bucket 1: 10% bucket 2: 10% bucket 3: 10% bucket 5: 10% bucket 4: 10% bucket 10: 10% bucket 11: 10% bucket 6: 10% bucket 9: 10% bucket 7: 10% bucket 8: 10% bucket 15: 10% bucket 14: 10% bucket 13: 10% bucket 12: 10% bucket 18: 10% bucket 26: 10% bucket 16: 10% bucket 17: 10% bucket 24: 10% bucket 20: 10% bucket 19: 10% bucket 25: 10% bucket 27: 10% bucket 22: 10% bucket 21: 10% bucket 23: 10% bucket 1: 20% bucket 2: 20% bucket 3: 20% bucket 5: 20% bucket 4: 20% bucket 10: 20% bucket 6: 20% bucket 11: 20% bucket 7: 20% bucket 8: 20% bucket 9: 20% bucket 15: 20% bucket 13: 20% bucket 14: 20% bucket 18: 20% bucket 12: 20% bucket 17: 20% bucket 16: 20% bucket 26: 20% bucket 24: 20% bucket 20: 20% bucket 19: 20% bucket 25: 20% bucket 27: 20% bucket 22: 20% bucket 21: 20% bucket 23: 20% bucket 1: 30% bucket 2: 30% bucket 3: 30% bucket 5: 30% bucket 4: 30% bucket 6: 30% bucket 10: 30% bucket 7: 30% bucket 11: 30% bucket 8: 30% bucket 9: 30% bucket 13: 30% bucket 15: 30% bucket 14: 30% bucket 12: 30% bucket 17: 30% bucket 18: 30% bucket 16: 30% bucket 26: 30% bucket 24: 30% bucket 19: 30% bucket 20: 30% bucket 25: 30% bucket 27: 30% bucket 22: 30% bucket 21: 30% bucket 23: 30% bucket 1: 40% bucket 2: 40% bucket 3: 40% bucket 5: 40% bucket 4: 40% bucket 6: 40% bucket 10: 40% bucket 7: 40% bucket 8: 40% bucket 11: 40% bucket 9: 40% bucket 13: 40% bucket 15: 40% bucket 14: 40% bucket 12: 40% bucket 17: 40% bucket 18: 40% bucket 16: 40% bucket 1: 50% bucket 26: 40% bucket 24: 40% bucket 19: 40% bucket 20: 40% bucket 25: 40% bucket 27: 40% bucket 22: 40% bucket 21: 40% bucket 2: 50% bucket 23: 40% bucket 3: 50% bucket 5: 50% bucket 4: 50% bucket 6: 50% bucket 7: 50% bucket 10: 50% bucket 8: 50% bucket 11: 50% bucket 9: 50% bucket 13: 50% bucket 15: 50% bucket 14: 50% bucket 1: 60% bucket 12: 50% bucket 17: 50% bucket 18: 50% bucket 16: 50% bucket 26: 50% bucket 24: 50% bucket 19: 50% bucket 20: 50% bucket 2: 60% bucket 25: 50% bucket 22: 50% bucket 27: 50% bucket 3: 60% bucket 21: 50% bucket 5: 60% bucket 4: 60% bucket 23: 50% bucket 6: 60% bucket 7: 60% bucket 10: 60% bucket 8: 60% bucket 11: 60% bucket 9: 60% bucket 1: 70% bucket 13: 60% bucket 15: 60% bucket 14: 60% bucket 12: 60% bucket 2: 70% bucket 17: 60% bucket 18: 60% bucket 16: 60% bucket 24: 60% bucket 26: 60% bucket 19: 60% bucket 20: 60% bucket 3: 70% bucket 25: 60% bucket 5: 70% bucket 22: 60% bucket 4: 70% bucket 27: 60% bucket 21: 60% bucket 6: 70% bucket 23: 60% bucket 7: 70% bucket 10: 70% bucket 1: 80% bucket 8: 70% bucket 11: 70% bucket 9: 70% bucket 13: 70% bucket 15: 70% bucket 2: 80% bucket 14: 70% bucket 12: 70% bucket 17: 70% bucket 3: 80% bucket 18: 70% bucket 16: 70% bucket 24: 70% bucket 19: 70% bucket 26: 70% bucket 5: 80% bucket 20: 70% bucket 4: 80% bucket 25: 70% bucket 27: 70% bucket 22: 70% bucket 6: 80% bucket 1: 90% bucket 21: 70% bucket 7: 80% bucket 10: 80% bucket 8: 80% bucket 23: 70% bucket 11: 80% bucket 9: 80% bucket 2: 90% bucket 13: 80% bucket 15: 80% bucket 12: 80% bucket 14: 80% bucket 3: 90% bucket 17: 80% bucket 5: 90% bucket 4: 90% bucket 18: 80% bucket 16: 80% bucket 24: 80% bucket 26: 80% bucket 19: 80% bucket 1: 100% Sorting block of length 7907 for bucket 1 (Using difference cover) bucket 20: 80% bucket 6: 90% bucket 25: 80% bucket 27: 80% bucket 22: 80% bucket 7: 90% bucket 10: 90% bucket 8: 90% bucket 21: 80% bucket 2: 100% Sorting block of length 21275 for bucket 2 (Using difference cover) bucket 11: 90% bucket 9: 90% bucket 23: 80% Sorting block time: 00:00:00 Returning block of 7908 for bucket 1 bucket 13: 90% bucket 3: 100% Sorting block of length 19387 for bucket 3 (Using difference cover) bucket 15: 90% bucket 12: 90% bucket 14: 90% bucket 5: 100% Sorting block of length 17368 for bucket 5 (Using difference cover) bucket 4: 100% Sorting block of length 24894 for bucket 4 (Using difference cover) bucket 17: 90% bucket 18: 90% bucket 16: 90% bucket 24: 90% bucket 19: 90% bucket 26: 90% bucket 20: 90% bucket 6: 100% Sorting block of length 14618 for bucket 6 (Using difference cover) Getting block 28 of 202 Reserving size (25350) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 25: 90% bucket 7: 100% Sorting block of length 25189 for bucket 7 (Using difference cover) bucket 10: 100% Sorting block of length 22951 for bucket 10 (Using difference cover) bucket 27: 90% bucket 22: 90% bucket 8: 100% Sorting block of length 22585 for bucket 8 (Using difference cover) bucket 11: 100% Sorting block of length 19987 for bucket 11 (Using difference cover) bucket 9: 100% Sorting block of length 18823 for bucket 9 (Using difference cover) bucket 21: 90% bucket 13: 100% Sorting block of length 18468 for bucket 13 (Using difference cover) Sorting block time: 00:00:00 Returning block of 21276 for bucket 2 bucket 15: 100% Sorting block of length 12582 for bucket 15 (Using difference cover) Sorting block time: 00:00:00 Returning block of 19388 for bucket 3 bucket 23: 90% Sorting block time: 00:00:00 Returning block of 17369 for bucket 5 bucket 12: 100% Sorting block of length 24342 for bucket 12 (Using difference cover) bucket 14: 100% Sorting block of length 17401 for bucket 14 (Using difference cover) bucket 17: 100% Sorting block of length 6694 for bucket 17 (Using difference cover) bucket 18: 100% Sorting block of length 21030 for bucket 18 (Using difference cover) Getting block 29 of 202 Reserving size (25350) for bucket 29 Calculating Z arrays for bucket 29 bucket 16: 100% Entering block accumulator loop for bucket 29: Sorting block of length 21086 for bucket 16 (Using difference cover) bucket 24: 100% Sorting block of length 4913 for bucket 24 (Using difference cover) bucket 19: 100% Sorting block of length 19253 for bucket 19 (Using difference cover) bucket 26: 100% Sorting block of length 14829 for bucket 26 (Using difference cover) bucket 20: 100% Sorting block of length 14672 for bucket 20 (Using difference cover) Getting block 30 of 202 Reserving size (25350) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 28: 10% bucket 25: 100% Sorting block of length 22617 for bucket 25 (Using difference cover) Getting block 31 of 202 Reserving size (25350) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: bucket 27: 100% Sorting block of length 13766 for bucket 27 (Using difference cover) bucket 22: 100% Sorting block of length 13093 for bucket 22 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14619 for bucket 6 bucket 21: 100% Sorting block of length 14758 for bucket 21 (Using difference cover) Getting block 32 of 202 Reserving size (25350) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: Sorting block time: 00:00:00 Returning block of 24895 for bucket 4 bucket 23: 100% Sorting block of length 23810 for bucket 23 (Using difference cover) bucket 29: 10% Getting block 33 of 202 Reserving size (25350) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: bucket 30: 10% bucket 28: 20% bucket 31: 10% Sorting block time: 00:00:00 Returning block of 4914 for bucket 24 bucket 32: 10% Getting block 34 of 202 Reserving size (25350) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: Sorting block time: 00:00:00 Returning block of 6695 for bucket 17 Getting block 35 of 202 Reserving size (25350) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: bucket 29: 20% bucket 33: 10% bucket 30: 20% bucket 28: 30% bucket 31: 20% Sorting block time: 00:00:00 Returning block of 24343 for bucket 12 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 18469 for bucket 13 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 19254 for bucket 19 Sorting block time: 00:00:00 Returning block of 14673 for bucket 20 Returning block of 21031 for bucket 18 Sorting block time: 00:00:00 Returning block of 22586 for bucket 8 Sorting block time: 00:00:00 Returning block of 12583 for bucket 15 Returning block of 19988 for bucket 11 Returning block of 25190 for bucket 7 Returning block of 13767 for bucket 27 Returning block of 18824 for bucket 9 Returning block of 14830 for bucket 26 Sorting block time: 00:00:00 Returning block of 13094 for bucket 22 Sorting block time: 00:00:00 Returning block of 17402 for bucket 14 bucket 32: 20% Sorting block time: 00:00:00 Returning block of 21087 for bucket 16 Getting block 36 of 202 Reserving size (25350) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: bucket 34: 10% Getting block 37 of 202 Reserving size (25350) for bucket 37 Calculating Z arrays for bucket 37 Getting block 38 of 202 Reserving size (25350) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 37: Entering block accumulator loop for bucket 38: Sorting block time: 00:00:00 Returning block of 14759 for bucket 21 Getting block 39 of 202 Reserving size (25350) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Getting block 40 of 202 Reserving size (25350) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: bucket 29: 30% Getting block 41 of 202 Reserving size (25350) for bucket 41 bucket 35: 10% Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: bucket 33: 20% Getting block 42 of 202 Reserving size (25350) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: bucket 28: 40% Getting block 43 of 202 Reserving size (25350) for bucket 43 Calculating Z arrays for bucket 43 bucket 30: 30% Entering block accumulator loop for bucket 43: Sorting block time: 00:00:00 Returning block of 22618 for bucket 25 Getting block 44 of 202 Reserving size (25350) for bucket 44 Calculating Z arrays for bucket 44 Sorting block time: 00:00:00 Returning block of 22952 for bucket 10 Entering block accumulator loop for bucket 44: bucket 31: 30% Getting block 45 of 202 Reserving size (25350) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Getting block 46 of 202 Reserving size (25350) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: Getting block 47 of 202 Reserving size (25350) for bucket 47 Getting block 48 of 202 Calculating Z arrays for bucket 47 Reserving size (25350) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 47: Entering block accumulator loop for bucket 48: Getting block 49 of 202 Reserving size (25350) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: Getting block 50 of 202 Reserving size (25350) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: Getting block 51 of 202 Reserving size (25350) for bucket 51 Calculating Z arrays for bucket 51 Sorting block time: 00:00:00 Returning block of 23811 for bucket 23 Entering block accumulator loop for bucket 51: bucket 32: 30% bucket 36: 10% Getting block 52 of 202 Reserving size (25350) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 34: 20% bucket 37: 10% Getting block 53 of 202 Reserving size (25350) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 38: 10% bucket 39: 10% bucket 40: 10% bucket 29: 40% bucket 41: 10% bucket 28: 50% bucket 35: 20% bucket 33: 30% bucket 30: 40% bucket 31: 40% bucket 42: 10% Getting block 54 of 202 Reserving size (25350) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 44: 10% bucket 45: 10% bucket 46: 10% bucket 48: 10% bucket 47: 10% bucket 49: 10% bucket 50: 10% bucket 51: 10% bucket 32: 40% bucket 36: 20% bucket 43: 10% bucket 34: 30% bucket 37: 20% bucket 38: 20% bucket 52: 10% bucket 39: 20% bucket 29: 50% bucket 40: 20% bucket 53: 10% bucket 28: 60% bucket 41: 20% bucket 30: 50% bucket 33: 40% bucket 31: 50% bucket 35: 30% bucket 42: 20% bucket 44: 20% bucket 54: 10% bucket 46: 20% bucket 45: 20% bucket 47: 20% bucket 48: 20% bucket 49: 20% bucket 32: 50% bucket 36: 30% bucket 50: 20% bucket 51: 20% bucket 34: 40% bucket 37: 30% bucket 29: 60% bucket 38: 30% bucket 39: 30% bucket 28: 70% bucket 40: 30% bucket 31: 60% bucket 30: 60% bucket 41: 30% bucket 33: 50% bucket 52: 20% bucket 53: 20% bucket 35: 40% bucket 42: 30% bucket 43: 20% bucket 44: 30% bucket 54: 20% bucket 46: 30% bucket 45: 30% bucket 47: 30% bucket 48: 30% bucket 32: 60% bucket 36: 40% bucket 49: 30% bucket 34: 50% bucket 51: 30% bucket 50: 30% bucket 37: 40% bucket 29: 70% bucket 28: 80% bucket 38: 40% bucket 31: 70% bucket 40: 40% bucket 39: 40% bucket 30: 70% bucket 41: 40% bucket 33: 60% bucket 35: 50% bucket 52: 30% bucket 42: 40% bucket 44: 40% bucket 46: 40% bucket 45: 40% bucket 54: 30% bucket 36: 50% bucket 32: 70% bucket 47: 40% bucket 48: 40% bucket 49: 40% bucket 43: 30% bucket 34: 60% bucket 29: 80% bucket 28: 90% bucket 37: 50% bucket 31: 80% bucket 30: 80% bucket 40: 50% bucket 38: 50% bucket 39: 50% bucket 41: 50% bucket 51: 40% bucket 50: 40% bucket 33: 70% bucket 35: 60% bucket 42: 50% bucket 52: 40% bucket 44: 50% bucket 46: 50% bucket 45: 50% bucket 36: 60% bucket 32: 80% bucket 54: 40% bucket 28: 100% bucket 34: 70% Sorting block of length 24556 for bucket 28 (Using difference cover) bucket 29: 90% bucket 47: 50% bucket 31: 90% bucket 37: 60% bucket 49: 50% bucket 48: 50% bucket 30: 90% bucket 53: 30% bucket 40: 60% bucket 41: 60% bucket 39: 60% bucket 38: 60% bucket 33: 80% bucket 51: 50% bucket 50: 50% bucket 35: 70% bucket 43: 40% bucket 42: 60% bucket 52: 50% bucket 44: 60% bucket 36: 70% bucket 46: 60% bucket 32: 90% bucket 45: 60% bucket 29: 100% Sorting block of length 24839 for bucket 29 (Using difference cover) bucket 31: 100% Sorting block of length 8354 for bucket 31 (Using difference cover) bucket 54: 50% bucket 34: 80% bucket 30: 100% Sorting block of length 20587 for bucket 30 (Using difference cover) bucket 37: 70% Sorting block time: 00:00:00 Returning block of 24557 for bucket 28 bucket 41: 70% bucket 47: 60% bucket 40: 70% bucket 33: 90% bucket 39: 70% bucket 49: 60% bucket 38: 70% bucket 48: 60% bucket 53: 40% Getting block 55 of 202 Reserving size (25350) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 35: 80% bucket 51: 60% Sorting block time: 00:00:00 Returning block of 8355 for bucket 31 bucket 50: 60% bucket 42: 70% bucket 52: 60% bucket 43: 50% bucket 44: 70% bucket 36: 80% bucket 32: 100% Sorting block of length 23949 for bucket 32 (Using difference cover) bucket 46: 70% bucket 45: 70% bucket 34: 90% Sorting block time: 00:00:00 Returning block of 20588 for bucket 30 bucket 37: 80% bucket 41: 80% bucket 54: 60% bucket 33: 100% Sorting block of length 15522 for bucket 33 (Using difference cover) bucket 40: 80% bucket 39: 80% bucket 38: 80% bucket 47: 70% bucket 49: 70% bucket 48: 70% bucket 53: 50% bucket 35: 90% Sorting block time: 00:00:00 Returning block of 24840 for bucket 29 bucket 55: 10% Getting block 56 of 202 Reserving size (25350) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 51: 70% bucket 42: 80% bucket 50: 70% Getting block 57 of 202 Reserving size (25350) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 36: 90% bucket 52: 70% Getting block 58 of 202 Reserving size (25350) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: Sorting block time: 00:00:00 Returning block of 23950 for bucket 32 Sorting block time: 00:00:00 Returning block of 15523 for bucket 33 bucket 44: 80% bucket 46: 80% Getting block 59 of 202 Reserving size (25350) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 34: 100% Sorting block of length 16934 for bucket 34 (Using difference cover) bucket 45: 80% bucket 37: 90% bucket 43: 60% bucket 41: 90% bucket 40: 90% bucket 39: 90% bucket 38: 90% bucket 54: 70% bucket 47: 80% bucket 49: 80% bucket 35: 100% Sorting block of length 23920 for bucket 35 (Using difference cover) bucket 53: 60% bucket 48: 80% bucket 55: 20% bucket 42: 90% bucket 51: 80% Sorting block time: 00:00:00 Returning block of 16935 for bucket 34 bucket 36: 100% Sorting block of length 16202 for bucket 36 (Using difference cover) Getting block 60 of 202 Reserving size (25350) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 57: 10% bucket 50: 80% bucket 44: 90% bucket 52: 80% Getting block 61 of 202 Reserving size (25350) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: bucket 56: 10% bucket 58: 10% bucket 46: 90% bucket 37: 100% bucket 41: 100% Sorting block of length 25283 for bucket 37 (Using difference cover) Sorting block of length 8152 for bucket 41 (Using difference cover) bucket 45: 90% bucket 40: 100% Sorting block of length 21568 for bucket 40 (Using difference cover) bucket 59: 10% bucket 39: 100% Sorting block of length 9999 for bucket 39 (Using difference cover) bucket 38: 100% Sorting block of length 25309 for bucket 38 (Using difference cover) bucket 43: 70% bucket 54: 80% bucket 49: 90% bucket 47: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 48: 90% Returning block of 23921 for bucket 35 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 16203 for bucket 36 bucket 53: 70% bucket 42: 100% bucket 55: 30% bucket 51: 90% Returning block of 8153 for bucket 41 bucket 44: 100% bucket 50: 90% Returning block of 10000 for bucket 39 bucket 57: 20% bucket 52: 90% bucket 60: 10% bucket 46: 100% bucket 58: 20% bucket 56: 20% bucket 45: 100% bucket 61: 10% bucket 59: 20% Returning block of 21569 for bucket 40 Sorting block of length 24156 for bucket 42 (Using difference cover) Sorting block time: 00:00:00 Getting block 62 of 202 Sorting block of length 20409 for bucket 44 (Using difference cover) Sorting block of length 20568 for bucket 46 (Using difference cover) Sorting block of length 17922 for bucket 45 (Using difference cover) Returning block of 25284 for bucket 37 Reserving size (25350) for bucket 62 bucket 54: 90% Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 49: 100% Sorting block of length 8937 for bucket 49 (Using difference cover) bucket 43: 80% bucket 47: 100% Sorting block of length 21363 for bucket 47 (Using difference cover) Getting block 63 of 202 Reserving size (25350) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 48: 100% Sorting block of length 20553 for bucket 48 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25310 for bucket 38 Getting block 64 of 202 Reserving size (25350) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: Getting block 65 of 202 Reserving size (25350) for bucket 65 Calculating Z arrays for bucket 65 Getting block 66 of 202 Entering block accumulator loop for bucket 65: Reserving size (25350) for bucket 66 bucket 53: 80% bucket 51: 100% bucket 52: 100% bucket 55: 40% bucket 50: 100% bucket 54: 100% bucket 57: 30% Calculating Z arrays for bucket 66 Getting block 67 of 202 Sorting block of length 23840 for bucket 51 (Using difference cover) Sorting block of length 17772 for bucket 52 (Using difference cover) Sorting block of length 21671 for bucket 50 (Using difference cover) bucket 59: 30% bucket 58: 30% Sorting block of length 24935 for bucket 54 (Using difference cover) Reserving size (25350) for bucket 67 bucket 60: 20% Entering block accumulator loop for bucket 66: bucket 56: 30% Calculating Z arrays for bucket 67 bucket 61: 20% Entering block accumulator loop for bucket 67: Sorting block time: 00:00:00 Returning block of 8938 for bucket 49 bucket 62: 10% bucket 43: 90% Getting block 68 of 202 Reserving size (25350) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 21364 for bucket 47 Sorting block time: 00:00:00 Returning block of 20554 for bucket 48 Returning block of 24157 for bucket 42 Getting block 69 of 202 Reserving size (25350) for bucket 69 Calculating Z arrays for bucket 69 bucket 63: 10% Entering block accumulator loop for bucket 69: Sorting block time: 00:00:00 Returning block of 20569 for bucket 46 bucket 64: 10% Getting block 70 of 202 Reserving size (25350) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: Getting block 71 of 202 Reserving size (25350) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: Getting block 72 of 202 Reserving size (25350) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 67: 10% bucket 53: 90% Sorting block time: 00:00:00 Returning block of 17923 for bucket 45 bucket 55: 50% Sorting block time: 00:00:00 Returning block of 20410 for bucket 44 bucket 57: 40% bucket 59: 40% bucket 58: 40% bucket 68: 10% bucket 56: 40% bucket 66: 10% bucket 65: 10% bucket 60: 30% Sorting block time: 00:00:00 Returning block of 23841 for bucket 51 bucket 43: 100% Sorting block of length 19562 for bucket 43 (Using difference cover) bucket 61: 30% bucket 69: 10% Getting block 73 of 202 Reserving size (25350) for bucket 73 Calculating Z arrays for bucket 73 Getting block 74 of 202 Entering block accumulator loop for bucket 73: Reserving size (25350) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: bucket 62: 20% Sorting block time: 00:00:00 Returning block of 24936 for bucket 54 bucket 70: 10% bucket 71: 10% Sorting block time: 00:00:00 Returning block of 17773 for bucket 52 Getting block 75 of 202 Reserving size (25350) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 63: 20% Getting block 76 of 202 Reserving size (25350) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 64: 20% Sorting block time: 00:00:00 Returning block of 21672 for bucket 50 Getting block 77 of 202 Reserving size (25350) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 72: 10% Getting block 78 of 202 Reserving size (25350) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 67: 20% Sorting block time: 00:00:00 Returning block of 19563 for bucket 43 bucket 68: 20% bucket 53: 100% Sorting block of length 19620 for bucket 53 (Using difference cover) bucket 55: 60% bucket 57: 50% bucket 69: 20% bucket 59: 50% Getting block 79 of 202 Reserving size (25350) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 58: 50% bucket 74: 10% bucket 73: 10% bucket 66: 20% bucket 70: 20% bucket 60: 40% bucket 71: 20% bucket 56: 50% bucket 61: 40% bucket 65: 20% bucket 75: 10% bucket 62: 30% bucket 76: 10% bucket 77: 10% bucket 63: 30% Getting block 80 of 202 Reserving size (25350) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 64: 30% bucket 72: 20% bucket 78: 10% Sorting block time: 00:00:00 Returning block of 19621 for bucket 53 bucket 67: 30% Getting block 81 of 202 Reserving size (25350) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 68: 30% bucket 69: 30% bucket 55: 70% bucket 79: 10% bucket 74: 20% bucket 71: 30% bucket 57: 60% bucket 59: 60% bucket 73: 20% bucket 58: 60% bucket 70: 30% bucket 66: 30% bucket 75: 20% bucket 60: 50% bucket 61: 50% bucket 56: 60% bucket 76: 20% bucket 65: 30% bucket 77: 20% bucket 62: 40% bucket 80: 10% bucket 78: 20% bucket 72: 30% bucket 63: 40% bucket 67: 40% bucket 64: 40% bucket 68: 40% bucket 81: 10% bucket 69: 40% bucket 79: 20% bucket 71: 40% bucket 55: 80% bucket 74: 30% bucket 70: 40% bucket 73: 30% bucket 57: 70% bucket 59: 70% bucket 58: 70% bucket 75: 30% bucket 66: 40% bucket 76: 30% bucket 60: 60% bucket 77: 30% bucket 80: 20% bucket 56: 70% bucket 61: 60% bucket 78: 30% bucket 65: 40% bucket 62: 50% bucket 72: 40% bucket 67: 50% bucket 68: 50% bucket 63: 50% bucket 64: 50% bucket 69: 50% bucket 81: 20% bucket 71: 50% bucket 79: 30% bucket 74: 40% bucket 70: 50% bucket 55: 90% bucket 73: 40% bucket 75: 40% bucket 57: 80% bucket 59: 80% bucket 80: 30% bucket 76: 40% bucket 58: 80% bucket 77: 40% bucket 66: 50% bucket 78: 40% bucket 60: 70% bucket 56: 80% bucket 72: 50% bucket 61: 70% bucket 67: 60% bucket 68: 60% bucket 62: 60% bucket 65: 50% bucket 71: 60% bucket 69: 60% bucket 79: 40% bucket 81: 30% bucket 63: 60% bucket 70: 60% bucket 74: 50% bucket 64: 60% bucket 55: 100% Sorting block of length 14954 for bucket 55 (Using difference cover) bucket 73: 50% bucket 75: 50% bucket 80: 40% bucket 76: 50% bucket 57: 90% bucket 77: 50% bucket 59: 90% bucket 78: 50% bucket 58: 90% bucket 66: 60% bucket 67: 70% bucket 72: 60% bucket 68: 70% bucket 56: 90% bucket 60: 80% Sorting block time: 00:00:00 Returning block of 14955 for bucket 55 bucket 61: 80% bucket 71: 70% bucket 79: 50% bucket 69: 70% bucket 81: 40% bucket 62: 70% bucket 65: 60% Getting block 82 of 202 Reserving size (25350) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 70: 70% bucket 74: 60% bucket 63: 70% bucket 73: 60% bucket 80: 50% bucket 75: 60% bucket 64: 70% bucket 78: 60% bucket 77: 60% bucket 76: 60% bucket 57: 100% Sorting block of length 4688 for bucket 57 (Using difference cover) bucket 59: 100% Sorting block of length 18738 for bucket 59 (Using difference cover) bucket 67: 80% bucket 58: 100% Sorting block of length 22497 for bucket 58 (Using difference cover) bucket 72: 70% bucket 68: 80% bucket 66: 70% Sorting block time: 00:00:00 Returning block of 4689 for bucket 57 bucket 71: 80% bucket 79: 60% bucket 56: 100% Sorting block of length 24290 for bucket 56 (Using difference cover) bucket 60: 90% bucket 69: 80% bucket 81: 50% Getting block 83 of 202 Reserving size (25350) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 61: 90% bucket 82: 10% bucket 70: 80% bucket 74: 70% bucket 62: 80% bucket 65: 70% bucket 80: 60% bucket 73: 70% Sorting block time: 00:00:00 Returning block of 18739 for bucket 59 bucket 75: 70% bucket 78: 70% bucket 77: 70% bucket 76: 70% bucket 63: 80% Getting block 84 of 202 Reserving size (25350) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: Sorting block time: 00:00:00 Returning block of 22498 for bucket 58 bucket 64: 80% bucket 67: 90% bucket 68: 90% bucket 72: 80% bucket 71: 90% Getting block 85 of 202 Reserving size (25350) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 79: 70% Sorting block time: 00:00:00 Returning block of 24291 for bucket 56 bucket 69: 90% bucket 81: 60% bucket 66: 80% bucket 83: 10% bucket 82: 20% bucket 70: 90% Getting block 86 of 202 Reserving size (25350) for bucket 86 Calculating Z arrays for bucket 86 bucket 60: 100% Sorting block of length 19853 for bucket 60 (Using difference cover) Entering block accumulator loop for bucket 86: bucket 74: 80% bucket 80: 70% bucket 61: 100% Sorting block of length 17151 for bucket 61 (Using difference cover) bucket 62: 90% bucket 73: 80% bucket 75: 80% bucket 78: 80% bucket 65: 80% bucket 77: 80% bucket 76: 80% bucket 84: 10% bucket 67: 100% Sorting block of length 17638 for bucket 67 (Using difference cover) bucket 68: 100% Sorting block of length 16100 for bucket 68 (Using difference cover) bucket 63: 90% bucket 71: 100% Sorting block of length 7465 for bucket 71 (Using difference cover) bucket 79: 80% bucket 64: 90% bucket 85: 10% bucket 69: 100% Sorting block of length 21179 for bucket 69 (Using difference cover) bucket 81: 70% Sorting block time: 00:00:00 Returning block of 19854 for bucket 60 bucket 72: 90% bucket 82: 30% bucket 70: 100% Sorting block of length 23282 for bucket 70 (Using difference cover) Sorting block time: 00:00:00 Returning block of 17152 for bucket 61 bucket 66: 90% bucket 80: 80% bucket 86: 10% Getting block 87 of 202 Reserving size (25350) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 74: 90% bucket 78: 90% Sorting block time: 00:00:00 Returning block of 7466 for bucket 71 bucket 75: 90% bucket 73: 90% bucket 83: 20% bucket 77: 90% bucket 62: 100% Sorting block of length 20373 for bucket 62 (Using difference cover) bucket 76: 90% Getting block 88 of 202 Reserving size (25350) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 65: 90% bucket 84: 20% Sorting block time: 00:00:00 Returning block of 16101 for bucket 68 Sorting block time: 00:00:00 Returning block of 17639 for bucket 67 bucket 79: 90% Getting block 89 of 202 Reserving size (25350) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: Getting block 90 of 202 Reserving size (25350) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 85: 20% bucket 63: 100% Sorting block time: 00:00:00 Sorting block of length 19842 for bucket 63 (Using difference cover) Returning block of 21180 for bucket 69 Getting block 91 of 202 bucket 81: 80% Reserving size (25350) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 82: 40% bucket 64: 100% Sorting block of length 21103 for bucket 64 (Using difference cover) bucket 72: 100% Sorting block of length 43396 for bucket 72 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23283 for bucket 70 bucket 80: 90% bucket 66: 100% Sorting block of length 15956 for bucket 66 (Using difference cover) bucket 74: 100% Sorting block of length 24797 for bucket 74 (Using difference cover) bucket 86: 20% bucket 87: 10% Getting block 92 of 202 Reserving size (25350) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: Getting block 93 of 202 Reserving size (25350) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: Sorting block time: 00:00:00 Returning block of 20374 for bucket 62 bucket 78: 100% Sorting block of length 18474 for bucket 78 (Using difference cover) bucket 75: 100% Sorting block of length 19834 for bucket 75 (Using difference cover) bucket 73: 100% Sorting block of length 23037 for bucket 73 (Using difference cover) bucket 83: 30% Getting block 94 of 202 bucket 77: 100% Reserving size (25350) for bucket 94 Sorting block of length 22923 for bucket 77 (Using difference cover) Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: bucket 76: 100% Sorting block of length 6071 for bucket 76 (Using difference cover) bucket 79: 100% bucket 88: 10% Sorting block of length 13173 for bucket 79 (Using difference cover) bucket 84: 30% Sorting block time: 00:00:00 Returning block of 19843 for bucket 63 bucket 65: 100% Sorting block of length 15185 for bucket 65 (Using difference cover) bucket 90: 10% bucket 89: 10% bucket 81: 90% bucket 85: 30% bucket 82: 50% bucket 91: 10% bucket 80: 100% Sorting block of length 17215 for bucket 80 (Using difference cover) Sorting block time: 00:00:00 Returning block of 15957 for bucket 66 Sorting block time: 00:00:00 Returning block of 21104 for bucket 64 Getting block 95 of 202 Reserving size (25350) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: Getting block 96 of 202 Reserving size (25350) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: Getting block 97 of 202 Reserving size (25350) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 18475 for bucket 78 Sorting block time: 00:00:00 Returning block of 24798 for bucket 74 bucket 92: 10% Returning block of 6072 for bucket 76 bucket 86: 30% bucket 87: 20% Sorting block time: 00:00:00 Returning block of 13174 for bucket 79 bucket 93: 10% Getting block 98 of 202 bucket 83: 40% Reserving size (25350) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: Sorting block time: 00:00:00 Returning block of 19835 for bucket 75 Getting block 99 of 202 Reserving size (25350) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: Getting block 100 of 202 Reserving size (25350) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: bucket 94: 10% Sorting block time: 00:00:00 Returning block of 22924 for bucket 77 Sorting block time: 00:00:00 Returning block of 15186 for bucket 65 bucket 84: 40% Sorting block time: 00:00:00 Returning block of 43397 for bucket 72 bucket 88: 20% Getting block 101 of 202 Reserving size (25350) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: Getting block 102 of 202 Reserving size (25350) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: Getting block 103 of 202 Reserving size (25350) for bucket 103 Calculating Z arrays for bucket 103 bucket 90: 20% Entering block accumulator loop for bucket 103: bucket 82: 60% bucket 81: 100% Sorting block of length 24872 for bucket 81 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23038 for bucket 73 bucket 89: 20% bucket 85: 40% Sorting block time: 00:00:00 Returning block of 17216 for bucket 80 bucket 91: 20% Getting block 104 of 202 Reserving size (25350) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: Getting block 105 of 202 Reserving size (25350) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: Getting block 106 of 202 Reserving size (25350) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 95: 10% bucket 96: 10% bucket 92: 20% bucket 86: 40% bucket 87: 30% bucket 97: 10% bucket 93: 20% Getting block 107 of 202 Reserving size (25350) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 83: 50% bucket 98: 10% bucket 94: 20% bucket 99: 10% bucket 100: 10% bucket 84: 50% bucket 82: 70% bucket 88: 30% bucket 90: 30% Sorting block time: 00:00:00 Returning block of 24873 for bucket 81 bucket 85: 50% bucket 102: 10% bucket 89: 30% bucket 91: 30% bucket 103: 10% bucket 101: 10% bucket 104: 10% bucket 105: 10% Getting block 108 of 202 Reserving size (25350) for bucket 108 Calculating Z arrays for bucket 108 bucket 95: 20% Entering block accumulator loop for bucket 108: bucket 106: 10% bucket 96: 20% bucket 92: 30% bucket 87: 40% bucket 97: 20% bucket 83: 60% bucket 93: 30% bucket 107: 10% bucket 98: 20% bucket 94: 30% bucket 82: 80% bucket 84: 60% bucket 90: 40% bucket 99: 20% bucket 100: 20% bucket 88: 40% bucket 85: 60% bucket 91: 40% bucket 89: 40% bucket 102: 20% bucket 103: 20% bucket 95: 30% bucket 104: 20% bucket 105: 20% bucket 101: 20% bucket 96: 30% bucket 92: 40% bucket 108: 10% bucket 87: 50% bucket 106: 20% bucket 83: 70% bucket 93: 40% bucket 97: 30% bucket 82: 90% bucket 94: 40% bucket 98: 30% bucket 84: 70% bucket 90: 50% bucket 107: 20% bucket 85: 70% bucket 88: 50% bucket 91: 50% bucket 89: 50% bucket 100: 30% bucket 99: 30% bucket 102: 30% bucket 95: 40% bucket 83: 80% bucket 92: 50% bucket 96: 40% bucket 103: 30% bucket 87: 60% bucket 104: 30% bucket 105: 30% bucket 108: 20% bucket 106: 30% bucket 93: 50% bucket 101: 30% bucket 97: 40% bucket 82: 100% Sorting block of length 24275 for bucket 82 (Using difference cover) bucket 94: 50% bucket 84: 80% bucket 98: 40% bucket 86: 50% bucket 90: 60% bucket 85: 80% bucket 91: 60% bucket 88: 60% bucket 89: 60% bucket 100: 40% bucket 107: 30% bucket 99: 40% bucket 102: 40% bucket 83: 90% bucket 92: 60% bucket 96: 50% bucket 95: 50% bucket 87: 70% bucket 103: 40% bucket 104: 40% bucket 105: 40% bucket 93: 60% Sorting block time: 00:00:00 Returning block of 24276 for bucket 82 bucket 106: 40% bucket 97: 50% Getting block 109 of 202 bucket 94: 60% Reserving size (25350) for bucket 109 bucket 84: 90% Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 101: 40% bucket 90: 70% bucket 86: 60% bucket 85: 90% bucket 98: 50% bucket 91: 70% bucket 88: 70% bucket 89: 70% bucket 83: 100% Sorting block of length 24674 for bucket 83 (Using difference cover) bucket 100: 50% bucket 102: 50% bucket 92: 70% bucket 96: 60% bucket 107: 40% bucket 99: 50% bucket 87: 80% bucket 95: 60% bucket 93: 70% bucket 104: 50% bucket 108: 30% bucket 103: 50% bucket 105: 50% bucket 97: 60% bucket 106: 50% bucket 84: 100% Sorting block of length 15180 for bucket 84 (Using difference cover) bucket 94: 70% bucket 90: 80% bucket 85: 100% Sorting block of length 21912 for bucket 85 (Using difference cover) bucket 86: 70% bucket 91: 80% bucket 109: 10% bucket 98: 60% bucket 89: 80% bucket 88: 80% bucket 101: 50% Sorting block time: 00:00:00 Returning block of 24675 for bucket 83 Getting block 110 of 202 Reserving size (25350) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 92: 80% bucket 100: 60% bucket 96: 70% Sorting block time: 00:00:00 Returning block of 15181 for bucket 84 bucket 87: 90% bucket 102: 60% bucket 95: 70% bucket 107: 50% Getting block 111 of 202 Reserving size (25350) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: bucket 99: 60% bucket 93: 80% Sorting block time: 00:00:00 Returning block of 21913 for bucket 85 bucket 104: 60% bucket 108: 40% bucket 105: 60% bucket 103: 60% bucket 97: 70% bucket 90: 90% bucket 94: 80% bucket 91: 90% Getting block 112 of 202 Reserving size (25350) for bucket 112 Calculating Z arrays for bucket 112 bucket 86: 80% Entering block accumulator loop for bucket 112: bucket 106: 60% bucket 98: 70% bucket 89: 90% bucket 109: 20% bucket 88: 90% bucket 101: 60% bucket 92: 90% bucket 96: 80% bucket 87: 100% Sorting block of length 9828 for bucket 87 (Using difference cover) bucket 100: 70% bucket 110: 10% bucket 95: 80% bucket 102: 70% bucket 93: 90% bucket 99: 70% bucket 107: 60% bucket 111: 10% bucket 90: 100% Sorting block of length 20840 for bucket 90 (Using difference cover) bucket 108: 50% bucket 104: 70% Sorting block time: 00:00:00 bucket 105: 70% Returning block of 9829 for bucket 87 bucket 91: 100% bucket 97: 80% Sorting block of length 9921 for bucket 91 (Using difference cover) bucket 94: 90% bucket 86: 90% bucket 103: 70% bucket 112: 10% Getting block 113 of 202 Reserving size (25350) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 106: 70% bucket 89: 100% Sorting block of length 18218 for bucket 89 (Using difference cover) bucket 98: 80% bucket 109: 30% bucket 88: 100% Sorting block of length 21985 for bucket 88 (Using difference cover) Sorting block time: 00:00:00 Returning block of 9922 for bucket 91 bucket 92: 100% Sorting block of length 22330 for bucket 92 (Using difference cover) Getting block 114 of 202 Reserving size (25350) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 96: 90% bucket 95: 90% bucket 100: 80% bucket 101: 70% bucket 102: 80% bucket 110: 20% Sorting block time: 00:00:00 Returning block of 20841 for bucket 90 bucket 93: 100% Sorting block of length 23090 for bucket 93 (Using difference cover) bucket 99: 80% Sorting block time: 00:00:00 Returning block of 18219 for bucket 89 bucket 107: 70% bucket 94: 100% Sorting block of length 14871 for bucket 94 (Using difference cover) bucket 86: 100% bucket 108: 60% Sorting block of length 24208 for bucket 86 (Using difference cover) bucket 97: 90% bucket 104: 80% bucket 111: 20% Getting block 115 of 202 Reserving size (25350) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 105: 80% Getting block 116 of 202 Reserving size (25350) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: Sorting block time: 00:00:00 Returning block of 21986 for bucket 88 bucket 103: 80% bucket 112: 20% bucket 113: 10% bucket 98: 90% bucket 106: 80% Getting block 117 of 202 Reserving size (25350) for bucket 117 Calculating Z arrays for bucket 117 Sorting block time: 00:00:00 Returning block of 22331 for bucket 92 Entering block accumulator loop for bucket 117: bucket 109: 40% Getting block 118 of 202 Reserving size (25350) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: bucket 96: 100% Sorting block of length 6710 for bucket 96 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14872 for bucket 94 bucket 114: 10% bucket 95: 100% Sorting block of length 19110 for bucket 95 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23091 for bucket 93 Getting block 119 of 202 Reserving size (25350) for bucket 119 Calculating Z arrays for bucket 119 bucket 100: 90% Entering block accumulator loop for bucket 119: bucket 102: 90% bucket 110: 30% Sorting block time: 00:00:00 Returning block of 6711 for bucket 96 bucket 101: 80% Sorting block time: 00:00:00 Returning block of 24209 for bucket 86 bucket 99: 90% Getting block 120 of 202 Reserving size (25350) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 97: 100% Sorting block of length 21764 for bucket 97 (Using difference cover) bucket 108: 70% Getting block 121 of 202 bucket 104: 90% Reserving size (25350) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 107: 80% bucket 105: 90% bucket 111: 30% bucket 116: 10% bucket 115: 10% bucket 103: 90% bucket 98: 100% Sorting block of length 25010 for bucket 98 (Using difference cover) bucket 112: 30% bucket 113: 20% bucket 106: 90% Sorting block time: 00:00:00 Returning block of 19111 for bucket 95 bucket 117: 10% bucket 109: 50% Getting block 122 of 202 Reserving size (25350) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 118: 10% bucket 114: 20% bucket 119: 10% bucket 100: 100% Sorting block of length 21453 for bucket 100 (Using difference cover) Sorting block time: 00:00:00 Returning block of 21765 for bucket 97 bucket 102: 100% Sorting block of length 4587 for bucket 102 (Using difference cover) bucket 110: 40% Getting block 123 of 202 Reserving size (25350) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: Getting block 124 of 202 bucket 99: 100% Reserving size (25350) for bucket 124 Sorting block of length 20123 for bucket 99 (Using difference cover) Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 120: 10% bucket 101: 90% Sorting block time: 00:00:00 Returning block of 4588 for bucket 102 bucket 108: 80% bucket 104: 100% Sorting block of length 19156 for bucket 104 (Using difference cover) bucket 121: 10% bucket 107: 90% bucket 105: 100% Sorting block of length 23224 for bucket 105 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25011 for bucket 98 Getting block 125 of 202 Reserving size (25350) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: bucket 115: 20% bucket 116: 20% bucket 103: 100% Sorting block of length 24034 for bucket 103 (Using difference cover) bucket 111: 40% bucket 112: 40% bucket 113: 30% bucket 106: 100% Sorting block of length 10754 for bucket 106 (Using difference cover) bucket 117: 20% bucket 109: 60% bucket 122: 10% bucket 118: 20% Sorting block time: 00:00:00 Returning block of 21454 for bucket 100 bucket 114: 30% Sorting block time: 00:00:00 Returning block of 20124 for bucket 99 bucket 119: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 10755 for bucket 106 Returning block of 19157 for bucket 104 Getting block 126 of 202 Reserving size (25350) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: bucket 110: 50% bucket 123: 10% Sorting block time: 00:00:00 Returning block of 23225 for bucket 105 Getting block 127 of 202 Reserving size (25350) for bucket 127 Calculating Z arrays for bucket 127 Getting block 128 of 202 Entering block accumulator loop for bucket 127: Reserving size (25350) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: bucket 120: 20% bucket 124: 10% Getting block 129 of 202 Reserving size (25350) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: bucket 108: 90% Getting block 130 of 202 Reserving size (25350) for bucket 130 Sorting block time: 00:00:00 Calculating Z arrays for bucket 130 Returning block of 24035 for bucket 103 bucket 121: 20% bucket 101: 100% bucket 125: 10% bucket 115: 30% bucket 107: 100% bucket 116: 30% bucket 112: 50% bucket 113: 40% bucket 111: 50% bucket 117: 30% bucket 109: 70% bucket 122: 20% bucket 118: 30% bucket 114: 40% bucket 119: 30% Getting block 131 of 202 Entering block accumulator loop for bucket 130: Sorting block of length 24183 for bucket 101 (Using difference cover) Sorting block of length 23858 for bucket 107 (Using difference cover) bucket 126: 10% bucket 110: 60% bucket 123: 20% bucket 127: 10% bucket 128: 10% Reserving size (25350) for bucket 131 bucket 120: 30% Getting block 132 of 202 Calculating Z arrays for bucket 131 Reserving size (25350) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 131: Entering block accumulator loop for bucket 132: bucket 124: 20% bucket 108: 100% Sorting block of length 12270 for bucket 108 (Using difference cover) Sorting block time: 00:00:00 Returning block of 12271 for bucket 108 bucket 129: 10% bucket 121: 30% bucket 115: 40% bucket 125: 20% bucket 117: 40% bucket 118: 40% Sorting block time: 00:00:00 Returning block of 24184 for bucket 101 bucket 119: 40% bucket 113: 50% bucket 112: 60% bucket 116: 40% bucket 122: 30% bucket 114: 50% bucket 109: 80% Sorting block time: 00:00:00 Returning block of 23859 for bucket 107 bucket 111: 60% Getting block 133 of 202 Reserving size (25350) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 110: 70% bucket 126: 20% bucket 123: 30% Getting block 134 of 202 Reserving size (25350) for bucket 134 Calculating Z arrays for bucket 134 bucket 127: 20% bucket 130: 10% bucket 128: 20% bucket 120: 40% Getting block 135 of 202 Reserving size (25350) for bucket 135 Entering block accumulator loop for bucket 134: Calculating Z arrays for bucket 135 bucket 124: 30% Entering block accumulator loop for bucket 135: bucket 132: 10% bucket 131: 10% bucket 121: 40% bucket 118: 50% bucket 115: 50% bucket 117: 50% bucket 129: 20% bucket 119: 50% bucket 122: 40% bucket 109: 90% bucket 112: 70% bucket 113: 60% bucket 125: 30% bucket 114: 60% bucket 116: 50% bucket 126: 30% bucket 110: 80% bucket 123: 40% bucket 120: 50% bucket 111: 70% bucket 127: 30% bucket 124: 40% bucket 130: 20% bucket 128: 30% bucket 135: 10% bucket 133: 10% bucket 132: 20% bucket 134: 10% bucket 131: 20% bucket 118: 60% bucket 121: 50% bucket 117: 60% bucket 115: 60% bucket 119: 60% bucket 122: 50% bucket 109: 100% Sorting block of length 25185 for bucket 109 (Using difference cover) bucket 129: 30% bucket 113: 70% bucket 112: 80% bucket 114: 70% bucket 116: 60% bucket 125: 40% bucket 110: 90% bucket 126: 40% bucket 123: 50% bucket 120: 60% bucket 127: 40% bucket 124: 50% bucket 128: 40% bucket 130: 30% bucket 135: 20% bucket 133: 20% bucket 111: 80% bucket 132: 30% bucket 134: 20% bucket 131: 30% Sorting block time: 00:00:00 Returning block of 25186 for bucket 109 bucket 118: 70% bucket 117: 70% bucket 119: 70% bucket 121: 60% bucket 115: 70% bucket 122: 60% bucket 113: 80% bucket 112: 90% bucket 129: 40% Getting block 136 of 202 Reserving size (25350) for bucket 136 bucket 114: 80% Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 125: 50% bucket 116: 70% bucket 126: 50% bucket 110: 100% Sorting block of length 11597 for bucket 110 (Using difference cover) bucket 120: 70% bucket 123: 60% bucket 127: 50% bucket 124: 60% bucket 130: 40% bucket 128: 50% bucket 135: 30% bucket 132: 40% bucket 134: 30% bucket 133: 30% bucket 111: 90% bucket 131: 40% Sorting block time: 00:00:00 Returning block of 11598 for bucket 110 Getting block 137 of 202 Reserving size (25350) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 118: 80% bucket 119: 80% bucket 121: 70% bucket 117: 80% bucket 122: 70% bucket 115: 80% bucket 113: 90% bucket 112: 100% Sorting block of length 20534 for bucket 112 (Using difference cover) bucket 114: 90% bucket 129: 50% bucket 136: 10% bucket 125: 60% bucket 116: 80% bucket 126: 60% bucket 120: 80% bucket 123: 70% bucket 124: 70% bucket 127: 60% bucket 135: 40% bucket 130: 50% bucket 128: 60% bucket 134: 40% bucket 132: 50% bucket 133: 40% bucket 131: 50% bucket 111: 100% Sorting block of length 17347 for bucket 111 (Using difference cover) Sorting block time: 00:00:00 Returning block of 20535 for bucket 112 bucket 137: 10% bucket 118: 90% Getting block 138 of 202 Reserving size (25350) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 119: 90% bucket 117: 90% bucket 121: 80% bucket 122: 80% bucket 115: 90% bucket 113: 100% Sorting block of length 16287 for bucket 113 (Using difference cover) bucket 114: 100% Sorting block of length 19049 for bucket 114 (Using difference cover) bucket 129: 60% bucket 136: 20% bucket 125: 70% bucket 116: 90% bucket 120: 90% bucket 126: 70% bucket 123: 80% Sorting block time: 00:00:00 Returning block of 17348 for bucket 111 bucket 127: 70% bucket 124: 80% bucket 135: 50% bucket 128: 70% bucket 130: 60% Getting block 139 of 202 Reserving size (25350) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 134: 50% bucket 132: 60% Sorting block time: 00:00:00 Returning block of 16288 for bucket 113 bucket 133: 50% Sorting block time: 00:00:00 Returning block of 19050 for bucket 114 bucket 131: 60% Getting block 140 of 202 Reserving size (25350) for bucket 140 Calculating Z arrays for bucket 140 bucket 137: 20% Entering block accumulator loop for bucket 140: bucket 118: 100% Sorting block of length 10995 for bucket 118 (Using difference cover) bucket 122: 90% bucket 119: 100% bucket 121: 90% bucket 138: 10% bucket 115: 100% bucket 117: 100% Sorting block of length 19902 for bucket 119 (Using difference cover) Sorting block of length 17270 for bucket 115 (Using difference cover) Sorting block of length 16171 for bucket 117 (Using difference cover) Getting block 141 of 202 bucket 129: 70% bucket 136: 30% bucket 125: 80% Reserving size (25350) for bucket 141 bucket 120: 100% bucket 116: 100% Calculating Z arrays for bucket 141 Sorting block of length 24242 for bucket 120 (Using difference cover) Sorting block of length 21318 for bucket 116 (Using difference cover) Entering block accumulator loop for bucket 141: bucket 126: 80% bucket 123: 90% Sorting block time: 00:00:00 Returning block of 10996 for bucket 118 bucket 127: 80% bucket 135: 60% bucket 124: 90% bucket 130: 70% bucket 128: 80% bucket 139: 10% bucket 134: 60% bucket 132: 70% bucket 133: 60% bucket 137: 30% bucket 140: 10% bucket 131: 70% Sorting block time: 00:00:00 Returning block of 16172 for bucket 117 Sorting block time: 00:00:00 Returning block of 17271 for bucket 115 Sorting block time: 00:00:00 Returning block of 19903 for bucket 119 bucket 122: 100% Sorting block of length 10381 for bucket 122 (Using difference cover) Sorting block time: 00:00:00 Returning block of 21319 for bucket 116 Sorting block time: 00:00:00 Returning block of 24243 for bucket 120 bucket 121: 100% Sorting block of length 21470 for bucket 121 (Using difference cover) bucket 138: 20% bucket 125: 90% bucket 136: 40% bucket 126: 90% bucket 129: 80% bucket 123: 100% Sorting block of length 20501 for bucket 123 (Using difference cover) bucket 141: 10% Getting block 142 of 202 Reserving size (25350) for bucket 142 Getting block 143 of 202 Calculating Z arrays for bucket 142 Reserving size (25350) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 142: Entering block accumulator loop for bucket 143: Sorting block time: 00:00:00 Returning block of 10382 for bucket 122 bucket 127: 90% bucket 135: 70% Getting block 144 of 202 Reserving size (25350) for bucket 144 Calculating Z arrays for bucket 144 bucket 124: 100% Entering block accumulator loop for bucket 144: Sorting block of length 17711 for bucket 124 (Using difference cover) Getting block 145 of 202 Reserving size (25350) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 128: 90% Getting block 146 of 202 Reserving size (25350) for bucket 146 Calculating Z arrays for bucket 146 bucket 130: 80% Entering block accumulator loop for bucket 146: Getting block 147 of 202 Reserving size (25350) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 139: 20% bucket 134: 70% bucket 132: 80% bucket 137: 40% Sorting block time: 00:00:00 Returning block of 21471 for bucket 121 bucket 140: 20% bucket 133: 70% bucket 131: 80% Sorting block time: 00:00:00 Returning block of 20502 for bucket 123 Getting block 148 of 202 Reserving size (25350) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: Getting block 149 of 202 Reserving size (25350) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: Sorting block time: 00:00:00 Returning block of 17712 for bucket 124 Getting block 150 of 202 Reserving size (25350) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 136: 50% bucket 138: 30% bucket 126: 100% Sorting block of length 8264 for bucket 126 (Using difference cover) bucket 129: 90% bucket 125: 100% Sorting block of length 19599 for bucket 125 (Using difference cover) bucket 141: 20% bucket 142: 10% bucket 143: 10% bucket 127: 100% Sorting block of length 23839 for bucket 127 (Using difference cover) bucket 144: 10% bucket 135: 80% bucket 145: 10% bucket 128: 100% Sorting block of length 20622 for bucket 128 (Using difference cover) bucket 130: 90% bucket 146: 10% Sorting block time: 00:00:00 Returning block of 8265 for bucket 126 bucket 147: 10% bucket 139: 30% Getting block 151 of 202 Reserving size (25350) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 134: 80% bucket 132: 90% bucket 137: 50% bucket 140: 30% Sorting block time: 00:00:00 Returning block of 19600 for bucket 125 bucket 133: 80% bucket 131: 90% bucket 148: 10% Getting block 152 of 202 Reserving size (25350) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: bucket 149: 10% bucket 150: 10% Sorting block time: 00:00:00 Returning block of 20623 for bucket 128 bucket 136: 60% bucket 138: 40% Sorting block time: 00:00:00 Returning block of 23840 for bucket 127 bucket 129: 100% Sorting block of length 16858 for bucket 129 (Using difference cover) Getting block 153 of 202 Reserving size (25350) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: Getting block 154 of 202 bucket 141: 30% Reserving size (25350) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 142: 20% bucket 144: 20% bucket 143: 20% bucket 135: 90% bucket 145: 20% bucket 130: 100% Sorting block of length 17769 for bucket 130 (Using difference cover) bucket 146: 20% bucket 147: 20% bucket 139: 40% bucket 151: 10% bucket 134: 90% bucket 132: 100% Sorting block of length 8657 for bucket 132 (Using difference cover) bucket 137: 60% Sorting block time: 00:00:00 Returning block of 16859 for bucket 129 bucket 140: 40% Getting block 155 of 202 Reserving size (25350) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: Getting block 156 of 202 Reserving size (25350) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 148: 20% bucket 131: 100% Sorting block of length 23392 for bucket 131 (Using difference cover) bucket 133: 90% Sorting block time: 00:00:00 Returning block of 17770 for bucket 130 bucket 152: 10% Sorting block time: 00:00:00 Returning block of 8658 for bucket 132 bucket 149: 20% bucket 150: 20% bucket 136: 70% bucket 138: 50% bucket 153: 10% bucket 154: 10% bucket 141: 40% Getting block 157 of 202 Reserving size (25350) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 142: 30% bucket 144: 30% Getting block 158 of 202 Reserving size (25350) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: bucket 145: 30% bucket 143: 30% bucket 135: 100% Sorting block of length 25048 for bucket 135 (Using difference cover) bucket 146: 30% bucket 147: 30% bucket 139: 50% bucket 151: 20% bucket 137: 70% Sorting block time: 00:00:00 Returning block of 23393 for bucket 131 bucket 140: 50% bucket 155: 10% Getting block 159 of 202 Reserving size (25350) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 148: 30% bucket 133: 100% Sorting block of length 37019 for bucket 133 (Using difference cover) bucket 156: 10% bucket 136: 80% bucket 149: 30% bucket 150: 30% bucket 152: 20% bucket 138: 60% bucket 134: 100% Sorting block of length 2400 for bucket 134 (Using difference cover) bucket 153: 20% Sorting block time: 00:00:00 Returning block of 25049 for bucket 135 bucket 154: 20% Sorting block time: 00:00:00 Returning block of 2401 for bucket 134 bucket 141: 50% bucket 157: 10% bucket 142: 40% bucket 144: 40% bucket 158: 10% bucket 145: 40% bucket 143: 40% bucket 146: 40% bucket 147: 40% Getting block 160 of 202 Reserving size (25350) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 139: 60% bucket 151: 30% bucket 137: 80% bucket 140: 60% bucket 155: 20% bucket 159: 10% bucket 148: 40% bucket 136: 90% bucket 156: 20% bucket 149: 40% bucket 150: 40% bucket 138: 70% bucket 153: 30% bucket 152: 30% Sorting block time: 00:00:00 Returning block of 37020 for bucket 133 bucket 154: 30% bucket 141: 60% bucket 157: 20% bucket 142: 50% bucket 144: 50% bucket 145: 50% bucket 158: 20% bucket 143: 50% bucket 146: 50% bucket 147: 50% bucket 160: 10% bucket 139: 70% bucket 151: 40% bucket 137: 90% Getting block 161 of 202 Reserving size (25350) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 140: 70% bucket 155: 30% bucket 159: 20% bucket 148: 50% bucket 136: 100% Sorting block of length 11849 for bucket 136 (Using difference cover) Getting block 162 of 202 Reserving size (25350) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 149: 50% bucket 150: 50% bucket 138: 80% bucket 153: 40% bucket 156: 30% bucket 154: 40% bucket 152: 40% bucket 144: 60% bucket 141: 70% bucket 142: 60% bucket 157: 30% bucket 145: 60% bucket 143: 60% bucket 158: 30% Sorting block time: 00:00:00 Returning block of 11850 for bucket 136 bucket 146: 60% bucket 160: 20% bucket 147: 60% Getting block 163 of 202 Reserving size (25350) for bucket 163 Calculating Z arrays for bucket 163 bucket 139: 80% Entering block accumulator loop for bucket 163: bucket 151: 50% bucket 137: 100% Sorting block of length 22640 for bucket 137 (Using difference cover) bucket 161: 10% bucket 155: 40% bucket 140: 80% bucket 159: 30% bucket 148: 60% bucket 162: 10% bucket 149: 60% bucket 138: 90% bucket 153: 50% bucket 150: 60% bucket 154: 50% bucket 144: 70% bucket 152: 50% bucket 142: 70% bucket 157: 40% bucket 141: 80% bucket 156: 40% bucket 145: 70% Sorting block time: 00:00:00 Returning block of 22641 for bucket 137 bucket 143: 70% bucket 158: 40% bucket 146: 70% bucket 160: 30% bucket 147: 70% bucket 163: 10% Getting block 164 of 202 Reserving size (25350) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 151: 60% bucket 139: 90% bucket 161: 20% bucket 155: 50% bucket 140: 90% bucket 159: 40% bucket 148: 70% bucket 162: 20% bucket 153: 60% bucket 138: 100% Sorting block of length 22245 for bucket 138 (Using difference cover) bucket 149: 70% bucket 150: 70% bucket 154: 60% bucket 144: 80% bucket 157: 50% bucket 142: 80% bucket 141: 90% bucket 156: 50% bucket 152: 60% bucket 145: 80% bucket 158: 50% bucket 143: 80% bucket 160: 40% bucket 146: 80% bucket 163: 20% bucket 147: 80% bucket 164: 10% bucket 139: 100% bucket 151: 70% Sorting block of length 6862 for bucket 139 (Using difference cover) bucket 161: 30% bucket 140: 100% bucket 155: 60% Sorting block of length 19580 for bucket 140 (Using difference cover) Sorting block time: 00:00:00 Returning block of 22246 for bucket 138 bucket 159: 50% Sorting block time: 00:00:00 Returning block of 6863 for bucket 139 bucket 148: 80% Getting block 165 of 202 Reserving size (25350) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 162: 30% Getting block 166 of 202 Reserving size (25350) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 153: 70% bucket 149: 80% bucket 154: 70% bucket 150: 80% bucket 144: 90% bucket 142: 90% bucket 157: 60% bucket 141: 100% Sorting block of length 23569 for bucket 141 (Using difference cover) bucket 156: 60% bucket 145: 90% bucket 152: 70% Sorting block time: 00:00:00 Returning block of 19581 for bucket 140 bucket 158: 60% bucket 143: 90% bucket 160: 50% bucket 146: 90% bucket 163: 30% bucket 147: 90% bucket 164: 20% bucket 161: 40% Getting block 167 of 202 Reserving size (25350) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: bucket 151: 80% bucket 155: 70% bucket 159: 60% bucket 148: 90% bucket 165: 10% bucket 162: 40% bucket 153: 80% bucket 149: 90% bucket 154: 80% bucket 166: 10% Sorting block time: 00:00:00 Returning block of 23570 for bucket 141 bucket 150: 90% bucket 144: 100% Sorting block of length 6386 for bucket 144 (Using difference cover) bucket 157: 70% bucket 142: 100% Sorting block of length 19025 for bucket 142 (Using difference cover) bucket 145: 100% Sorting block of length 21327 for bucket 145 (Using difference cover) bucket 156: 70% Getting block 168 of 202 Reserving size (25350) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 163: 40% bucket 158: 70% Sorting block time: 00:00:00 Returning block of 6387 for bucket 144 bucket 160: 60% bucket 146: 100% bucket 152: 80% Sorting block of length 15381 for bucket 146 (Using difference cover) bucket 147: 100% Sorting block of length 24897 for bucket 147 (Using difference cover) bucket 164: 30% bucket 143: 100% Sorting block of length 24757 for bucket 143 (Using difference cover) bucket 161: 50% bucket 167: 10% bucket 151: 90% bucket 155: 80% Sorting block time: 00:00:00 Returning block of 19026 for bucket 142 bucket 159: 70% bucket 148: 100% Sorting block of length 12810 for bucket 148 (Using difference cover) bucket 153: 90% bucket 165: 20% bucket 162: 50% Sorting block time: 00:00:00 Returning block of 21328 for bucket 145 Sorting block time: 00:00:00 Returning block of 15382 for bucket 146 bucket 154: 90% bucket 149: 100% Sorting block of length 18067 for bucket 149 (Using difference cover) bucket 166: 20% bucket 150: 100% Sorting block of length 11267 for bucket 150 (Using difference cover) Getting block 169 of 202 Reserving size (25350) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 157: 80% Getting block 170 of 202 Reserving size (25350) for bucket 170 Getting block 171 of 202 Calculating Z arrays for bucket 170 Reserving size (25350) for bucket 171 Calculating Z arrays for bucket 171 Getting block 172 of 202 Entering block accumulator loop for bucket 170: Reserving size (25350) for bucket 172 Entering block accumulator loop for bucket 171: Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: Sorting block time: 00:00:00 Returning block of 24898 for bucket 147 bucket 168: 10% Sorting block time: 00:00:00 Returning block of 24758 for bucket 143 bucket 163: 50% Sorting block time: 00:00:00 Returning block of 12811 for bucket 148 bucket 160: 70% bucket 158: 80% bucket 164: 40% bucket 156: 80% bucket 152: 90% bucket 167: 20% bucket 161: 60% Sorting block time: 00:00:00 Returning block of 11268 for bucket 150 Getting block 173 of 202 Reserving size (25350) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: Getting block 174 of 202 Reserving size (25350) for bucket 174 Calculating Z arrays for bucket 174 bucket 151: 100% Entering block accumulator loop for bucket 174: Sorting block of length 21394 for bucket 151 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 155: 90% Returning block of 18068 for bucket 149 bucket 159: 80% bucket 153: 100% bucket 165: 30% bucket 162: 60% bucket 154: 100% bucket 166: 30% bucket 169: 10% bucket 157: 90% bucket 170: 10% bucket 171: 10% bucket 172: 10% bucket 168: 20% bucket 163: 60% Returning block of 21395 for bucket 151 bucket 160: 80% bucket 158: 90% bucket 164: 50% bucket 156: 90% bucket 167: 30% bucket 161: 70% bucket 152: 100% bucket 173: 10% bucket 174: 10% Getting block 175 of 202 Getting block 176 of 202 Sorting block of length 19632 for bucket 153 (Using difference cover) Sorting block of length 20534 for bucket 154 (Using difference cover) Sorting block of length 23959 for bucket 152 (Using difference cover) bucket 165: 40% bucket 155: 100% bucket 162: 70% bucket 163: 70% bucket 159: 90% bucket 164: 60% bucket 160: 90% bucket 170: 20% bucket 157: 100% bucket 172: 20% bucket 171: 20% bucket 166: 40% bucket 169: 20% bucket 158: 100% bucket 167: 40% bucket 168: 30% bucket 161: 80% bucket 156: 100% bucket 173: 20% Reserving size (25350) for bucket 175 bucket 174: 20% Reserving size (25350) for bucket 176 Getting block 177 of 202 Getting block 178 of 202 Sorting block of length 19204 for bucket 155 (Using difference cover) Sorting block of length 20198 for bucket 157 (Using difference cover) Sorting block of length 19666 for bucket 158 (Using difference cover) Sorting block of length 12286 for bucket 156 (Using difference cover) Calculating Z arrays for bucket 175 Calculating Z arrays for bucket 176 Reserving size (25350) for bucket 177 Reserving size (25350) for bucket 178 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 175: Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 176: Entering block accumulator loop for bucket 177: Entering block accumulator loop for bucket 178: Sorting block time: 00:00:00 Returning block of 12287 for bucket 156 Getting block 179 of 202 Reserving size (25350) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: Sorting block time: 00:00:00 Returning block of 19633 for bucket 153 Sorting block time: 00:00:00 Returning block of 19205 for bucket 155 Sorting block time: 00:00:00 Returning block of 20535 for bucket 154 Sorting block time: 00:00:00 Returning block of 20199 for bucket 157 Sorting block time: 00:00:00 Returning block of 19667 for bucket 158 Sorting block time: 00:00:00 Returning block of 23960 for bucket 152 Getting block 180 of 202 bucket 163: 80% Reserving size (25350) for bucket 180 Calculating Z arrays for bucket 180 Getting block 181 of 202 bucket 164: 70% Reserving size (25350) for bucket 181 Entering block accumulator loop for bucket 180: Calculating Z arrays for bucket 181 bucket 165: 50% Entering block accumulator loop for bucket 181: bucket 167: 50% bucket 161: 90% bucket 160: 100% Sorting block of length 20392 for bucket 160 (Using difference cover) bucket 162: 80% bucket 170: 30% bucket 159: 100% bucket 172: 30% bucket 171: 30% Sorting block of length 22398 for bucket 159 (Using difference cover) bucket 169: 30% Getting block 182 of 202 Reserving size (25350) for bucket 182 Calculating Z arrays for bucket 182 bucket 168: 40% Entering block accumulator loop for bucket 182: bucket 177: 10% bucket 166: 50% bucket 174: 30% bucket 173: 30% Getting block 183 of 202 bucket 178: 10% Reserving size (25350) for bucket 183 Calculating Z arrays for bucket 183 bucket 175: 10% Entering block accumulator loop for bucket 183: bucket 176: 10% Getting block 184 of 202 Reserving size (25350) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: Getting block 185 of 202 Reserving size (25350) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: Sorting block time: 00:00:00 Returning block of 20393 for bucket 160 Sorting block time: 00:00:00 Returning block of 22399 for bucket 159 bucket 163: 90% bucket 179: 10% bucket 180: 10% bucket 181: 10% bucket 164: 80% bucket 167: 60% bucket 161: 100% bucket 165: 60% Sorting block of length 21563 for bucket 161 (Using difference cover) bucket 170: 40% bucket 172: 40% bucket 162: 90% bucket 171: 40% bucket 177: 20% bucket 169: 40% bucket 182: 10% bucket 173: 40% bucket 168: 50% bucket 178: 20% bucket 174: 40% bucket 183: 10% bucket 175: 20% bucket 166: 60% bucket 184: 10% bucket 176: 20% bucket 185: 10% Getting block 186 of 202 Reserving size (25350) for bucket 186 Getting block 187 of 202 Calculating Z arrays for bucket 186 Reserving size (25350) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 186: Entering block accumulator loop for bucket 187: Sorting block time: 00:00:00 Returning block of 21564 for bucket 161 Getting block 188 of 202 Reserving size (25350) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 163: 100% Sorting block of length 10953 for bucket 163 (Using difference cover) bucket 180: 20% bucket 181: 20% bucket 164: 90% bucket 167: 70% bucket 165: 70% bucket 170: 50% bucket 177: 30% bucket 179: 20% bucket 172: 50% bucket 162: 100% Sorting block of length 18713 for bucket 162 (Using difference cover) bucket 171: 50% bucket 169: 50% bucket 182: 20% bucket 173: 50% bucket 178: 30% bucket 168: 60% bucket 183: 20% bucket 174: 50% bucket 175: 30% bucket 166: 70% bucket 185: 20% bucket 176: 30% Sorting block time: 00:00:00 Returning block of 10954 for bucket 163 bucket 186: 10% bucket 187: 10% bucket 184: 20% Sorting block time: 00:00:00 Returning block of 18714 for bucket 162 Getting block 189 of 202 Reserving size (25350) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 188: 10% bucket 180: 30% bucket 181: 30% bucket 164: 100% Sorting block of length 21181 for bucket 164 (Using difference cover) bucket 167: 80% bucket 177: 40% bucket 179: 30% bucket 170: 60% bucket 172: 60% bucket 165: 80% bucket 169: 60% bucket 178: 40% bucket 173: 60% bucket 182: 30% bucket 168: 70% bucket 183: 30% bucket 174: 60% bucket 175: 40% bucket 171: 60% bucket 166: 80% bucket 176: 40% bucket 185: 30% bucket 186: 20% bucket 187: 20% bucket 184: 30% Sorting block time: 00:00:00 Returning block of 21182 for bucket 164 Getting block 190 of 202 Reserving size (25350) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 180: 40% bucket 189: 10% bucket 179: 40% Getting block 191 of 202 Reserving size (25350) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: bucket 181: 40% bucket 169: 70% bucket 167: 90% bucket 188: 20% bucket 177: 50% bucket 170: 70% bucket 165: 90% bucket 172: 70% bucket 178: 50% bucket 182: 40% bucket 173: 70% bucket 183: 40% bucket 168: 80% bucket 174: 70% bucket 175: 50% bucket 166: 90% bucket 171: 70% bucket 176: 50% bucket 186: 30% bucket 185: 40% bucket 187: 30% bucket 184: 40% bucket 180: 50% bucket 179: 50% bucket 190: 10% bucket 169: 80% bucket 189: 20% bucket 191: 10% bucket 181: 50% bucket 167: 100% Sorting block of length 9510 for bucket 167 (Using difference cover) bucket 177: 60% bucket 188: 30% bucket 165: 100% bucket 178: 60% Sorting block of length 15353 for bucket 165 (Using difference cover) bucket 172: 80% bucket 170: 80% bucket 182: 50% bucket 173: 80% bucket 183: 50% bucket 168: 90% bucket 175: 60% bucket 174: 80% bucket 171: 80% bucket 166: 100% Sorting block of length 21272 for bucket 166 (Using difference cover) bucket 186: 40% Sorting block time: 00:00:00 Returning block of 9511 for bucket 167 bucket 176: 60% bucket 187: 40% bucket 185: 50% Getting block 192 of 202 Reserving size (25350) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 180: 60% bucket 179: 60% bucket 184: 50% bucket 169: 90% Sorting block time: 00:00:00 Returning block of 15354 for bucket 165 Getting block 193 of 202 Reserving size (25350) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: bucket 190: 20% bucket 189: 30% bucket 181: 60% bucket 191: 20% bucket 177: 70% Sorting block time: 00:00:00 Returning block of 21273 for bucket 166 bucket 188: 40% bucket 178: 70% bucket 172: 90% bucket 170: 90% bucket 182: 60% Getting block 194 of 202 Reserving size (25350) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 183: 60% bucket 173: 90% bucket 175: 70% bucket 168: 100% bucket 174: 90% Sorting block of length 22232 for bucket 168 (Using difference cover) bucket 171: 90% bucket 180: 70% bucket 186: 50% bucket 179: 70% bucket 176: 70% bucket 185: 60% bucket 187: 50% bucket 192: 10% bucket 169: 100% Sorting block of length 22355 for bucket 169 (Using difference cover) bucket 184: 60% bucket 193: 10% bucket 190: 30% bucket 181: 70% bucket 189: 40% bucket 191: 30% Sorting block time: 00:00:00 Returning block of 22233 for bucket 168 bucket 177: 80% bucket 188: 50% bucket 178: 80% bucket 172: 100% Sorting block of length 14018 for bucket 172 (Using difference cover) bucket 170: 100% Sorting block of length 18788 for bucket 170 (Using difference cover) bucket 182: 70% Getting block 195 of 202 bucket 180: 80% Reserving size (25350) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 179: 80% bucket 194: 10% bucket 183: 70% Sorting block time: 00:00:00 Returning block of 22356 for bucket 169 bucket 173: 100% Sorting block of length 18812 for bucket 173 (Using difference cover) bucket 175: 80% bucket 174: 100% Sorting block of length 22554 for bucket 174 (Using difference cover) bucket 171: 100% Sorting block of length 13769 for bucket 171 (Using difference cover) bucket 186: 60% Getting block 196 of 202 Reserving size (25350) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 185: 70% bucket 176: 80% bucket 192: 20% bucket 187: 60% Sorting block time: 00:00:00 Returning block of 14019 for bucket 172 bucket 184: 70% Sorting block time: 00:00:00 Returning block of 13770 for bucket 171 Getting block 197 of 202 Reserving size (25350) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: Sorting block time: 00:00:00 Returning block of 18789 for bucket 170 bucket 193: 20% bucket 181: 80% Getting block 198 of 202 Reserving size (25350) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 190: 40% bucket 177: 90% bucket 191: 40% bucket 180: 90% bucket 189: 50% bucket 179: 90% Sorting block time: 00:00:00 Returning block of 22555 for bucket 174 Getting block 199 of 202 Reserving size (25350) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: bucket 188: 60% Getting block 200 of 202 Reserving size (25350) for bucket 200 Calculating Z arrays for bucket 200 bucket 195: 10% bucket 182: 80% Entering block accumulator loop for bucket 200: bucket 196: 10% bucket 194: 20% bucket 178: 90% bucket 183: 80% Sorting block time: 00:00:00 Returning block of 18813 for bucket 173 bucket 175: 90% bucket 186: 70% bucket 185: 80% bucket 192: 30% bucket 176: 90% bucket 187: 70% bucket 180: 100% Sorting block of length 12117 for bucket 180 (Using difference cover) bucket 184: 80% bucket 179: 100% Sorting block of length 13350 for bucket 179 (Using difference cover) bucket 197: 10% bucket 193: 30% bucket 181: 90% bucket 198: 10% bucket 177: 100% Sorting block of length 19461 for bucket 177 (Using difference cover) bucket 191: 50% bucket 196: 20% bucket 189: 60% bucket 199: 10% bucket 190: 50% bucket 188: 70% Sorting block time: 00:00:00 Returning block of 12118 for bucket 180 bucket 200: 10% bucket 195: 20% bucket 182: 90% bucket 178: 100% Sorting block of length 18701 for bucket 178 (Using difference cover) bucket 194: 30% bucket 183: 90% Getting block 201 of 202 Reserving size (25350) for bucket 201 Calculating Z arrays for bucket 201 Sorting block time: 00:00:00 Returning block of 13351 for bucket 179 Entering block accumulator loop for bucket 201: bucket 175: 100% Sorting block of length 21829 for bucket 175 (Using difference cover) bucket 186: 80% Getting block 202 of 202 Reserving size (25350) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 185: 90% bucket 192: 40% Sorting block time: 00:00:00 Returning block of 19462 for bucket 177 bucket 176: 100% Sorting block of length 17174 for bucket 176 (Using difference cover) bucket 187: 80% Sorting block time: 00:00:00 Returning block of 18702 for bucket 178 bucket 196: 30% bucket 184: 90% bucket 198: 20% bucket 181: 100% bucket 193: 40% Sorting block of length 14775 for bucket 181 (Using difference cover) bucket 197: 20% bucket 202: 10% bucket 191: 60% Sorting block time: 00:00:00 Returning block of 21830 for bucket 175 bucket 199: 20% bucket 189: 70% bucket 190: 60% bucket 201: 10% bucket 200: 20% bucket 195: 30% bucket 182: 100% Sorting block of length 25275 for bucket 182 (Using difference cover) bucket 188: 80% bucket 194: 40% bucket 183: 100% Sorting block of length 23148 for bucket 183 (Using difference cover) Sorting block time: 00:00:00 Returning block of 17175 for bucket 176 bucket 186: 90% Sorting block time: 00:00:00 Returning block of 14776 for bucket 181 bucket 185: 100% Sorting block of length 22645 for bucket 185 (Using difference cover) bucket 192: 50% bucket 202: 20% bucket 196: 40% bucket 187: 90% bucket 184: 100% Sorting block of length 23923 for bucket 184 (Using difference cover) bucket 198: 30% bucket 193: 50% bucket 201: 20% bucket 197: 30% bucket 191: 70% Sorting block time: 00:00:00 Returning block of 23149 for bucket 183 Sorting block time: 00:00:00 Returning block of 25276 for bucket 182 bucket 199: 30% bucket 189: 80% bucket 190: 70% bucket 200: 30% bucket 202: 30% bucket 195: 40% bucket 188: 90% bucket 194: 50% Sorting block time: 00:00:00 Returning block of 22646 for bucket 185 bucket 186: 100% Sorting block of length 4471 for bucket 186 (Using difference cover) bucket 196: 50% bucket 192: 60% Sorting block time: 00:00:00 Returning block of 4472 for bucket 186 Sorting block time: 00:00:00 Returning block of 23924 for bucket 184 bucket 201: 30% bucket 202: 40% bucket 187: 100% Sorting block of length 24292 for bucket 187 (Using difference cover) bucket 198: 40% bucket 193: 60% bucket 197: 40% bucket 191: 80% bucket 199: 40% bucket 190: 80% bucket 189: 90% bucket 200: 40% bucket 195: 50% bucket 188: 100% bucket 194: 60% Sorting block of length 14143 for bucket 188 (Using difference cover) bucket 196: 60% bucket 202: 50% bucket 192: 70% bucket 201: 40% Sorting block time: 00:00:00 Returning block of 24293 for bucket 187 Sorting block time: 00:00:00 Returning block of 14144 for bucket 188 bucket 198: 50% bucket 197: 50% bucket 193: 70% bucket 199: 50% bucket 191: 90% bucket 190: 90% bucket 196: 70% bucket 200: 50% bucket 189: 100% Sorting block of length 20255 for bucket 189 (Using difference cover) bucket 202: 60% bucket 195: 60% bucket 194: 70% bucket 201: 50% bucket 192: 80% bucket 202: 70% Sorting block time: 00:00:00 Returning block of 20256 for bucket 189 bucket 198: 60% bucket 196: 80% bucket 197: 60% bucket 199: 60% bucket 193: 80% bucket 191: 100% Sorting block of length 16376 for bucket 191 (Using difference cover) bucket 190: 100% Sorting block of length 23441 for bucket 190 (Using difference cover) bucket 200: 60% bucket 195: 70% bucket 201: 60% bucket 194: 80% bucket 202: 80% bucket 192: 90% Sorting block time: 00:00:00 Returning block of 16377 for bucket 191 bucket 196: 90% Sorting block time: 00:00:00 Returning block of 23442 for bucket 190 bucket 198: 70% bucket 199: 70% bucket 197: 70% bucket 202: 90% bucket 193: 90% bucket 201: 70% bucket 200: 70% bucket 195: 80% bucket 194: 90% bucket 192: 100% Sorting block of length 13961 for bucket 192 (Using difference cover) bucket 196: 100% Sorting block of length 24617 for bucket 196 (Using difference cover) bucket 202: 100% Sorting block of length 22818 for bucket 202 (Using difference cover) bucket 201: 80% bucket 198: 80% bucket 199: 80% bucket 197: 80% Sorting block time: 00:00:00 Returning block of 13962 for bucket 192 bucket 193: 100% Sorting block of length 18995 for bucket 193 (Using difference cover) bucket 200: 80% bucket 195: 90% Sorting block time: 00:00:00 Returning block of 22819 for bucket 202 Sorting block time: 00:00:00 Returning block of 24618 for bucket 196 bucket 194: 100% Sorting block of length 25105 for bucket 194 (Using difference cover) bucket 201: 90% Sorting block time: 00:00:00 Returning block of 18996 for bucket 193 bucket 198: 90% bucket 199: 90% bucket 197: 90% bucket 200: 90% Sorting block time: 00:00:00 Returning block of 25106 for bucket 194 bucket 195: 100% Sorting block of length 25121 for bucket 195 (Using difference cover) bucket 201: 100% Sorting block of length 23878 for bucket 201 (Using difference cover) bucket 198: 100% Sorting block of length 21461 for bucket 198 (Using difference cover) bucket 199: 100% Sorting block of length 24821 for bucket 199 (Using difference cover) bucket 197: 100% Sorting block of length 14097 for bucket 197 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25122 for bucket 195 bucket 200: 100% Sorting block of length 23936 for bucket 200 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23879 for bucket 201 Sorting block time: 00:00:00 Returning block of 14098 for bucket 197 Sorting block time: 00:00:00 Returning block of 21462 for bucket 198 Sorting block time: 00:00:00 Returning block of 24822 for bucket 199 Sorting block time: 00:00:00 Returning block of 23937 for bucket 200 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1210749 fchr[G]: 1210749 fchr[T]: 1897502 fchr[$]: 3785646 Preparing indexing of GA converted genome in /gscratch/srlab/sr320/data/olurida-bs/v082/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 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 5461730 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 946416 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 3785646 bwtLen: 3785647 sz: 946412 bwtSz: 946412 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 236603 offsSz: 946412 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 19717 numLines: 19717 ebwtTotLen: 1261888 ebwtTotSz: 1261888 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:00 Reading reference sizes Time reading reference sizes: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences 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 to join reference sequences: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 33800 Using parameters --bmax 25350 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 25350 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 33800 Using parameters --bmax 25350 --dcv 1024 Doing ahead-of-time memory usage test Invoking Larsson-Sadakane on ranks time: 00:00:00 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 Passed! Constructing with these parameters: --bmax 25350 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Splitting and merging Splitting and merging time: 00:00:00 Split 39, merged 129; iterating... V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Splitting and merging Splitting and merging time: 00:00:00 Split 19, merged 22; iterating... Invoking Larsson-Sadakane on ranks time: 00:00:00 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 8, merged 10; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 37, merged 130; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 4; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 16, merged 16; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 3; iterating... Avg bucket size: 18556.1 (target: 25349) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 204 Reserving size (25350) for bucket 1 Getting block 2 of 204 Getting block 3 of 204 Getting block 4 of 204 Getting block 5 of 204 Calculating Z arrays for bucket 1 Reserving size (25350) for bucket 2 Reserving size (25350) for bucket 3 Getting block 6 of 204 Reserving size (25350) for bucket 4 Getting block 7 of 204 Reserving size (25350) for bucket 5 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 Entering block accumulator loop for bucket 1: Getting block 21 of 204 Getting block 22 of 204 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 2 Reserving size (25350) for bucket 6 Getting block 23 of 204 Getting block 24 of 204 Calculating Z arrays for bucket 4 Reserving size (25350) for bucket 7 Calculating Z arrays for bucket 5 Reserving size (25350) for bucket 8 Reserving size (25350) for bucket 9 Reserving size (25350) for bucket 10 Reserving size (25350) for bucket 11 Reserving size (25350) for bucket 12 Reserving size (25350) for bucket 13 Reserving size (25350) for bucket 14 Reserving size (25350) for bucket 15 Reserving size (25350) for bucket 16 Reserving size (25350) for bucket 17 Reserving size (25350) for bucket 18 Reserving size (25350) for bucket 19 Reserving size (25350) for bucket 20 Reserving size (25350) for bucket 21 Reserving size (25350) for bucket 22 Getting block 25 of 204 Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 2: Reserving size (25350) for bucket 23 Calculating Z arrays for bucket 6 Reserving size (25350) for bucket 24 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 4: Calculating Z arrays for bucket 8 Entering block accumulator loop for bucket 5: 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 Getting block 26 of 204 Calculating Z arrays for bucket 14 Calculating Z arrays for bucket 16 Calculating Z arrays for bucket 15 Calculating Z arrays for bucket 18 Calculating Z arrays for bucket 17 Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 Reserving size (25350) for bucket 25 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 24 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: Reserving size (25350) for bucket 26 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 15: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 21: Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 24: Getting block 27 of 204 Splitting and merging Splitting and merging time: 00:00:00 Split 7, merged 11; iterating... Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 25: Reserving size (25350) for bucket 27 bucket 1: 10% bucket 2: 10% bucket 3: 10% bucket 4: 10% bucket 5: 10% bucket 6: 10% bucket 8: 10% bucket 10: 10% bucket 9: 10% bucket 7: 10% bucket 12: 10% bucket 11: 10% Entering block accumulator loop for bucket 26: bucket 14: 10% bucket 13: 10% bucket 15: 10% bucket 18: 10% bucket 17: 10% bucket 16: 10% bucket 20: 10% bucket 19: 10% bucket 21: 10% bucket 22: 10% Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 3; iterating... bucket 23: 10% Calculating Z arrays for bucket 27 bucket 1: 20% bucket 24: 10% bucket 2: 20% bucket 3: 20% bucket 4: 20% bucket 5: 20% bucket 6: 20% bucket 8: 20% bucket 10: 20% bucket 9: 20% bucket 7: 20% bucket 12: 20% bucket 11: 20% Entering block accumulator loop for bucket 27: bucket 14: 20% bucket 13: 20% bucket 15: 20% bucket 18: 20% bucket 17: 20% bucket 16: 20% bucket 19: 20% bucket 21: 20% bucket 22: 20% bucket 25: 10% bucket 20: 20% bucket 1: 30% bucket 2: 30% bucket 3: 30% bucket 4: 30% bucket 6: 30% bucket 5: 30% bucket 8: 30% bucket 10: 30% bucket 9: 30% bucket 7: 30% bucket 12: 30% bucket 24: 20% bucket 11: 30% bucket 26: 10% bucket 23: 20% bucket 27: 10% bucket 14: 30% bucket 13: 30% bucket 15: 30% bucket 18: 30% bucket 17: 30% bucket 16: 30% bucket 1: 40% bucket 2: 40% bucket 6: 40% bucket 10: 40% bucket 7: 40% bucket 11: 40% bucket 27: 20% bucket 15: 40% bucket 17: 40% bucket 1: 50% bucket 2: 50% bucket 6: 50% bucket 10: 50% bucket 7: 50% bucket 11: 50% bucket 27: 30% bucket 1: 60% bucket 15: 50% bucket 17: 50% bucket 2: 60% bucket 6: 60% bucket 10: 60% bucket 7: 60% bucket 11: 60% bucket 1: 70% bucket 27: 40% bucket 2: 70% bucket 15: 60% bucket 19: 30% bucket 21: 30% bucket 25: 20% bucket 22: 30% bucket 6: 70% bucket 10: 70% bucket 4: 40% bucket 5: 40% bucket 7: 70% bucket 8: 40% bucket 11: 70% bucket 12: 40% bucket 1: 80% bucket 2: 80% bucket 13: 40% bucket 15: 70% bucket 18: 40% bucket 16: 40% bucket 27: 50% bucket 19: 40% bucket 21: 40% bucket 22: 40% bucket 6: 80% bucket 25: 30% bucket 4: 50% bucket 10: 80% bucket 5: 50% bucket 7: 80% bucket 8: 50% bucket 12: 50% bucket 11: 80% bucket 1: 90% bucket 2: 90% bucket 13: 50% bucket 15: 80% bucket 18: 50% bucket 16: 50% bucket 6: 90% bucket 19: 50% bucket 4: 60% bucket 21: 50% bucket 25: 40% bucket 5: 60% bucket 10: 90% bucket 22: 50% bucket 8: 60% bucket 7: 90% bucket 1: 100% bucket 12: 60% bucket 11: 90% bucket 2: 100% bucket 23: 30% bucket 3: 40% Sorting block of length 22633 for bucket 1 (Using difference cover) bucket 13: 60% bucket 17: 60% bucket 15: 90% bucket 6: 100% Sorting block of length 14338 for bucket 2 (Using difference cover) bucket 24: 30% bucket 14: 40% bucket 27: 60% Splitting and merging bucket 9: 40% Splitting and merging time: 00:00:00 Split 2, merged 3; iterating... bucket 18: 60% bucket 4: 70% bucket 16: 60% Avg bucket size: 18647.5 (target: 25349) bucket 5: 70% Converting suffix-array elements to index image bucket 10: 100% Allocating ftab, absorbFtab bucket 19: 60% bucket 21: 60% bucket 8: 70% bucket 25: 50% bucket 7: 100% bucket 22: 60% bucket 12: 70% bucket 11: 100% bucket 20: 30% Sorting block of length 10141 for bucket 6 (Using difference cover) bucket 23: 40% bucket 26: 20% Sorting block of length 18099 for bucket 10 (Using difference cover) Sorting block of length 17905 for bucket 7 (Using difference cover) Sorting block of length 24255 for bucket 11 (Using difference cover) bucket 3: 50% Entering Ebwt loop Getting block 1 of 203 bucket 15: 100% Sorting block of length 20607 for bucket 15 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14339 for bucket 2 bucket 24: 40% Getting block 2 of 203 Sorting block time: 00:00:00 Returning block of 22634 for bucket 1 bucket 9: 50% bucket 26: 30% bucket 23: 50% bucket 3: 60% bucket 27: 70% Reserving size (25350) for bucket 1 bucket 17: 70% bucket 14: 50% bucket 24: 50% bucket 9: 60% bucket 3: 70% bucket 13: 70% bucket 26: 40% bucket 23: 60% Getting block 28 of 204 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (25350) for bucket 28 Getting block 29 of 204 Returning block of 17906 for bucket 7 Returning block of 10142 for bucket 6 Calculating Z arrays for bucket 28 Reserving size (25350) for bucket 29 Reserving size (25350) for bucket 2 Getting block 3 of 203 Getting block 4 of 203 Getting block 5 of 203 Getting block 6 of 203 Getting block 7 of 203 Getting block 8 of 203 Getting block 9 of 203 Getting block 10 of 203 Getting block 11 of 203 Getting block 12 of 203 Getting block 13 of 203 Calculating Z arrays for bucket 1 Getting block 14 of 203 Getting block 15 of 203 Getting block 16 of 203 Getting block 17 of 203 Getting block 18 of 203 Getting block 19 of 203 Getting block 20 of 203 Getting block 21 of 203 Getting block 22 of 203 Getting block 23 of 203 Calculating Z arrays for bucket 2 Reserving size (25350) for bucket 3 Getting block 24 of 203 Reserving size (25350) for bucket 4 Reserving size (25350) for bucket 5 Reserving size (25350) for bucket 6 Reserving size (25350) for bucket 7 Reserving size (25350) for bucket 8 Reserving size (25350) for bucket 9 Reserving size (25350) for bucket 10 Reserving size (25350) for bucket 11 Reserving size (25350) for bucket 12 Reserving size (25350) for bucket 13 Entering block accumulator loop for bucket 1: Reserving size (25350) for bucket 14 Reserving size (25350) for bucket 15 Reserving size (25350) for bucket 16 Getting block 25 of 203 Reserving size (25350) for bucket 17 Reserving size (25350) for bucket 18 Reserving size (25350) for bucket 19 Getting block 26 of 203 Getting block 27 of 203 Reserving size (25350) for bucket 20 Reserving size (25350) for bucket 21 Reserving size (25350) for bucket 22 Reserving size (25350) for bucket 23 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 2: Reserving size (25350) for bucket 24 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 Reserving size (25350) for bucket 25 Calculating Z arrays for bucket 17 Calculating Z arrays for bucket 18 Calculating Z arrays for bucket 19 Reserving size (25350) for bucket 26 Reserving size (25350) for bucket 27 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: Calculating Z arrays for bucket 24 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: Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 18: Calculating Z arrays for bucket 26 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 26: Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 27: 80% Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 28: bucket 17: 80% Returning block of 24256 for bucket 11 Entering block accumulator loop for bucket 27: bucket 4: 10% bucket 4: 80% bucket 5: 80% bucket 8: 80% bucket 9: 70% bucket 18: 70% bucket 16: 70% bucket 24: 60% bucket 19: 70% Returning block of 18100 for bucket 10 bucket 20: 40% bucket 3: 80% bucket 13: 80% bucket 1: 10% bucket 22: 70% bucket 2: 10% bucket 12: 80% bucket 3: 10% bucket 25: 60% bucket 6: 10% Returning block of 20608 for bucket 15 bucket 21: 70% bucket 26: 50% Entering block accumulator loop for bucket 29: bucket 5: 10% Getting block 30 of 204 bucket 14: 60% bucket 23: 70% bucket 17: 90% bucket 27: 90% Getting block 31 of 204 bucket 4: 90% bucket 5: 90% bucket 3: 90% bucket 8: 90% bucket 9: 80% bucket 13: 90% bucket 8: 10% bucket 7: 10% bucket 10: 10% bucket 9: 10% bucket 13: 10% bucket 15: 10% bucket 12: 10% bucket 11: 10% bucket 17: 10% bucket 14: 10% bucket 16: 10% bucket 12: 90% bucket 16: 80% bucket 18: 80% bucket 24: 70% bucket 19: 80% bucket 4: 20% bucket 18: 10% bucket 19: 10% bucket 21: 10% bucket 20: 10% bucket 22: 10% bucket 24: 10% bucket 23: 10% bucket 25: 10% bucket 1: 20% bucket 6: 20% bucket 2: 20% bucket 3: 20% bucket 5: 20% bucket 7: 20% bucket 8: 20% bucket 10: 20% bucket 13: 20% bucket 9: 20% bucket 15: 20% bucket 12: 20% bucket 11: 20% bucket 26: 10% bucket 17: 20% bucket 20: 50% bucket 14: 20% bucket 16: 20% bucket 4: 30% bucket 18: 20% bucket 19: 20% bucket 21: 20% bucket 25: 70% bucket 22: 80% Reserving size (25350) for bucket 30 Getting block 32 of 204 bucket 21: 80% bucket 26: 60% Reserving size (25350) for bucket 31 bucket 3: 100% bucket 27: 10% bucket 22: 20% bucket 20: 20% bucket 1: 30% bucket 6: 30% bucket 3: 30% bucket 2: 30% bucket 5: 30% bucket 4: 100% bucket 5: 100% bucket 8: 100% bucket 28: 10% bucket 9: 90% bucket 17: 100% bucket 23: 20% bucket 25: 20% bucket 24: 20% bucket 7: 30% bucket 8: 30% bucket 10: 30% bucket 13: 30% bucket 9: 30% bucket 15: 30% bucket 12: 30% bucket 17: 30% bucket 13: 100% bucket 14: 30% bucket 26: 20% bucket 4: 40% bucket 16: 30% bucket 18: 30% bucket 19: 30% bucket 21: 30% bucket 11: 30% bucket 1: 40% bucket 3: 40% bucket 6: 40% bucket 2: 40% bucket 5: 40% bucket 20: 30% bucket 27: 100% bucket 23: 80% bucket 14: 70% bucket 12: 100% bucket 16: 90% bucket 29: 10% bucket 22: 30% bucket 27: 20% bucket 18: 90% bucket 7: 40% bucket 19: 90% bucket 24: 80% bucket 20: 60% Calculating Z arrays for bucket 30 Reserving size (25350) for bucket 32 bucket 21: 90% bucket 22: 90% bucket 25: 80% bucket 25: 30% bucket 24: 30% bucket 4: 50% bucket 8: 40% Calculating Z arrays for bucket 31 Getting block 33 of 204 Getting block 34 of 204 Sorting block of length 12461 for bucket 3 (Using difference cover) bucket 10: 40% Sorting block of length 24844 for bucket 4 bucket 13: 40% (Using difference cover) bucket 9: 40% Sorting block of length 22844 for bucket 5 bucket 15: 40% (Using difference cover) bucket 12: 40% bucket 17: 40% bucket 14: 40% bucket 11: 40% bucket 18: 40% bucket 19: 40% bucket 26: 30% bucket 21: 40% bucket 1: 50% bucket 3: 50% bucket 6: 50% bucket 2: 50% bucket 5: 50% bucket 20: 40% Sorting block of length 21253 for bucket 8 (Using difference cover) bucket 7: 50% bucket 22: 40% bucket 4: 60% bucket 16: 40% bucket 26: 70% Sorting block of length 20406 for bucket 17 (Using difference cover) bucket 9: 100% bucket 28: 20% Sorting block of length 23169 for bucket 13 (Using difference cover) Sorting block of length 12025 for bucket 27 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 24170 for bucket 12 (Using difference cover) bucket 16: 100% Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 30: bucket 29: 20% bucket 23: 90% bucket 18: 100% bucket 14: 80% bucket 19: 100% bucket 24: 90% bucket 20: 70% bucket 21: 100% Reserving size (25350) for bucket 33 Entering block accumulator loop for bucket 31: bucket 8: 50% bucket 23: 30% Sorting block time: 00:00:00 Reserving size (25350) for bucket 34 bucket 22: 100% bucket 25: 90% Sorting block of length 17916 for bucket 9 (Using difference cover) Returning block of 12462 for bucket 3 Returning block of 12026 for bucket 27 bucket 26: 80% bucket 25: 40% bucket 24: 40% bucket 27: 30% bucket 10: 50% bucket 13: 50% bucket 9: 50% bucket 15: 50% bucket 12: 50% bucket 17: 50% bucket 1: 60% bucket 14: 50% bucket 3: 60% bucket 6: 60% bucket 2: 60% bucket 11: 50% bucket 5: 60% bucket 18: 50% bucket 19: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 28: 30% Sorting block of length 17005 for bucket 16 (Using difference cover) Entering block accumulator loop for bucket 32: Sorting block of length 17565 for bucket 18 (Using difference cover) bucket 26: 40% bucket 20: 50% Sorting block of length 14750 for bucket 19 bucket 21: 50% (Using difference cover) bucket 4: 70% Sorting block of length 21176 for bucket 21 (Using difference cover) Calculating Z arrays for bucket 33 Returning block of 21254 for bucket 8 Calculating Z arrays for bucket 34 Sorting block of length 21699 for bucket 22 (Using difference cover) bucket 7: 60% bucket 22: 50% bucket 20: 80% bucket 23: 40% bucket 10: 60% Sorting block time: 00:00:00 Returning block of 23170 for bucket 13 Returning block of 22845 for bucket 5 Returning block of 20407 for bucket 17 bucket 24: 100% Returning block of 24845 for bucket 4 bucket 29: 30% bucket 23: 100% bucket 25: 100% bucket 26: 90% Returning block of 17917 for bucket 9 bucket 14: 90% Returning block of 24171 for bucket 12 Entering block accumulator loop for bucket 33: Getting block 35 of 204 Entering block accumulator loop for bucket 34: bucket 28: 40% Getting block 36 of 204 bucket 13: 60% bucket 25: 50% bucket 27: 40% bucket 24: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 31: 10% bucket 30: 10% Returning block of 17006 for bucket 16 Sorting block of length 24101 for bucket 24 (Using difference cover) bucket 16: 50% bucket 1: 70% Sorting block of length 14500 for bucket 23 bucket 3: 70% (Using difference cover) Sorting block of length 15514 for bucket 25 (Using difference cover) Reserving size (25350) for bucket 35 Getting block 37 of 204 Reserving size (25350) for bucket 36 bucket 6: 70% bucket 2: 70% bucket 9: 60% bucket 5: 70% bucket 15: 60% bucket 12: 60% bucket 17: 60% bucket 14: 60% bucket 18: 60% bucket 19: 60% bucket 8: 60% bucket 4: 80% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 20: 90% Sorting block time: 00:00:00 Returning block of 14751 for bucket 19 bucket 26: 100% bucket 29: 40% Returning block of 21700 for bucket 22 Returning block of 17566 for bucket 18 bucket 32: 10% Returning block of 21177 for bucket 21 Calculating Z arrays for bucket 35 Reserving size (25350) for bucket 37 Calculating Z arrays for bucket 36 Getting block 38 of 204 Getting block 39 of 204 Getting block 40 of 204 Getting block 41 of 204 bucket 7: 70% bucket 11: 60% bucket 21: 60% Getting block 42 of 204 bucket 20: 60% bucket 22: 60% bucket 26: 50% bucket 13: 70% bucket 27: 50% bucket 25: 60% bucket 28: 50% bucket 24: 60% bucket 10: 70% bucket 3: 80% bucket 1: 80% Getting block 43 of 204 Returning block of 14501 for bucket 23 bucket 30: 20% Returning block of 15515 for bucket 25 bucket 31: 20% bucket 33: 10% Returning block of 24102 for bucket 24 Sorting block of length 20797 for bucket 26 (Using difference cover) Entering block accumulator loop for bucket 35: Calculating Z arrays for bucket 37 bucket 16: 60% Reserving size (25350) for bucket 38 Entering block accumulator loop for bucket 36: Reserving size (25350) for bucket 39 Reserving size (25350) for bucket 40 bucket 34: 10% Reserving size (25350) for bucket 41 Reserving size (25350) for bucket 42 Getting block 44 of 204 bucket 23: 50% bucket 4: 90% Sorting block time: 00:00:00 bucket 20: 100% bucket 14: 100% bucket 29: 50% bucket 32: 20% Reserving size (25350) for bucket 43 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 37: Calculating Z arrays for bucket 39 Calculating Z arrays for bucket 40 Calculating Z arrays for bucket 41 Calculating Z arrays for bucket 42 Reserving size (25350) for bucket 44 Getting block 45 of 204 Returning block of 20798 for bucket 26 bucket 31: 30% Sorting block of length 15170 for bucket 20 (Using difference cover) Getting block 46 of 204 bucket 34: 20% bucket 28: 60% bucket 6: 80% bucket 2: 80% bucket 5: 80% bucket 9: 70% bucket 15: 70% Sorting block time: 00:00:00 bucket 33: 20% bucket 8: 70% bucket 12: 70% bucket 17: 70% bucket 14: 70% bucket 18: 70% bucket 19: 70% Getting block 47 of 204 Getting block 48 of 204 Sorting block of length 10774 for bucket 14 (Using difference cover) Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 38: Entering block accumulator loop for bucket 39: Entering block accumulator loop for bucket 40: bucket 29: 60% bucket 32: 30% bucket 30: 30% bucket 35: 10% bucket 36: 10% bucket 7: 80% bucket 13: 80% bucket 21: 70% bucket 20: 70% bucket 22: 70% bucket 26: 60% bucket 25: 70% bucket 27: 60% bucket 3: 90% bucket 10: 80% bucket 11: 70% bucket 24: 70% bucket 1: 90% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 41: Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 42: Reserving size (25350) for bucket 45 Getting block 49 of 204 Getting block 50 of 204 Getting block 51 of 204 Reserving size (25350) for bucket 46 bucket 16: 70% bucket 4: 100% bucket 23: 60% bucket 2: 90% bucket 5: 90% bucket 9: 80% bucket 15: 80% bucket 8: 80% bucket 12: 80% bucket 17: 80% bucket 14: 80% bucket 18: 80% bucket 19: 80% Returning block of 15171 for bucket 20 bucket 28: 70% bucket 7: 90% bucket 31: 40% bucket 3: 100% bucket 34: 30% bucket 13: 90% bucket 10: 90% bucket 33: 30% bucket 21: 80% bucket 20: 80% bucket 22: 80% bucket 25: 80% bucket 26: 70% bucket 27: 70% Sorting block of length 20633 for bucket 4 (Using difference cover) Reserving size (25350) for bucket 47 Reserving size (25350) for bucket 48 bucket 6: 90% bucket 1: 100% bucket 11: 80% bucket 24: 80% bucket 2: 100% Sorting block time: 00:00:00 bucket 5: 100% bucket 9: 90% bucket 15: 90% bucket 12: 90% bucket 17: 90% Entering block accumulator loop for bucket 43: bucket 16: 80% bucket 14: 90% bucket 18: 90% bucket 23: 70% bucket 19: 90% Sorting block of length 22092 for bucket 3 (Using difference cover) Sorting block of length 22323 for bucket 1 (Using difference cover) Sorting block of length 9224 for bucket 2 (Using difference cover) Returning block of 20634 for bucket 4 Sorting block of length 24741 for bucket 5 (Using difference cover) bucket 7: 100% Returning block of 10775 for bucket 14 bucket 29: 70% bucket 32: 40% bucket 37: 10% bucket 36: 20% bucket 10: 100% bucket 13: 100% bucket 11: 90% bucket 21: 90% bucket 20: 90% bucket 22: 90% bucket 25: 90% bucket 26: 80% bucket 24: 90% Sorting block of length 24436 for bucket 7 (Using difference cover) bucket 8: 90% bucket 15: 100% bucket 17: 100% Sorting block of length 23415 for bucket 10 (Using difference cover) Sorting block of length 8885 for bucket 13 (Using difference cover) bucket 23: 80% bucket 6: 100% Sorting block of length 10328 for bucket 15 (Using difference cover) Getting block 28 of 203 Sorting block of length 13305 for bucket 17 (Using difference cover) Entering block accumulator loop for bucket 44: Calculating Z arrays for bucket 45 Reserving size (25350) for bucket 49 Reserving size (25350) for bucket 50 Reserving size (25350) for bucket 51 Calculating Z arrays for bucket 46 Getting block 52 of 204 bucket 35: 20% Calculating Z arrays for bucket 47 Calculating Z arrays for bucket 48 bucket 30: 40% bucket 31: 50% bucket 34: 40% bucket 16: 90% Sorting block of length 12811 for bucket 6 (Using difference cover) Reserving size (25350) for bucket 28 bucket 9: 100% bucket 12: 100% bucket 27: 80% bucket 14: 100% bucket 33: 40% bucket 28: 80% bucket 39: 10% bucket 38: 10% bucket 29: 80% bucket 40: 10% bucket 32: 50% bucket 37: 20% bucket 36: 30% Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 45: Calculating Z arrays for bucket 50 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 46: Reserving size (25350) for bucket 52 Entering block accumulator loop for bucket 47: Getting block 53 of 204 Entering block accumulator loop for bucket 48: bucket 42: 10% bucket 41: 10% bucket 30: 50% bucket 31: 60% Sorting block time: 00:00:00 bucket 20: 100% bucket 18: 100% Calculating Z arrays for bucket 28 bucket 34: 50% Sorting block of length 21160 for bucket 9 (Using difference cover) Sorting block of length 20543 for bucket 12 (Using difference cover) Sorting block of length 18579 for bucket 14 (Using difference cover) bucket 8: 100% bucket 25: 100% Returning block of 9225 for bucket 2 bucket 19: 100% bucket 16: 100% bucket 11: 100% bucket 23: 90% Sorting block of length 25276 for bucket 20 (Using difference cover) Sorting block of length 25035 for bucket 18 (Using difference cover) Entering block accumulator loop for bucket 28: bucket 21: 100% bucket 26: 90% bucket 24: 100% bucket 22: 100% Sorting block of length 20232 for bucket 8 (Using difference cover) Sorting block of length 12619 for bucket 25 (Using difference cover) Sorting block of length 22749 for bucket 19 (Using difference cover) Sorting block of length 17645 for bucket 16 (Using difference cover) Sorting block of length 19595 for bucket 11 (Using difference cover) bucket 27: 90% Sorting block of length 16678 for bucket 21 (Using difference cover) Sorting block of length 22241 for bucket 24 (Using difference cover) Sorting block of length 24222 for bucket 22 (Using difference cover) Getting block 54 of 204 Entering block accumulator loop for bucket 49: Entering block accumulator loop for bucket 50: Getting block 29 of 203 Reserving size (25350) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: Entering block accumulator loop for bucket 51: bucket 28: 90% bucket 33: 50% Calculating Z arrays for bucket 52 Reserving size (25350) for bucket 53 bucket 23: 100% Sorting block of length 15028 for bucket 23 (Using difference cover) bucket 29: 10% bucket 26: 100% Sorting block of length 24571 for bucket 26 (Using difference cover) bucket 27: 100% Sorting block of length 21064 for bucket 27 (Using difference cover) bucket 43: 10% bucket 35: 30% bucket 39: 20% bucket 38: 20% bucket 40: 20% bucket 32: 60% bucket 37: 30% bucket 36: 40% bucket 44: 10% bucket 30: 60% bucket 42: 20% bucket 41: 20% bucket 31: 70% bucket 29: 90% bucket 34: 60% bucket 29: 20% Reserving size (25350) for bucket 54 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 52: bucket 45: 10% bucket 46: 10% bucket 28: 100% bucket 33: 60% bucket 47: 10% bucket 29: 100% bucket 30: 70% bucket 32: 70% bucket 37: 40% bucket 43: 20% bucket 31: 80% bucket 44: 20% bucket 35: 40% bucket 39: 30% bucket 40: 30% bucket 36: 50% bucket 38: 30% Sorting block time: 00:00:00 Returning block of 22093 for bucket 3 bucket 34: 70% bucket 28: 10% Calculating Z arrays for bucket 54 bucket 42: 30% Entering block accumulator loop for bucket 53: bucket 41: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 29: 30% Sorting block time: 00:00:00 Returning block of 24742 for bucket 5 Returning block of 20544 for bucket 12 Returning block of 19596 for bucket 11 Sorting block of length 13340 for bucket 28 (Using difference cover) bucket 48: 10% Sorting block of length 14825 for bucket 29 (Using difference cover) Sorting block time: 00:00:00 Returning block of 24437 for bucket 7 bucket 33: 70% bucket 30: 80% bucket 31: 90% bucket 45: 20% bucket 46: 20% bucket 37: 50% bucket 28: 20% Getting block 30 of 203 Returning block of 22324 for bucket 1 Returning block of 23416 for bucket 10 bucket 47: 20% bucket 32: 80% bucket 39: 40% bucket 38: 40% bucket 36: 60% bucket 40: 40% bucket 43: 30% bucket 29: 40% Reserving size (25350) for bucket 30 Getting block 31 of 203 Getting block 32 of 203 Getting block 33 of 203 Getting block 34 of 203 Sorting block time: 00:00:00 bucket 49: 10% bucket 51: 10% bucket 35: 50% bucket 50: 10% bucket 44: 30% Sorting block time: 00:00:00 bucket 34: 80% Entering block accumulator loop for bucket 54: bucket 42: 40% bucket 41: 40% bucket 52: 10% bucket 30: 90% bucket 37: 60% bucket 33: 80% bucket 45: 30% bucket 46: 30% bucket 48: 20% bucket 31: 100% Returning block of 13341 for bucket 28 Returning block of 14826 for bucket 29 bucket 32: 90% bucket 39: 50% bucket 38: 50% bucket 40: 50% bucket 36: 70% bucket 28: 30% Calculating Z arrays for bucket 30 Reserving size (25350) for bucket 31 Reserving size (25350) for bucket 32 Reserving size (25350) for bucket 33 bucket 43: 40% Reserving size (25350) for bucket 34 Getting block 35 of 203 Getting block 36 of 203 bucket 47: 30% Sorting block of length 12126 for bucket 31 (Using difference cover) bucket 29: 50% Calculating Z arrays for bucket 31 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 30: Calculating Z arrays for bucket 33 Calculating Z arrays for bucket 34 Reserving size (25350) for bucket 35 Reserving size (25350) for bucket 36 bucket 35: 60% bucket 44: 40% bucket 51: 20% bucket 50: 20% bucket 30: 100% bucket 37: 70% bucket 33: 90% bucket 42: 50% bucket 41: 50% bucket 45: 40% bucket 46: 40% bucket 53: 10% bucket 52: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 28: 40% Entering block accumulator loop for bucket 31: Entering block accumulator loop for bucket 32: Entering block accumulator loop for bucket 33: Calculating Z arrays for bucket 35 Sorting block time: 00:00:00 bucket 48: 30% bucket 39: 60% bucket 38: 60% bucket 40: 60% bucket 32: 100% bucket 36: 80% bucket 43: 50% Entering block accumulator loop for bucket 34: Calculating Z arrays for bucket 36 Returning block of 12620 for bucket 25 Returning block of 8886 for bucket 13 Sorting block time: 00:00:00 bucket 29: 60% Getting block 55 of 204 bucket 54: 10% Entering block accumulator loop for bucket 35: Sorting block time: 00:00:00 Entering block accumulator loop for bucket 36: Returning block of 21161 for bucket 9 bucket 28: 50% bucket 30: 10% Getting block 56 of 204 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 29: 70% Returning block of 12812 for bucket 6 Getting block 37 of 203 Getting block 38 of 203 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 22750 for bucket 19 Returning block of 22242 for bucket 24 bucket 28: 60% bucket 30: 20% Reserving size (25350) for bucket 37 Sorting block time: 00:00:00 bucket 29: 80% Reserving size (25350) for bucket 38 Returning block of 13306 for bucket 17 Returning block of 24223 for bucket 22 bucket 35: 10% Returning block of 20233 for bucket 8 Sorting block of length 13674 for bucket 30 (Using difference cover) Returning block of 12127 for bucket 31 bucket 47: 40% Sorting block of length 24058 for bucket 32 (Using difference cover) bucket 34: 90% bucket 35: 70% bucket 42: 60% bucket 49: 20% bucket 37: 80% bucket 33: 100% Getting block 39 of 203 Sorting block time: 00:00:00 Calculating Z arrays for bucket 37 Getting block 40 of 203 bucket 36: 10% bucket 44: 50% bucket 34: 10% bucket 41: 60% bucket 46: 50% bucket 45: 50% bucket 51: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 10329 for bucket 15 bucket 53: 20% bucket 28: 70% bucket 50: 30% Calculating Z arrays for bucket 38 bucket 52: 30% bucket 30: 30% Reserving size (25350) for bucket 39 bucket 39: 70% bucket 38: 70% bucket 40: 70% bucket 43: 60% Returning block of 17646 for bucket 16 Entering block accumulator loop for bucket 37: Reserving size (25350) for bucket 40 Getting block 41 of 203 bucket 31: 10% bucket 33: 10% bucket 29: 90% Reserving size (25350) for bucket 55 bucket 36: 90% bucket 48: 40% bucket 54: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 32: 10% bucket 35: 20% Returning block of 21065 for bucket 27 Returning block of 15029 for bucket 23 Returning block of 25277 for bucket 20 bucket 36: 20% Getting block 42 of 203 Entering block accumulator loop for bucket 38: Calculating Z arrays for bucket 39 Reserving size (25350) for bucket 56 Sorting block of length 22146 for bucket 33 (Using difference cover) bucket 37: 90% Sorting block time: 00:00:00 bucket 35: 80% Sorting block time: 00:00:00 Calculating Z arrays for bucket 40 bucket 47: 50% bucket 28: 80% bucket 44: 60% bucket 34: 20% bucket 30: 40% Reserving size (25350) for bucket 41 bucket 34: 100% bucket 46: 60% bucket 45: 60% bucket 51: 40% bucket 50: 40% Returning block of 18580 for bucket 14 Returning block of 16679 for bucket 21 bucket 29: 100% Returning block of 25036 for bucket 18 bucket 31: 20% Getting block 43 of 203 Getting block 44 of 203 Getting block 45 of 203 bucket 33: 20% Reserving size (25350) for bucket 42 Getting block 46 of 203 Entering block accumulator loop for bucket 39: Returning block of 24572 for bucket 26 bucket 32: 20% bucket 35: 30% Sorting block time: 00:00:00 bucket 53: 30% bucket 52: 40% bucket 49: 30% Calculating Z arrays for bucket 55 bucket 39: 80% bucket 38: 80% bucket 40: 80% bucket 36: 100% bucket 54: 30% bucket 36: 30% bucket 37: 10% Getting block 47 of 203 Entering block accumulator loop for bucket 40: Calculating Z arrays for bucket 41 Calculating Z arrays for bucket 56 bucket 28: 90% Getting block 57 of 204 bucket 42: 70% bucket 48: 50% bucket 43: 70% Returning block of 13675 for bucket 30 Sorting block of length 22262 for bucket 34 (Using difference cover) bucket 41: 70% Returning block of 22147 for bucket 33 bucket 44: 70% bucket 35: 90% Sorting block of length 7928 for bucket 29 (Using difference cover) Reserving size (25350) for bucket 43 Reserving size (25350) for bucket 44 Reserving size (25350) for bucket 45 Calculating Z arrays for bucket 42 Sorting block time: 00:00:00 bucket 47: 60% bucket 46: 70% bucket 45: 70% bucket 50: 50% Sorting block time: 00:00:00 bucket 30: 50% Reserving size (25350) for bucket 46 bucket 51: 50% Entering block accumulator loop for bucket 55: Sorting block of length 20698 for bucket 36 (Using difference cover) Sorting block time: 00:00:00 bucket 37: 100% Sorting block time: 00:00:00 bucket 39: 90% bucket 40: 90% bucket 38: 90% bucket 52: 50% bucket 54: 40% Reserving size (25350) for bucket 57 Getting block 48 of 203 Getting block 49 of 203 Getting block 50 of 203 bucket 31: 30% bucket 38: 10% Reserving size (25350) for bucket 47 bucket 34: 30% Entering block accumulator loop for bucket 56: bucket 42: 80% bucket 32: 30% bucket 43: 80% bucket 35: 40% Returning block of 24059 for bucket 32 bucket 36: 40% bucket 48: 60% Getting block 51 of 203 bucket 44: 80% Getting block 52 of 203 Entering block accumulator loop for bucket 41: bucket 28: 100% Calculating Z arrays for bucket 43 Calculating Z arrays for bucket 44 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 42: Returning block of 7929 for bucket 29 Calculating Z arrays for bucket 46 Getting block 53 of 203 Getting block 54 of 203 bucket 35: 100% bucket 33: 30% bucket 37: 20% bucket 30: 60% bucket 39: 10% bucket 41: 80% bucket 53: 40% bucket 49: 40% bucket 47: 70% bucket 46: 80% bucket 45: 80% bucket 50: 60% Returning block of 20699 for bucket 36 Sorting block of length 10054 for bucket 37 (Using difference cover) Returning block of 22263 for bucket 34 Calculating Z arrays for bucket 57 Reserving size (25350) for bucket 48 Reserving size (25350) for bucket 49 Reserving size (25350) for bucket 50 Calculating Z arrays for bucket 47 bucket 31: 40% Reserving size (25350) for bucket 51 Reserving size (25350) for bucket 52 Sorting block of length 19567 for bucket 28 (Using difference cover) Entering block accumulator loop for bucket 43: Entering block accumulator loop for bucket 44: Sorting block time: 00:00:00 bucket 51: 60% bucket 39: 100% bucket 40: 100% bucket 38: 100% bucket 52: 60% bucket 54: 50% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 45: Entering block accumulator loop for bucket 46: bucket 32: 40% bucket 35: 50% bucket 36: 50% Getting block 58 of 204 Getting block 59 of 204 bucket 42: 90% bucket 44: 90% bucket 43: 90% bucket 48: 70% Reserving size (25350) for bucket 53 Sorting block of length 10841 for bucket 35 (Using difference cover) Entering block accumulator loop for bucket 57: Returning block of 10055 for bucket 37 bucket 41: 90% bucket 45: 90% bucket 46: 90% bucket 50: 70% bucket 49: 50% Sorting block time: 00:00:00 Sorting block of length 14873 for bucket 39 (Using difference cover) Reserving size (25350) for bucket 54 bucket 55: 10% bucket 40: 10% Sorting block of length 20787 for bucket 40 bucket 34: 40% (Using difference cover) Sorting block of length 19404 for bucket 38 (Using difference cover) bucket 53: 50% bucket 33: 40% bucket 47: 80% bucket 51: 70% bucket 54: 60% Reserving size (25350) for bucket 58 Reserving size (25350) for bucket 59 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 60 of 204 bucket 52: 70% Getting block 61 of 204 Getting block 62 of 204 Returning block of 10842 for bucket 35 Sorting block time: 00:00:00 bucket 42: 100% bucket 44: 100% bucket 30: 70% bucket 37: 30% Calculating Z arrays for bucket 48 Calculating Z arrays for bucket 49 bucket 43: 100% bucket 41: 100% bucket 56: 10% bucket 45: 100% bucket 46: 100% bucket 48: 80% bucket 49: 60% Calculating Z arrays for bucket 58 Calculating Z arrays for bucket 59 bucket 50: 80% Returning block of 14874 for bucket 39 Returning block of 19405 for bucket 38 Reserving size (25350) for bucket 60 Reserving size (25350) for bucket 61 Reserving size (25350) for bucket 62 Getting block 63 of 204 Returning block of 20788 for bucket 40 Sorting block of length 14019 for bucket 42 (Using difference cover) Sorting block of length 8029 for bucket 44 (Using difference cover) Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 47: Calculating Z arrays for bucket 51 Calculating Z arrays for bucket 52 bucket 55: 20% bucket 53: 60% Sorting block time: 00:00:00 bucket 47: 90% bucket 54: 70% bucket 51: 80% Sorting block of length 19973 for bucket 43 (Using difference cover) Sorting block of length 21124 for bucket 41 (Using difference cover) Sorting block of length 19277 for bucket 45 (Using difference cover) Sorting block of length 21036 for bucket 46 (Using difference cover) Entering block accumulator loop for bucket 58: Entering block accumulator loop for bucket 59: Calculating Z arrays for bucket 60 Calculating Z arrays for bucket 61 Calculating Z arrays for bucket 62 Reserving size (25350) for bucket 63 bucket 52: 80% bucket 38: 20% Returning block of 19568 for bucket 28 bucket 31: 50% bucket 39: 20% bucket 41: 10% Sorting block time: 00:00:00 Returning block of 8030 for bucket 44 bucket 32: 50% bucket 35: 60% bucket 36: 60% bucket 56: 20% bucket 49: 70% bucket 48: 90% Calculating Z arrays for bucket 53 bucket 42: 10% Calculating Z arrays for bucket 54 Getting block 64 of 204 Getting block 55 of 203 bucket 50: 90% bucket 33: 50% bucket 57: 10% Entering block accumulator loop for bucket 60: Entering block accumulator loop for bucket 61: Calculating Z arrays for bucket 63 Getting block 65 of 204 Getting block 66 of 204 Entering block accumulator loop for bucket 62: Returning block of 14020 for bucket 42 bucket 53: 70% bucket 47: 100% Sorting block time: 00:00:00 bucket 54: 80% bucket 52: 90% bucket 40: 20% Entering block accumulator loop for bucket 48: Entering block accumulator loop for bucket 49: bucket 55: 30% Reserving size (25350) for bucket 64 Reserving size (25350) for bucket 65 Entering block accumulator loop for bucket 50: Entering block accumulator loop for bucket 51: Entering block accumulator loop for bucket 52: bucket 30: 80% bucket 37: 40% bucket 34: 50% bucket 43: 10% bucket 31: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 63: Reserving size (25350) for bucket 66 Getting block 67 of 204 Getting block 68 of 204 bucket 48: 100% Sorting block of length 5275 for bucket 47 (Using difference cover) bucket 49: 80% bucket 56: 30% Returning block of 19974 for bucket 43 bucket 44: 10% bucket 38: 30% bucket 39: 30% bucket 41: 20% bucket 46: 10% bucket 32: 60% bucket 35: 70% bucket 36: 70% Sorting block time: 00:00:00 bucket 51: 90% Entering block accumulator loop for bucket 53: Reserving size (25350) for bucket 55 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 54: bucket 45: 10% Calculating Z arrays for bucket 65 Returning block of 21125 for bucket 41 Returning block of 21037 for bucket 46 Returning block of 19278 for bucket 45 bucket 50: 100% bucket 57: 20% bucket 54: 90% bucket 53: 80% bucket 58: 10% bucket 59: 10% bucket 52: 100% bucket 61: 10% bucket 60: 10% bucket 33: 60% bucket 42: 20% Calculating Z arrays for bucket 66 Reserving size (25350) for bucket 67 Reserving size (25350) for bucket 68 Sorting block of length 24174 for bucket 48 (Using difference cover) Getting block 56 of 203 bucket 40: 30% bucket 31: 70% bucket 30: 90% bucket 37: 50% bucket 43: 20% Sorting block time: 00:00:00 Returning block of 5276 for bucket 47 bucket 47: 10% bucket 56: 40% bucket 49: 90% Entering block accumulator loop for bucket 64: bucket 62: 10% Entering block accumulator loop for bucket 65: Sorting block of length 20606 for bucket 50 (Using difference cover) Sorting block of length 16387 for bucket 52 (Using difference cover) bucket 55: 40% bucket 32: 70% bucket 36: 80% Sorting block time: 00:00:00 bucket 51: 100% bucket 54: 100% bucket 60: 20% bucket 58: 20% bucket 57: 30% bucket 59: 20% bucket 61: 20% Getting block 69 of 204 Sorting block time: 00:00:00 Calculating Z arrays for bucket 67 Calculating Z arrays for bucket 55 bucket 35: 80% bucket 41: 30% bucket 44: 20% bucket 38: 40% bucket 46: 20% bucket 34: 60% bucket 48: 10% Entering block accumulator loop for bucket 66: Calculating Z arrays for bucket 68 Getting block 70 of 204 bucket 53: 90% Returning block of 24175 for bucket 48 bucket 39: 40% bucket 33: 70% bucket 42: 30% bucket 49: 10% bucket 45: 20% bucket 51: 10% Reserving size (25350) for bucket 56 bucket 50: 10% Getting block 71 of 204 bucket 31: 80% Getting block 72 of 204 bucket 63: 10% Returning block of 16388 for bucket 52 bucket 49: 100% Sorting block of length 19554 for bucket 51 (Using difference cover) bucket 56: 50% Sorting block time: 00:00:00 Sorting block of length 21940 for bucket 54 (Using difference cover) bucket 52: 10% bucket 30: 100% bucket 47: 20% bucket 40: 40% bucket 37: 60% bucket 43: 30% bucket 32: 80% bucket 36: 90% Entering block accumulator loop for bucket 55: bucket 35: 90% bucket 54: 10% bucket 48: 20% Getting block 73 of 204 Reserving size (25350) for bucket 69 Returning block of 20607 for bucket 50 bucket 53: 10% bucket 41: 40% bucket 34: 70% bucket 38: 50% Calculating Z arrays for bucket 56 Sorting block time: 00:00:00 bucket 55: 50% Entering block accumulator loop for bucket 67: bucket 44: 30% bucket 46: 30% bucket 39: 50% bucket 31: 90% bucket 49: 20% bucket 50: 20% bucket 51: 20% Sorting block of length 18099 for bucket 30 (Using difference cover) bucket 62: 20% bucket 60: 30% Sorting block time: 00:00:00 bucket 42: 40% bucket 33: 80% bucket 32: 90% bucket 40: 50% bucket 35: 100% bucket 36: 100% bucket 45: 30% Entering block accumulator loop for bucket 56: bucket 52: 20% Entering block accumulator loop for bucket 68: bucket 57: 40% bucket 58: 30% bucket 59: 30% bucket 61: 30% Reserving size (25350) for bucket 70 Getting block 74 of 204 Reserving size (25350) for bucket 71 Reserving size (25350) for bucket 72 Sorting block of length 8143 for bucket 49 (Using difference cover) bucket 54: 20% bucket 48: 30% bucket 37: 70% bucket 43: 40% bucket 47: 30% Returning block of 18100 for bucket 30 bucket 53: 20% Sorting block time: 00:00:00 Returning block of 19555 for bucket 51 bucket 53: 100% bucket 56: 60% bucket 31: 100% bucket 41: 50% bucket 64: 10% Reserving size (25350) for bucket 73 Calculating Z arrays for bucket 69 bucket 39: 60% Sorting block of length 23172 for bucket 35 (Using difference cover) bucket 63: 20% bucket 65: 10% Returning block of 21941 for bucket 54 bucket 55: 60% bucket 60: 40% Sorting block time: 00:00:00 Sorting block of length 13218 for bucket 36 (Using difference cover) Calculating Z arrays for bucket 70 Reserving size (25350) for bucket 74 Calculating Z arrays for bucket 71 Calculating Z arrays for bucket 72 Getting block 75 of 204 Getting block 76 of 204 Returning block of 8144 for bucket 49 Sorting block of length 20969 for bucket 53 (Using difference cover) bucket 62: 30% bucket 57: 50% bucket 66: 10% Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 69: bucket 58: 40% bucket 59: 40% bucket 61: 40% Getting block 77 of 204 bucket 56: 70% bucket 38: 60% bucket 55: 10% Sorting block time: 00:00:00 bucket 64: 20% bucket 55: 70% bucket 60: 50% bucket 67: 10% Calculating Z arrays for bucket 74 Sorting block time: 00:00:00 bucket 49: 30% bucket 50: 30% bucket 51: 30% bucket 44: 40% bucket 46: 40% bucket 33: 90% bucket 32: 100% Sorting block of length 24041 for bucket 31 (Using difference cover) bucket 40: 60% Entering block accumulator loop for bucket 70: Entering block accumulator loop for bucket 71: Reserving size (25350) for bucket 75 Entering block accumulator loop for bucket 72: Reserving size (25350) for bucket 76 Getting block 78 of 204 Entering block accumulator loop for bucket 73: bucket 63: 30% Reserving size (25350) for bucket 77 bucket 65: 20% Returning block of 20970 for bucket 53 bucket 57: 60% bucket 66: 20% bucket 68: 10% bucket 56: 80% Sorting block time: 00:00:00 bucket 52: 30% bucket 42: 50% bucket 34: 80% bucket 48: 40% bucket 37: 80% bucket 43: 50% Getting block 79 of 204 Entering block accumulator loop for bucket 74: bucket 58: 50% bucket 59: 50% bucket 41: 60% Returning block of 23173 for bucket 35 bucket 47: 40% bucket 39: 70% bucket 61: 50% bucket 45: 40% Calculating Z arrays for bucket 75 Returning block of 13219 for bucket 36 bucket 54: 30% bucket 55: 20% Getting block 57 of 203 Sorting block of length 8157 for bucket 32 (Using difference cover) bucket 38: 70% bucket 33: 100% Calculating Z arrays for bucket 76 Reserving size (25350) for bucket 78 bucket 60: 60% Calculating Z arrays for bucket 77 bucket 67: 20% Getting block 80 of 204 bucket 64: 30% Sorting block time: 00:00:00 Returning block of 24042 for bucket 31 bucket 40: 70% bucket 69: 10% bucket 56: 90% bucket 56: 10% bucket 46: 50% bucket 49: 40% bucket 50: 40% bucket 51: 40% bucket 53: 30% bucket 44: 50% Reserving size (25350) for bucket 79 bucket 57: 70% bucket 66: 30% bucket 68: 20% bucket 63: 40% bucket 52: 40% bucket 48: 50% bucket 37: 90% bucket 42: 60% bucket 43: 60% bucket 34: 90% Reserving size (25350) for bucket 57 Sorting block of length 19654 for bucket 33 (Using difference cover) Entering block accumulator loop for bucket 75: bucket 65: 30% Sorting block time: 00:00:00 bucket 39: 80% bucket 41: 70% bucket 47: 50% Returning block of 8158 for bucket 32 bucket 55: 30% bucket 54: 40% bucket 62: 40% bucket 38: 80% bucket 40: 80% bucket 46: 60% bucket 56: 20% bucket 50: 50% bucket 49: 50% bucket 51: 50% bucket 53: 40% bucket 70: 10% bucket 44: 60% bucket 71: 10% Getting block 58 of 203 Calculating Z arrays for bucket 78 Getting block 59 of 203 Entering block accumulator loop for bucket 76: Calculating Z arrays for bucket 57 Returning block of 19655 for bucket 33 Entering block accumulator loop for bucket 77: Reserving size (25350) for bucket 80 bucket 58: 60% Getting block 81 of 204 bucket 59: 60% bucket 52: 50% bucket 61: 60% bucket 48: 60% bucket 72: 10% bucket 43: 70% bucket 73: 10% bucket 37: 100% bucket 60: 70% bucket 42: 70% bucket 55: 80% Getting block 60 of 203 bucket 67: 30% bucket 34: 100% bucket 45: 50% bucket 64: 40% bucket 69: 20% bucket 56: 100% Calculating Z arrays for bucket 79 bucket 74: 10% bucket 39: 90% bucket 55: 40% bucket 54: 50% Reserving size (25350) for bucket 58 Reserving size (25350) for bucket 59 Entering block accumulator loop for bucket 57: bucket 47: 60% bucket 41: 80% bucket 40: 90% bucket 38: 90% bucket 46: 70% bucket 44: 70% bucket 57: 80% bucket 66: 40% bucket 68: 30% bucket 63: 50% bucket 56: 30% bucket 65: 40% Entering block accumulator loop for bucket 78: bucket 62: 50% bucket 70: 20% bucket 71: 20% Calculating Z arrays for bucket 80 Reserving size (25350) for bucket 81 bucket 50: 60% bucket 49: 60% bucket 51: 60% Sorting block of length 17540 for bucket 37 (Using difference cover) Reserving size (25350) for bucket 60 bucket 72: 20% Sorting block of length 11629 for bucket 56 (Using difference cover) Sorting block of length 13957 for bucket 34 (Using difference cover) Getting block 61 of 203 bucket 53: 50% bucket 43: 80% bucket 48: 70% Calculating Z arrays for bucket 58 Calculating Z arrays for bucket 59 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 79: bucket 73: 20% bucket 55: 90% bucket 58: 70% bucket 59: 70% bucket 61: 70% bucket 60: 80% bucket 67: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 52: 60% bucket 42: 80% bucket 64: 50% bucket 69: 30% bucket 74: 20% Calculating Z arrays for bucket 81 Getting block 62 of 203 bucket 39: 100% bucket 47: 70% bucket 55: 50% bucket 54: 60% bucket 40: 100% bucket 38: 100% bucket 44: 80% bucket 46: 80% Entering block accumulator loop for bucket 80: bucket 41: 90% bucket 75: 10% bucket 57: 90% bucket 66: 50% bucket 68: 40% bucket 63: 60% bucket 76: 10% bucket 77: 10% bucket 56: 40% Calculating Z arrays for bucket 60 bucket 70: 30% bucket 71: 30% bucket 62: 60% bucket 65: 50% Returning block of 11630 for bucket 56 bucket 45: 60% Reserving size (25350) for bucket 61 bucket 72: 30% Entering block accumulator loop for bucket 81: bucket 73: 30% bucket 55: 100% bucket 67: 50% bucket 58: 80% bucket 59: 80% bucket 60: 90% bucket 61: 80% bucket 78: 10% Entering block accumulator loop for bucket 58: Entering block accumulator loop for bucket 59: Returning block of 17541 for bucket 37 Returning block of 13958 for bucket 34 bucket 50: 70% bucket 49: 70% bucket 51: 70% bucket 43: 90% bucket 48: 80% bucket 57: 10% bucket 53: 60% bucket 69: 40% bucket 74: 30% Reserving size (25350) for bucket 62 Sorting block of length 21109 for bucket 39 (Using difference cover) Sorting block of length 24226 for bucket 40 (Using difference cover) Sorting block of length 17732 for bucket 38 (Using difference cover) bucket 52: 70% bucket 42: 90% bucket 47: 80% bucket 55: 60% bucket 44: 90% Entering block accumulator loop for bucket 60: bucket 64: 60% bucket 68: 50% bucket 77: 20% bucket 46: 90% bucket 54: 70% Calculating Z arrays for bucket 61 bucket 75: 20% bucket 57: 100% bucket 66: 60% bucket 63: 70% bucket 70: 40% bucket 71: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 41: 100% bucket 56: 50% Calculating Z arrays for bucket 62 Sorting block of length 24849 for bucket 55 (Using difference cover) bucket 79: 10% Sorting block time: 00:00:00 bucket 45: 70% bucket 43: 100% bucket 48: 90% bucket 49: 80% bucket 51: 80% bucket 57: 20% bucket 53: 70% bucket 50: 80% bucket 62: 70% bucket 65: 60% Entering block accumulator loop for bucket 61: Sorting block time: 00:00:00 bucket 76: 20% bucket 67: 60% bucket 78: 20% bucket 72: 40% bucket 73: 40% bucket 58: 90% bucket 59: 90% bucket 60: 100% bucket 61: 90% Returning block of 17733 for bucket 38 Returning block of 21110 for bucket 39 bucket 47: 90% bucket 44: 100% bucket 55: 70% bucket 52: 80% bucket 54: 80% bucket 46: 100% bucket 80: 10% bucket 69: 50% bucket 74: 40% Sorting block of length 25329 for bucket 57 (Using difference cover) bucket 68: 60% bucket 77: 30% bucket 64: 70% bucket 75: 30% bucket 66: 70% bucket 63: 80% bucket 70: 50% bucket 71: 50% bucket 81: 10% bucket 79: 20% bucket 42: 100% Sorting block of length 22158 for bucket 41 (Using difference cover) Getting block 63 of 203 Getting block 64 of 203 Entering block accumulator loop for bucket 62: Returning block of 24227 for bucket 40 Sorting block of length 25336 for bucket 43 (Using difference cover) bucket 56: 60% bucket 59: 10% bucket 49: 90% bucket 48: 100% bucket 50: 90% bucket 51: 90% bucket 60: 10% Sorting block time: 00:00:00 Getting block 82 of 204 Returning block of 24850 for bucket 55 Sorting block of length 16143 for bucket 60 (Using difference cover) bucket 62: 80% bucket 65: 70% bucket 78: 30% bucket 67: 70% bucket 76: 30% bucket 73: 50% bucket 72: 50% bucket 59: 100% bucket 58: 100% bucket 61: 100% Sorting block time: 00:00:01 bucket 57: 30% bucket 53: 80% bucket 58: 10% Sorting block of length 9270 for bucket 44 (Using difference cover) Sorting block of length 23124 for bucket 46 (Using difference cover) Sorting block time: 00:00:01 bucket 80: 20% bucket 69: 60% bucket 68: 70% bucket 77: 40% bucket 74: 50% Returning block of 25330 for bucket 57 bucket 64: 80% bucket 70: 60% Sorting block time: 00:00:01 Sorting block time: 00:00:01 Sorting block time: 00:00:01 bucket 45: 80% bucket 55: 80% bucket 75: 40% bucket 71: 60% bucket 81: 20% bucket 79: 30% bucket 54: 90% bucket 52: 90% bucket 47: 100% Sorting block of length 22947 for bucket 42 (Using difference cover) Reserving size (25350) for bucket 63 Reserving size (25350) for bucket 64 Sorting block of length 19560 for bucket 48 (Using difference cover) Returning block of 25337 for bucket 43 bucket 49: 100% bucket 56: 70% bucket 50: 100% bucket 59: 20% Reserving size (25350) for bucket 82 bucket 66: 80% bucket 63: 90% Sorting block of length 19117 for bucket 59 (Using difference cover) Sorting block of length 21488 for bucket 58 (Using difference cover) Sorting block time: 00:00:01 bucket 51: 100% bucket 60: 20% Returning block of 9271 for bucket 44 Returning block of 22159 for bucket 41 Getting block 65 of 203 Getting block 66 of 203 Sorting block of length 22521 for bucket 61 (Using difference cover) Sorting block time: 00:00:01 bucket 61: 10% bucket 57: 40% bucket 53: 90% Returning block of 23125 for bucket 46 Sorting block of length 16822 for bucket 47 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 16144 for bucket 60 bucket 78: 40% bucket 67: 80% bucket 73: 60% bucket 72: 60% bucket 62: 90% bucket 65: 80% bucket 76: 40% Sorting block time: 00:00:00 Calculating Z arrays for bucket 63 Sorting block time: 00:00:00 bucket 80: 30% bucket 69: 70% bucket 77: 50% bucket 68: 80% bucket 74: 60% bucket 70: 70% bucket 64: 90% bucket 79: 40% Calculating Z arrays for bucket 64 Sorting block of length 17239 for bucket 49 (Using difference cover) bucket 58: 20% bucket 55: 90% bucket 45: 90% Sorting block of length 16095 for bucket 50 (Using difference cover) Calculating Z arrays for bucket 82 Returning block of 19561 for bucket 48 bucket 71: 70% bucket 54: 100% bucket 81: 30% bucket 52: 100% Sorting block of length 17555 for bucket 51 (Using difference cover) Getting block 67 of 203 bucket 62: 10% Reserving size (25350) for bucket 65 Reserving size (25350) for bucket 66 Returning block of 22948 for bucket 42 bucket 75: 50% bucket 66: 90% bucket 63: 100% Returning block of 19118 for bucket 59 Returning block of 21489 for bucket 58 Getting block 83 of 204 Getting block 84 of 204 bucket 56: 80% bucket 59: 30% bucket 60: 30% Returning block of 16823 for bucket 47 Entering block accumulator loop for bucket 63: Returning block of 22522 for bucket 61 bucket 78: 50% bucket 67: 90% bucket 76: 50% bucket 73: 70% bucket 72: 70% bucket 62: 100% bucket 65: 90% bucket 80: 40% bucket 69: 80% bucket 77: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 61: 20% bucket 68: 90% bucket 57: 50% bucket 70: 80% bucket 53: 100% bucket 79: 50% Entering block accumulator loop for bucket 64: Getting block 68 of 203 Sorting block of length 21263 for bucket 54 (Using difference cover) Sorting block of length 9969 for bucket 52 (Using difference cover) Entering block accumulator loop for bucket 82: Reserving size (25350) for bucket 67 Sorting block of length 24687 for bucket 63 Calculating Z arrays for bucket 65 (Using difference cover) Calculating Z arrays for bucket 66 bucket 64: 100% Getting block 69 of 203 bucket 74: 70% bucket 81: 40% bucket 71: 80% bucket 75: 60% Reserving size (25350) for bucket 83 Reserving size (25350) for bucket 84 bucket 66: 100% Getting block 85 of 204 Sorting block of length 19420 for bucket 62 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 70 of 203 bucket 55: 100% bucket 45: 100% Getting block 71 of 203 bucket 58: 30% bucket 62: 20% Returning block of 16096 for bucket 50 Returning block of 17240 for bucket 49 Returning block of 17556 for bucket 51 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 67: 100% bucket 72: 80% bucket 59: 40% bucket 56: 90% bucket 60: 40% Sorting block of length 20618 for bucket 53 (Using difference cover) Reserving size (25350) for bucket 68 bucket 73: 80% Calculating Z arrays for bucket 67 bucket 78: 60% Entering block accumulator loop for bucket 65: Reserving size (25350) for bucket 69 bucket 65: 100% Entering block accumulator loop for bucket 66: bucket 76: 60% bucket 68: 100% bucket 70: 90% bucket 69: 90% bucket 77: 70% bucket 79: 60% Sorting block of length 23770 for bucket 64 (Using difference cover) bucket 80: 50% Calculating Z arrays for bucket 83 Calculating Z arrays for bucket 84 Sorting block of length 23824 for bucket 66 (Using difference cover) Reserving size (25350) for bucket 85 Getting block 86 of 204 bucket 74: 80% Sorting block time: 00:00:00 bucket 61: 30% bucket 57: 60% Returning block of 9970 for bucket 52 Returning block of 21264 for bucket 54 Returning block of 19421 for bucket 62 Returning block of 24688 for bucket 63 Getting block 87 of 204 Reserving size (25350) for bucket 70 Getting block 72 of 203 Sorting block of length 18162 for bucket 55 (Using difference cover) Sorting block of length 21954 for bucket 45 (Using difference cover) Reserving size (25350) for bucket 71 Getting block 73 of 203 bucket 58: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 81: 50% bucket 75: 70% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 63: 10% Getting block 88 of 204 Sorting block of length 24134 for bucket 67 (Using difference cover) bucket 71: 90% bucket 72: 90% Sorting block of length 25050 for bucket 65 (Using difference cover) Sorting block of length 15587 for bucket 68 (Using difference cover) bucket 78: 70% bucket 70: 100% bucket 76: 70% Getting block 74 of 203 bucket 62: 30% Calculating Z arrays for bucket 68 Sorting block time: 00:00:00 bucket 69: 100% bucket 79: 70% Entering block accumulator loop for bucket 67: Calculating Z arrays for bucket 69 Returning block of 20619 for bucket 53 bucket 59: 50% bucket 60: 50% bucket 56: 100% bucket 64: 10% Calculating Z arrays for bucket 70 Sorting block time: 00:00:00 bucket 73: 90% Entering block accumulator loop for bucket 83: bucket 77: 80% Entering block accumulator loop for bucket 84: Calculating Z arrays for bucket 85 Reserving size (25350) for bucket 86 Reserving size (25350) for bucket 87 Sorting block time: 00:00:00 bucket 80: 60% Returning block of 23771 for bucket 64 Returning block of 23825 for bucket 66 bucket 82: 10% bucket 74: 90% bucket 81: 60% bucket 75: 80% Reserving size (25350) for bucket 72 Calculating Z arrays for bucket 71 Reserving size (25350) for bucket 88 Sorting block of length 23996 for bucket 70 Reserving size (25350) for bucket 73 (Using difference cover) Getting block 75 of 203 Returning block of 15588 for bucket 68 Getting block 76 of 203 bucket 72: 100% Getting block 77 of 203 Sorting block of length 25145 for bucket 69 Returning block of 18163 for bucket 55 (Using difference cover) Returning block of 21955 for bucket 45 bucket 61: 40% bucket 57: 70% bucket 71: 100% bucket 58: 50% bucket 78: 80% bucket 63: 20% Reserving size (25350) for bucket 74 Entering block accumulator loop for bucket 68: Entering block accumulator loop for bucket 69: Sorting block of length 18613 for bucket 56 (Using difference cover) Entering block accumulator loop for bucket 70: bucket 62: 40% bucket 59: 60% Sorting block time: 00:00:00 bucket 60: 60% bucket 64: 20% bucket 65: 10% bucket 66: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 76: 80% Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 71: Calculating Z arrays for bucket 73 Reserving size (25350) for bucket 75 Reserving size (25350) for bucket 76 Reserving size (25350) for bucket 77 Getting block 78 of 203 Getting block 79 of 203 Returning block of 25051 for bucket 65 Calculating Z arrays for bucket 74 Getting block 80 of 203 Returning block of 18614 for bucket 56 bucket 61: 50% bucket 58: 60% Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 85: Calculating Z arrays for bucket 87 Returning block of 24135 for bucket 67 bucket 79: 80% bucket 77: 90% Getting block 89 of 204 bucket 73: 100% Getting block 90 of 204 bucket 80: 70% bucket 81: 70% bucket 59: 70% bucket 62: 50% bucket 74: 100% bucket 75: 90% bucket 57: 80% bucket 63: 30% Entering block accumulator loop for bucket 72: Calculating Z arrays for bucket 75 Calculating Z arrays for bucket 88 Sorting block of length 23889 for bucket 72 (Using difference cover) Entering block accumulator loop for bucket 73: bucket 82: 20% Calculating Z arrays for bucket 76 Sorting block of length 19662 for bucket 71 Calculating Z arrays for bucket 77 (Using difference cover) bucket 78: 90% Returning block of 23997 for bucket 70 Reserving size (25350) for bucket 78 Reserving size (25350) for bucket 79 bucket 60: 70% bucket 64: 30% bucket 65: 20% Reserving size (25350) for bucket 80 Getting block 81 of 203 Returning block of 25146 for bucket 69 bucket 76: 90% Entering block accumulator loop for bucket 74: Getting block 82 of 203 bucket 67: 10% bucket 61: 60% bucket 68: 10% bucket 70: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 83: 10% bucket 69: 10% bucket 84: 10% bucket 58: 70% bucket 66: 20% Entering block accumulator loop for bucket 86: Entering block accumulator loop for bucket 87: Reserving size (25350) for bucket 89 Sorting block of length 14647 for bucket 73 (Using difference cover) Reserving size (25350) for bucket 90 Getting block 91 of 204 Getting block 92 of 204 Sorting block of length 24427 for bucket 74 (Using difference cover) bucket 79: 90% bucket 77: 100% bucket 81: 80% bucket 80: 80% bucket 75: 100% Entering block accumulator loop for bucket 88: Getting block 93 of 204 Returning block of 19663 for bucket 71 Entering block accumulator loop for bucket 75: Entering block accumulator loop for bucket 76: Entering block accumulator loop for bucket 77: Calculating Z arrays for bucket 78 Calculating Z arrays for bucket 79 Calculating Z arrays for bucket 80 Reserving size (25350) for bucket 81 Reserving size (25350) for bucket 82 Getting block 83 of 203 bucket 62: 60% bucket 59: 80% Sorting block time: 00:00:00 bucket 78: 100% bucket 57: 90% bucket 76: 100% bucket 71: 10% Returning block of 23890 for bucket 72 bucket 64: 40% bucket 82: 30% bucket 60: 80% Getting block 94 of 204 bucket 65: 30% bucket 67: 20% Sorting block time: 00:00:00 bucket 83: 20% bucket 63: 40% bucket 61: 70% bucket 68: 20% bucket 70: 20% bucket 69: 20% bucket 58: 80% bucket 66: 30% Entering block accumulator loop for bucket 78: Entering block accumulator loop for bucket 79: Entering block accumulator loop for bucket 80: Calculating Z arrays for bucket 81 Calculating Z arrays for bucket 82 bucket 84: 20% Calculating Z arrays for bucket 89 Reserving size (25350) for bucket 83 bucket 73: 10% bucket 74: 10% bucket 72: 10% bucket 59: 90% bucket 62: 70% bucket 57: 100% bucket 60: 90% bucket 64: 50% bucket 65: 40% bucket 71: 20% bucket 67: 30% bucket 58: 90% Calculating Z arrays for bucket 90 Reserving size (25350) for bucket 91 bucket 85: 10% bucket 61: 80% bucket 63: 50% bucket 68: 30% bucket 66: 40% bucket 75: 10% bucket 77: 10% bucket 70: 30% Reserving size (25350) for bucket 92 Getting block 95 of 204 Sorting block of length 23506 for bucket 77 (Using difference cover) Sorting block of length 23275 for bucket 75 (Using difference cover) Reserving size (25350) for bucket 93 Returning block of 14648 for bucket 73 bucket 76: 10% bucket 79: 100% Entering block accumulator loop for bucket 81: bucket 80: 90% bucket 69: 30% bucket 81: 90% Entering block accumulator loop for bucket 82: Calculating Z arrays for bucket 83 Sorting block of length 23817 for bucket 78 (Using difference cover) Sorting block of length 13541 for bucket 57 (Using difference cover) bucket 59: 100% bucket 60: 100% bucket 64: 60% bucket 58: 100% bucket 62: 80% bucket 65: 50% bucket 73: 20% bucket 74: 20% bucket 67: 40% bucket 72: 20% bucket 71: 30% bucket 61: 90% Sorting block of length 16506 for bucket 76 (Using difference cover) Sorting block time: 00:00:00 Reserving size (25350) for bucket 94 Getting block 96 of 204 Returning block of 24428 for bucket 74 bucket 82: 40% Sorting block time: 00:00:00 bucket 63: 60% bucket 66: 50% bucket 68: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 97 of 204 bucket 83: 30% Entering block accumulator loop for bucket 89: bucket 87: 10% bucket 75: 20% bucket 77: 20% bucket 70: 40% Sorting block time: 00:00:00 bucket 86: 10% Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 90: bucket 84: 30% bucket 85: 20% Entering block accumulator loop for bucket 83: Sorting block of length 24015 for bucket 59 (Using difference cover) Sorting block of length 10355 for bucket 60 (Using difference cover) Sorting block of length 15549 for bucket 58 (Using difference cover) bucket 80: 10% bucket 69: 40% bucket 78: 10% Calculating Z arrays for bucket 92 Reserving size (25350) for bucket 95 Calculating Z arrays for bucket 93 Getting block 98 of 204 bucket 76: 20% Sorting block of length 25067 for bucket 79 bucket 79: 10% (Using difference cover) Returning block of 13542 for bucket 57 bucket 80: 100% bucket 62: 90% bucket 81: 100% bucket 64: 70% bucket 88: 10% bucket 65: 60% Returning block of 16507 for bucket 76 bucket 67: 50% bucket 61: 100% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 73: 30% bucket 72: 30% bucket 74: 30% bucket 71: 40% Sorting block time: 00:00:00 Calculating Z arrays for bucket 94 Reserving size (25350) for bucket 96 Getting block 99 of 204 Returning block of 23818 for bucket 78 Returning block of 23507 for bucket 77 bucket 63: 70% bucket 68: 50% Reserving size (25350) for bucket 97 Returning block of 23276 for bucket 75 bucket 82: 50% bucket 66: 60% bucket 83: 40% bucket 75: 30% Entering block accumulator loop for bucket 91: bucket 77: 30% bucket 87: 20% bucket 70: 50% bucket 82: 10% Entering block accumulator loop for bucket 92: Calculating Z arrays for bucket 95 bucket 84: 40% Entering block accumulator loop for bucket 93: bucket 86: 20% Reserving size (25350) for bucket 98 Getting block 100 of 204 bucket 81: 10% Sorting block of length 21587 for bucket 80 Sorting block of length 15918 for bucket 61 (Using difference cover) (Using difference cover) Sorting block of length 9089 for bucket 81 Returning block of 10356 for bucket 60 (Using difference cover) Returning block of 24016 for bucket 59 bucket 85: 30% bucket 88: 20% Returning block of 15550 for bucket 58 Returning block of 25068 for bucket 79 bucket 80: 20% Calculating Z arrays for bucket 96 bucket 78: 20% Entering block accumulator loop for bucket 94: bucket 62: 100% Reserving size (25350) for bucket 99 bucket 65: 70% bucket 64: 80% Calculating Z arrays for bucket 97 Getting block 101 of 204 Sorting block time: 00:00:00 bucket 76: 30% bucket 67: 60% bucket 79: 20% bucket 69: 50% bucket 73: 40% bucket 71: 50% bucket 74: 40% bucket 72: 40% bucket 63: 80% bucket 68: 60% bucket 75: 40% bucket 77: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 89: 10% bucket 83: 50% bucket 82: 60% bucket 87: 30% Entering block accumulator loop for bucket 95: Calculating Z arrays for bucket 98 Reserving size (25350) for bucket 100 Getting block 102 of 204 Entering block accumulator loop for bucket 96: Calculating Z arrays for bucket 99 Getting block 103 of 204 bucket 66: 70% bucket 82: 20% Getting block 84 of 203 Sorting block of length 20095 for bucket 62 (Using difference cover) bucket 70: 60% Getting block 104 of 204 Entering block accumulator loop for bucket 97: Reserving size (25350) for bucket 101 Returning block of 9090 for bucket 81 bucket 86: 30% bucket 84: 50% bucket 90: 10% Returning block of 21588 for bucket 80 Sorting block time: 00:00:00 Returning block of 15919 for bucket 61 bucket 85: 40% bucket 88: 30% Getting block 105 of 204 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 98: Reserving size (25350) for bucket 102 bucket 83: 10% bucket 64: 90% bucket 65: 80% bucket 80: 30% bucket 78: 30% bucket 81: 20% bucket 67: 70% bucket 76: 40% bucket 69: 60% bucket 79: 30% bucket 73: 50% bucket 74: 50% bucket 71: 60% bucket 72: 50% Entering block accumulator loop for bucket 99: Reserving size (25350) for bucket 84 Reserving size (25350) for bucket 103 Returning block of 20096 for bucket 62 bucket 91: 10% Reserving size (25350) for bucket 104 bucket 63: 90% bucket 75: 50% bucket 77: 50% bucket 68: 70% Getting block 85 of 203 Calculating Z arrays for bucket 101 bucket 83: 60% bucket 89: 20% bucket 87: 40% bucket 82: 70% Getting block 86 of 203 Getting block 87 of 203 bucket 66: 80% bucket 82: 30% Calculating Z arrays for bucket 84 bucket 70: 70% bucket 65: 90% bucket 64: 100% bucket 78: 40% Getting block 106 of 204 bucket 94: 10% bucket 92: 10% bucket 93: 10% Reserving size (25350) for bucket 105 Entering block accumulator loop for bucket 100: Calculating Z arrays for bucket 102 bucket 86: 40% bucket 83: 20% bucket 90: 20% bucket 67: 80% Reserving size (25350) for bucket 85 bucket 76: 50% bucket 69: 70% bucket 73: 60% bucket 71: 70% bucket 79: 40% bucket 80: 40% bucket 85: 50% bucket 63: 100% bucket 75: 60% bucket 72: 60% bucket 77: 60% bucket 68: 80% bucket 88: 40% bucket 95: 10% bucket 84: 60% bucket 96: 10% Reserving size (25350) for bucket 86 bucket 81: 30% bucket 74: 60% Calculating Z arrays for bucket 103 Calculating Z arrays for bucket 104 bucket 91: 20% Entering block accumulator loop for bucket 101: bucket 83: 70% bucket 89: 30% bucket 87: 50% bucket 82: 80% Reserving size (25350) for bucket 106 bucket 97: 10% Calculating Z arrays for bucket 105 Getting block 107 of 204 Getting block 108 of 204 Entering block accumulator loop for bucket 102: bucket 92: 20% bucket 90: 30% bucket 94: 20% bucket 93: 20% bucket 86: 50% Reserving size (25350) for bucket 87 Getting block 88 of 203 Entering block accumulator loop for bucket 84: Sorting block of length 11260 for bucket 64 (Using difference cover) bucket 98: 10% bucket 85: 60% bucket 84: 70% bucket 88: 50% bucket 95: 20% bucket 96: 20% Entering block accumulator loop for bucket 103: Entering block accumulator loop for bucket 104: bucket 89: 40% bucket 83: 80% bucket 87: 60% bucket 82: 90% bucket 91: 30% Sorting block time: 00:00:00 Getting block 89 of 203 bucket 65: 100% bucket 66: 90% bucket 70: 80% bucket 82: 40% Calculating Z arrays for bucket 106 Reserving size (25350) for bucket 107 Entering block accumulator loop for bucket 105: Reserving size (25350) for bucket 108 bucket 99: 10% bucket 90: 40% bucket 92: 30% bucket 86: 60% bucket 94: 30% bucket 93: 30% Calculating Z arrays for bucket 85 bucket 78: 50% bucket 67: 90% bucket 97: 20% bucket 100: 10% bucket 98: 20% bucket 84: 80% bucket 85: 70% bucket 88: 60% bucket 83: 90% bucket 87: 70% bucket 95: 30% bucket 89: 50% bucket 82: 100% Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 106: Calculating Z arrays for bucket 108 bucket 91: 40% bucket 96: 30% bucket 101: 10% Sorting block of length 22442 for bucket 63 (Using difference cover) bucket 83: 30% Sorting block time: 00:00:00 bucket 73: 70% bucket 76: 60% bucket 90: 50% bucket 86: 70% bucket 92: 40% bucket 94: 40% bucket 80: 50% bucket 69: 80% bucket 71: 80% bucket 102: 10% bucket 93: 40% bucket 99: 20% Sorting block of length 18854 for bucket 82 (Using difference cover) bucket 79: 50% bucket 75: 70% bucket 68: 90% bucket 77: 70% Calculating Z arrays for bucket 86 bucket 72: 70% bucket 74: 70% Calculating Z arrays for bucket 87 Reserving size (25350) for bucket 88 bucket 81: 40% Returning block of 11261 for bucket 64 Reserving size (25350) for bucket 89 Sorting block of length 18728 for bucket 65 (Using difference cover) bucket 70: 90% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 107: Entering block accumulator loop for bucket 108: bucket 83: 100% bucket 84: 90% bucket 88: 70% bucket 85: 80% bucket 87: 80% bucket 95: 40% bucket 89: 60% bucket 97: 30% bucket 91: 50% bucket 96: 40% bucket 104: 10% bucket 103: 10% bucket 100: 20% bucket 105: 10% bucket 101: 20% bucket 98: 30% Returning block of 18855 for bucket 82 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 85: bucket 66: 100% bucket 82: 50% bucket 67: 100% bucket 78: 60% Returning block of 22443 for bucket 63 bucket 90: 60% bucket 86: 80% bucket 92: 50% bucket 94: 50% bucket 93: 50% bucket 102: 20% bucket 99: 30% bucket 83: 40% Entering block accumulator loop for bucket 86: Sorting block of length 24769 for bucket 83 (Using difference cover) bucket 106: 10% Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 87: Calculating Z arrays for bucket 89 bucket 73: 80% bucket 80: 60% bucket 69: 90% bucket 76: 70% bucket 71: 90% bucket 75: 80% bucket 77: 80% bucket 79: 60% bucket 68: 100% bucket 72: 80% Returning block of 18729 for bucket 65 bucket 84: 10% bucket 81: 50% bucket 70: 100% Sorting block of length 9708 for bucket 66 (Using difference cover) Sorting block of length 18723 for bucket 67 (Using difference cover) bucket 74: 80% Sorting block time: 00:00:00 bucket 88: 80% bucket 78: 70% bucket 82: 60% Entering block accumulator loop for bucket 88: Getting block 90 of 203 Entering block accumulator loop for bucket 89: bucket 84: 100% bucket 85: 90% bucket 87: 90% bucket 89: 70% bucket 95: 50% bucket 91: 60% bucket 96: 50% bucket 97: 40% bucket 104: 20% bucket 103: 20% bucket 105: 20% bucket 100: 30% bucket 98: 40% bucket 101: 30% bucket 90: 70% bucket 92: 60% bucket 86: 90% bucket 94: 60% bucket 93: 60% bucket 99: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 14021 for bucket 68 (Using difference cover) Sorting block of length 20026 for bucket 70 (Using difference cover) bucket 83: 50% bucket 102: 30% bucket 108: 10% bucket 107: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 91 of 203 bucket 75: 90% bucket 80: 70% bucket 73: 90% bucket 77: 90% Returning block of 24770 for bucket 83 bucket 106: 20% Reserving size (25350) for bucket 90 bucket 69: 100% bucket 76: 80% bucket 85: 10% bucket 84: 20% bucket 71: 100% bucket 81: 60% bucket 79: 70% Returning block of 9709 for bucket 66 Returning block of 18724 for bucket 67 bucket 72: 90% bucket 78: 80% bucket 82: 70% bucket 86: 10% bucket 87: 10% Getting block 109 of 204 Sorting block of length 12986 for bucket 84 (Using difference cover) bucket 88: 90% bucket 85: 100% bucket 87: 100% bucket 89: 80% bucket 95: 60% bucket 91: 70% bucket 96: 60% bucket 97: 50% bucket 98: 50% bucket 104: 30% bucket 100: 40% bucket 103: 30% bucket 105: 30% bucket 101: 40% bucket 92: 70% bucket 94: 70% bucket 90: 80% Returning block of 14022 for bucket 68 Returning block of 20027 for bucket 70 bucket 74: 90% Sorting block time: 00:00:00 bucket 93: 70% bucket 86: 100% bucket 99: 50% Getting block 92 of 203 Reserving size (25350) for bucket 91 bucket 83: 60% Calculating Z arrays for bucket 90 Sorting block of length 14959 for bucket 69 (Using difference cover) Sorting block of length 15298 for bucket 71 (Using difference cover) bucket 102: 40% bucket 108: 20% bucket 107: 20% bucket 106: 30% bucket 75: 100% bucket 77: 100% bucket 80: 80% bucket 73: 100% bucket 76: 90% bucket 85: 20% Reserving size (25350) for bucket 109 Sorting block of length 16002 for bucket 85 (Using difference cover) Sorting block of length 23367 for bucket 87 (Using difference cover) Returning block of 12987 for bucket 84 bucket 88: 100% bucket 95: 70% bucket 89: 90% Sorting block of length 17644 for bucket 86 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 84: 30% (Using difference cover) bucket 88: 10% bucket 91: 80% bucket 89: 10% bucket 96: 70% bucket 79: 80% bucket 81: 70% bucket 78: 90% bucket 87: 20% bucket 97: 60% bucket 86: 20% bucket 92: 80% bucket 82: 80% bucket 94: 80% bucket 90: 90% Reserving size (25350) for bucket 92 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 90: Getting block 93 of 203 Getting block 94 of 203 Sorting block of length 11733 for bucket 75 (Using difference cover) Sorting block of length 16728 for bucket 77 (Using difference cover) Sorting block of length 21279 for bucket 73 (Using difference cover) bucket 72: 100% Returning block of 14960 for bucket 69 Returning block of 15299 for bucket 71 bucket 98: 60% bucket 74: 100% bucket 100: 50% bucket 83: 70% bucket 103: 40% bucket 80: 90% bucket 76: 100% bucket 85: 30% bucket 84: 40% bucket 78: 100% bucket 79: 90% bucket 88: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 110 of 204 bucket 104: 40% Sorting block time: 00:00:00 bucket 105: 40% bucket 101: 50% bucket 93: 80% bucket 99: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 89: 20% bucket 87: 30% bucket 102: 50% bucket 106: 40% bucket 82: 90% bucket 86: 30% Calculating Z arrays for bucket 109 bucket 108: 30% Sorting block of length 23708 for bucket 88 (Using difference cover) bucket 107: 30% bucket 89: 100% bucket 95: 80% bucket 91: 90% bucket 90: 100% bucket 96: 80% bucket 92: 90% bucket 94: 90% bucket 97: 70% Getting block 95 of 203 Getting block 96 of 203 Sorting block time: 00:00:00 Returning block of 16003 for bucket 85 Returning block of 17645 for bucket 86 Reserving size (25350) for bucket 110 Calculating Z arrays for bucket 92 Returning block of 23368 for bucket 87 Entering block accumulator loop for bucket 91: bucket 98: 70% Reserving size (25350) for bucket 93 bucket 100: 60% Reserving size (25350) for bucket 94 bucket 103: 50% Sorting block of length 18959 for bucket 72 bucket 104: 50% (Using difference cover) bucket 93: 90% bucket 99: 70% bucket 105: 50% bucket 101: 60% bucket 81: 80% Sorting block of length 17954 for bucket 74 (Using difference cover) Sorting block of length 20077 for bucket 76 (Using difference cover) Sorting block of length 20752 for bucket 78 (Using difference cover) Returning block of 11734 for bucket 75 Returning block of 16729 for bucket 77 bucket 102: 60% bucket 106: 50% Returning block of 21280 for bucket 73 bucket 84: 50% bucket 80: 100% bucket 85: 40% bucket 88: 30% bucket 83: 80% bucket 89: 30% bucket 79: 100% bucket 86: 40% Entering block accumulator loop for bucket 109: Getting block 111 of 204 Sorting block of length 23829 for bucket 89 (Using difference cover) Sorting block of length 17672 for bucket 90 (Using difference cover) Returning block of 23709 for bucket 88 bucket 95: 90% bucket 91: 100% bucket 92: 100% bucket 94: 100% Calculating Z arrays for bucket 110 bucket 96: 90% bucket 97: 80% Sorting block time: 00:00:00 bucket 108: 40% Sorting block time: 00:00:00 bucket 107: 40% bucket 93: 100% bucket 100: 70% bucket 99: 80% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (25350) for bucket 95 bucket 104: 60% bucket 103: 60% bucket 105: 60% Reserving size (25350) for bucket 111 Sorting block of length 21149 for bucket 91 (Using difference cover) Sorting block of length 16715 for bucket 92 (Using difference cover) Sorting block of length 7844 for bucket 94 (Using difference cover) Entering block accumulator loop for bucket 110: bucket 101: 70% Reserving size (25350) for bucket 96 Returning block of 17673 for bucket 90 bucket 98: 80% bucket 82: 100% bucket 87: 40% Entering block accumulator loop for bucket 92: Calculating Z arrays for bucket 93 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 102: 70% bucket 95: 100% Returning block of 23830 for bucket 89 Getting block 112 of 204 Getting block 113 of 204 Getting block 114 of 204 Sorting block of length 18932 for bucket 93 (Using difference cover) bucket 96: 100% bucket 97: 90% bucket 106: 60% Calculating Z arrays for bucket 111 Getting block 115 of 204 Returning block of 7845 for bucket 94 Returning block of 16716 for bucket 92 bucket 100: 80% bucket 108: 50% bucket 99: 90% bucket 107: 50% Returning block of 21150 for bucket 91 Calculating Z arrays for bucket 94 Getting block 97 of 203 Getting block 98 of 203 bucket 90: 10% Sorting block of length 15800 for bucket 80 (Using difference cover) Sorting block of length 25075 for bucket 79 (Using difference cover) Returning block of 20078 for bucket 76 Sorting block time: 00:00:00 bucket 104: 70% Returning block of 17955 for bucket 74 bucket 103: 70% Returning block of 20753 for bucket 78 Sorting block of length 19358 for bucket 95 Returning block of 18960 for bucket 72 (Using difference cover) Reserving size (25350) for bucket 112 Reserving size (25350) for bucket 113 Reserving size (25350) for bucket 114 bucket 109: 10% Sorting block of length 22930 for bucket 96 (Using difference cover) Entering block accumulator loop for bucket 111: bucket 84: 60% bucket 81: 90% bucket 89: 40% bucket 88: 40% bucket 86: 50% Sorting block time: 00:00:00 bucket 101: 80% bucket 98: 90% Reserving size (25350) for bucket 115 Getting block 116 of 204 bucket 105: 70% Returning block of 18933 for bucket 93 bucket 97: 100% bucket 102: 80% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Calculating Z arrays for bucket 95 Calculating Z arrays for bucket 112 bucket 85: 50% bucket 106: 70% bucket 110: 10% Calculating Z arrays for bucket 96 bucket 83: 90% Sorting block time: 00:00:00 Calculating Z arrays for bucket 113 Calculating Z arrays for bucket 114 bucket 99: 100% bucket 100: 90% bucket 108: 60% bucket 107: 60% Returning block of 19359 for bucket 95 bucket 104: 80% Getting block 117 of 204 Calculating Z arrays for bucket 115 Reserving size (25350) for bucket 116 Getting block 118 of 204 Getting block 119 of 204 Getting block 120 of 204 Sorting block of length 14239 for bucket 97 bucket 109: 20% bucket 103: 80% Entering block accumulator loop for bucket 112: Returning block of 22931 for bucket 96 bucket 98: 100% bucket 105: 80% Sorting block of length 10860 for bucket 82 (Using difference cover) Entering block accumulator loop for bucket 93: bucket 87: 50% bucket 91: 10% bucket 102: 90% bucket 110: 20% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 94: Reserving size (25350) for bucket 97 Reserving size (25350) for bucket 98 (Using difference cover) Getting block 99 of 203 Getting block 100 of 203 Getting block 101 of 203 Returning block of 15801 for bucket 80 Returning block of 25076 for bucket 79 bucket 90: 20% Entering block accumulator loop for bucket 95: bucket 84: 70% bucket 89: 50% bucket 88: 50% bucket 81: 100% bucket 85: 60% Entering block accumulator loop for bucket 113: Sorting block of length 12776 for bucket 99 (Using difference cover) Entering block accumulator loop for bucket 114: Entering block accumulator loop for bucket 96: bucket 106: 80% bucket 86: 60% bucket 83: 100% Returning block of 10861 for bucket 82 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (25350) for bucket 117 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 115: Reserving size (25350) for bucket 118 Reserving size (25350) for bucket 119 Reserving size (25350) for bucket 120 Getting block 121 of 204 bucket 101: 90% Sorting block of length 22737 for bucket 98 (Using difference cover) bucket 100: 100% bucket 108: 70% bucket 107: 70% bucket 111: 10% bucket 104: 90% bucket 103: 90% bucket 109: 30% bucket 105: 90% bucket 87: 60% bucket 92: 10% bucket 91: 20% Sorting block time: 00:00:00 bucket 102: 100% bucket 110: 30% Calculating Z arrays for bucket 97 Calculating Z arrays for bucket 98 Reserving size (25350) for bucket 99 Reserving size (25350) for bucket 100 Reserving size (25350) for bucket 101 Getting block 102 of 203 Getting block 103 of 203 Getting block 104 of 203 Sorting block of length 15328 for bucket 81 (Using difference cover) Returning block of 12777 for bucket 99 Returning block of 14240 for bucket 97 Calculating Z arrays for bucket 117 Getting block 105 of 203 Sorting block of length 24805 for bucket 83 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 84: 80% bucket 90: 30% bucket 88: 60% bucket 89: 60% bucket 86: 70% Entering block accumulator loop for bucket 116: Calculating Z arrays for bucket 118 bucket 106: 90% Calculating Z arrays for bucket 119 Calculating Z arrays for bucket 120 Reserving size (25350) for bucket 121 Getting block 122 of 204 Getting block 123 of 204 bucket 85: 70% bucket 93: 10% bucket 87: 70% bucket 92: 20% bucket 91: 30% Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 97: Entering block accumulator loop for bucket 98: Calculating Z arrays for bucket 100 Sorting block of length 21959 for bucket 100 (Using difference cover) Returning block of 22738 for bucket 98 bucket 111: 20% bucket 104: 100% bucket 112: 10% bucket 108: 80% bucket 103: 100% bucket 109: 40% Sorting block of length 19317 for bucket 102 (Using difference cover) bucket 107: 80% bucket 101: 100% bucket 105: 100% bucket 110: 40% Entering block accumulator loop for bucket 117: Calculating Z arrays for bucket 101 Reserving size (25350) for bucket 102 Reserving size (25350) for bucket 103 Reserving size (25350) for bucket 104 Reserving size (25350) for bucket 105 Getting block 106 of 203 Returning block of 15329 for bucket 81 Returning block of 24806 for bucket 83 Getting block 107 of 203 Getting block 108 of 203 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 113: 10% bucket 115: 10% bucket 114: 10% bucket 94: 10% bucket 95: 10% bucket 96: 10% Entering block accumulator loop for bucket 99: Entering block accumulator loop for bucket 118: Entering block accumulator loop for bucket 119: Calculating Z arrays for bucket 121 Reserving size (25350) for bucket 122 Entering block accumulator loop for bucket 120: Reserving size (25350) for bucket 123 Sorting block of length 12464 for bucket 104 (Using difference cover) bucket 106: 100% Sorting block of length 16977 for bucket 103 (Using difference cover) Sorting block of length 16725 for bucket 101 (Using difference cover) Sorting block of length 13177 for bucket 105 (Using difference cover) Returning block of 19318 for bucket 102 Getting block 124 of 204 Getting block 125 of 204 Returning block of 21960 for bucket 100 bucket 111: 30% bucket 108: 90% bucket 107: 90% bucket 110: 50% bucket 109: 50% bucket 112: 20% Entering block accumulator loop for bucket 100: bucket 84: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 113: 20% bucket 90: 40% bucket 114: 20% bucket 88: 70% Entering block accumulator loop for bucket 121: bucket 89: 70% Calculating Z arrays for bucket 122 bucket 86: 80% Calculating Z arrays for bucket 123 bucket 85: 80% Sorting block time: 00:00:00 Sorting block of length 24618 for bucket 106 Entering block accumulator loop for bucket 101: (Using difference cover) Calculating Z arrays for bucket 102 Calculating Z arrays for bucket 103 bucket 91: 40% Getting block 126 of 204 Reserving size (25350) for bucket 124 Reserving size (25350) for bucket 125 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 12465 for bucket 104 bucket 92: 30% Returning block of 13178 for bucket 105 Calculating Z arrays for bucket 104 bucket 116: 10% Calculating Z arrays for bucket 105 bucket 108: 100% Reserving size (25350) for bucket 106 bucket 117: 10% Reserving size (25350) for bucket 107 bucket 107: 100% Reserving size (25350) for bucket 108 bucket 110: 60% bucket 111: 40% bucket 93: 20% bucket 94: 20% bucket 96: 20% bucket 97: 10% bucket 95: 20% bucket 98: 10% Entering block accumulator loop for bucket 122: Returning block of 16978 for bucket 103 bucket 109: 60% Entering block accumulator loop for bucket 123: Reserving size (25350) for bucket 126 Calculating Z arrays for bucket 124 Calculating Z arrays for bucket 125 Getting block 127 of 204 bucket 112: 30% Returning block of 16726 for bucket 101 bucket 115: 20% Returning block of 24619 for bucket 106 bucket 119: 10% bucket 120: 10% bucket 114: 30% bucket 113: 30% Getting block 128 of 204 bucket 118: 10% Sorting block of length 15873 for bucket 108 (Using difference cover) Sorting block of length 23637 for bucket 107 (Using difference cover) bucket 121: 10% bucket 87: 80% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 116: 20% bucket 110: 70% bucket 117: 20% Calculating Z arrays for bucket 126 bucket 111: 50% Entering block accumulator loop for bucket 124: Entering block accumulator loop for bucket 102: Entering block accumulator loop for bucket 103: bucket 84: 100% bucket 85: 90% bucket 86: 90% Entering block accumulator loop for bucket 125: Reserving size (25350) for bucket 127 bucket 109: 70% Reserving size (25350) for bucket 128 Getting block 129 of 204 bucket 90: 50% bucket 88: 80% bucket 89: 80% Entering block accumulator loop for bucket 104: Entering block accumulator loop for bucket 105: Calculating Z arrays for bucket 106 Calculating Z arrays for bucket 107 Calculating Z arrays for bucket 108 Getting block 109 of 203 bucket 91: 50% Getting block 110 of 203 bucket 92: 40% bucket 115: 30% bucket 112: 40% Returning block of 15874 for bucket 108 Returning block of 23638 for bucket 107 bucket 119: 20% bucket 120: 20% bucket 121: 20% bucket 114: 40% bucket 113: 40% Entering block accumulator loop for bucket 126: bucket 94: 30% bucket 97: 20% bucket 95: 30% bucket 99: 10% bucket 98: 20% bucket 96: 30% bucket 93: 30% bucket 118: 20% bucket 122: 10% bucket 123: 10% bucket 100: 10% bucket 87: 90% Sorting block of length 17481 for bucket 84 (Using difference cover) Entering block accumulator loop for bucket 106: Entering block accumulator loop for bucket 107: Calculating Z arrays for bucket 127 Getting block 130 of 204 Getting block 131 of 204 Getting block 132 of 204 Calculating Z arrays for bucket 128 Reserving size (25350) for bucket 129 bucket 110: 80% bucket 117: 30% Sorting block time: 00:00:00 Reserving size (25350) for bucket 109 Entering block accumulator loop for bucket 108: Reserving size (25350) for bucket 110 bucket 85: 100% bucket 86: 100% bucket 111: 60% bucket 116: 30% bucket 109: 80% bucket 101: 10% bucket 89: 90% bucket 88: 90% bucket 92: 50% bucket 90: 60% bucket 95: 40% bucket 97: 30% bucket 96: 40% bucket 94: 40% bucket 98: 30% bucket 99: 20% Getting block 133 of 204 bucket 115: 40% bucket 112: 50% bucket 119: 30% bucket 121: 30% bucket 120: 30% bucket 113: 50% bucket 114: 50% bucket 124: 10% bucket 118: 30% bucket 91: 60% Returning block of 17482 for bucket 84 bucket 105: 10% bucket 122: 20% bucket 123: 20% Calculating Z arrays for bucket 109 Calculating Z arrays for bucket 110 Sorting block of length 20022 for bucket 85 (Using difference cover) Sorting block of length 22179 for bucket 86 (Using difference cover) bucket 104: 10% bucket 87: 100% bucket 100: 20% bucket 102: 10% bucket 103: 10% Entering block accumulator loop for bucket 127: Reserving size (25350) for bucket 130 Reserving size (25350) for bucket 131 Reserving size (25350) for bucket 132 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 128: bucket 125: 10% bucket 110: 90% bucket 117: 40% bucket 116: 40% bucket 111: 70% bucket 109: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 93: 40% bucket 89: 100% bucket 88: 100% bucket 92: 60% bucket 101: 20% bucket 107: 10% bucket 106: 10% bucket 90: 70% bucket 97: 40% bucket 94: 50% bucket 96: 50% bucket 95: 50% bucket 98: 40% Entering block accumulator loop for bucket 109: Reserving size (25350) for bucket 133 Getting block 134 of 204 Getting block 135 of 204 bucket 126: 10% bucket 119: 40% bucket 121: 40% Entering block accumulator loop for bucket 110: bucket 115: 50% bucket 112: 60% bucket 120: 40% bucket 124: 20% bucket 113: 60% bucket 114: 60% Calculating Z arrays for bucket 130 Calculating Z arrays for bucket 131 Calculating Z arrays for bucket 132 bucket 118: 40% bucket 122: 30% bucket 123: 30% Entering block accumulator loop for bucket 129: Sorting block of length 22928 for bucket 87 (Using difference cover) bucket 91: 70% bucket 99: 30% Returning block of 20023 for bucket 85 bucket 105: 20% Returning block of 22180 for bucket 86 bucket 108: 10% bucket 104: 20% bucket 103: 20% bucket 125: 20% bucket 110: 100% bucket 117: 50% bucket 116: 50% bucket 109: 100% Calculating Z arrays for bucket 133 Sorting block time: 00:00:00 Sorting block of length 14314 for bucket 89 (Using difference cover) Sorting block of length 14617 for bucket 88 (Using difference cover) bucket 102: 20% bucket 100: 30% Getting block 111 of 203 bucket 107: 20% bucket 111: 80% Reserving size (25350) for bucket 134 Reserving size (25350) for bucket 135 Entering block accumulator loop for bucket 130: Entering block accumulator loop for bucket 131: Entering block accumulator loop for bucket 132: bucket 119: 50% bucket 121: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 106: 20% bucket 92: 70% bucket 93: 50% bucket 101: 30% bucket 97: 50% bucket 90: 80% bucket 96: 60% bucket 94: 60% bucket 95: 60% bucket 98: 50% bucket 126: 20% bucket 120: 50% Returning block of 22929 for bucket 87 Reserving size (25350) for bucket 111 bucket 108: 20% bucket 104: 30% bucket 115: 60% bucket 91: 80% bucket 113: 70% bucket 99: 40% Returning block of 14315 for bucket 89 bucket 112: 70% Returning block of 14618 for bucket 88 bucket 114: 70% bucket 103: 30% bucket 127: 10% bucket 107: 30% bucket 118: 50% bucket 109: 10% bucket 122: 40% bucket 123: 40% bucket 100: 40% bucket 102: 30% bucket 105: 30% bucket 110: 10% bucket 106: 30% bucket 90: 90% Sorting block of length 13354 for bucket 110 (Using difference cover) Sorting block of length 21168 for bucket 109 (Using difference cover) Entering block accumulator loop for bucket 133: bucket 128: 10% bucket 124: 30% Calculating Z arrays for bucket 134 Calculating Z arrays for bucket 135 bucket 92: 80% bucket 97: 60% bucket 96: 70% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 117: 60% bucket 125: 30% bucket 116: 60% bucket 111: 90% bucket 119: 60% Getting block 112 of 203 bucket 121: 60% bucket 93: 60% bucket 129: 10% bucket 94: 70% bucket 126: 30% bucket 95: 70% bucket 120: 60% bucket 122: 50% bucket 123: 50% bucket 115: 70% bucket 127: 20% bucket 113: 80% bucket 114: 80% bucket 118: 60% Entering block accumulator loop for bucket 134: Entering block accumulator loop for bucket 135: bucket 112: 80% Getting block 113 of 203 bucket 101: 40% Calculating Z arrays for bucket 111 bucket 98: 60% bucket 108: 30% bucket 107: 40% bucket 104: 40% bucket 109: 20% bucket 91: 90% bucket 103: 40% bucket 99: 50% Returning block of 13355 for bucket 110 Returning block of 21169 for bucket 109 bucket 124: 40% bucket 130: 10% bucket 100: 50% bucket 102: 40% bucket 110: 20% bucket 131: 10% bucket 128: 20% bucket 119: 70% bucket 120: 70% bucket 121: 70% bucket 117: 70% bucket 125: 40% bucket 116: 70% bucket 129: 20% bucket 132: 10% bucket 111: 100% bucket 105: 40% bucket 106: 40% bucket 90: 100% bucket 92: 90% bucket 96: 80% bucket 126: 40% bucket 122: 60% bucket 123: 60% bucket 115: 80% bucket 114: 90% bucket 113: 90% bucket 127: 30% Reserving size (25350) for bucket 112 bucket 97: 70% bucket 118: 70% bucket 94: 80% bucket 133: 10% bucket 93: 70% bucket 112: 90% bucket 95: 80% bucket 124: 50% bucket 130: 20% Sorting block of length 15579 for bucket 111 (Using difference cover) bucket 119: 80% bucket 120: 80% bucket 121: 80% bucket 116: 80% bucket 125: 50% bucket 117: 80% Reserving size (25350) for bucket 113 bucket 131: 20% Entering block accumulator loop for bucket 111: bucket 107: 50% bucket 104: 50% bucket 108: 40% bucket 103: 50% bucket 91: 100% bucket 98: 70% bucket 101: 50% Sorting block time: 00:00:00 bucket 132: 20% bucket 129: 30% bucket 134: 10% bucket 128: 30% bucket 135: 10% bucket 122: 70% bucket 123: 70% bucket 113: 100% Getting block 136 of 204 bucket 114: 100% bucket 126: 50% bucket 127: 40% bucket 118: 80% bucket 112: 100% bucket 133: 20% Getting block 114 of 203 Getting block 115 of 203 Getting block 116 of 203 bucket 99: 60% bucket 109: 30% bucket 110: 30% Sorting block of length 24774 for bucket 90 (Using difference cover) Getting block 137 of 204 Returning block of 15580 for bucket 111 bucket 120: 90% bucket 119: 90% bucket 121: 90% bucket 124: 60% bucket 125: 60% bucket 116: 90% bucket 117: 90% bucket 130: 30% bucket 131: 30% bucket 115: 90% Sorting block of length 25082 for bucket 113 (Using difference cover) Sorting block time: 00:00:00 bucket 105: 50% bucket 100: 60% bucket 102: 50% bucket 106: 50% bucket 96: 90% Sorting block time: 00:00:00 Reserving size (25350) for bucket 136 Sorting block of length 19263 for bucket 114 (Using difference cover) Sorting block of length 11043 for bucket 112 (Using difference cover) bucket 132: 30% bucket 122: 80% bucket 123: 80% bucket 128: 40% bucket 129: 40% bucket 118: 90% bucket 127: 50% Calculating Z arrays for bucket 112 bucket 126: 60% bucket 134: 20% bucket 133: 30% bucket 92: 100% bucket 94: 90% bucket 97: 80% bucket 95: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (25350) for bucket 137 bucket 135: 20% bucket 120: 100% bucket 119: 100% bucket 121: 100% bucket 125: 70% bucket 124: 70% bucket 116: 100% bucket 117: 100% bucket 130: 40% Returning block of 25083 for bucket 113 Calculating Z arrays for bucket 136 bucket 115: 100% bucket 131: 40% Returning block of 11044 for bucket 112 Returning block of 19264 for bucket 114 bucket 122: 90% Calculating Z arrays for bucket 113 bucket 123: 90% bucket 132: 40% bucket 128: 50% bucket 118: 100% bucket 127: 60% bucket 129: 50% bucket 126: 70% bucket 133: 40% bucket 93: 80% Sorting block of length 23274 for bucket 91 (Using difference cover) bucket 107: 60% Sorting block time: 00:00:00 bucket 108: 50% bucket 104: 60% Calculating Z arrays for bucket 137 bucket 103: 60% bucket 98: 80% bucket 101: 60% Getting block 138 of 204 Sorting block of length 23350 for bucket 120 (Using difference cover) Sorting block of length 4749 for bucket 119 (Using difference cover) Sorting block of length 24907 for bucket 121 (Using difference cover) Sorting block of length 20412 for bucket 116 (Using difference cover) Sorting block of length 8769 for bucket 117 (Using difference cover) bucket 134: 30% Sorting block of length 8382 for bucket 115 (Using difference cover) Entering block accumulator loop for bucket 136: bucket 122: 100% bucket 125: 80% bucket 124: 80% bucket 131: 50% bucket 130: 50% Sorting block of length 20829 for bucket 118 (Using difference cover) bucket 135: 30% Reserving size (25350) for bucket 114 Reserving size (25350) for bucket 115 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 123: 100% bucket 128: 60% bucket 127: 70% bucket 132: 50% bucket 129: 60% bucket 126: 80% bucket 133: 50% Reserving size (25350) for bucket 116 Returning block of 24775 for bucket 90 bucket 110: 40% bucket 99: 70% bucket 109: 40% bucket 105: 60% bucket 106: 60% bucket 96: 100% Entering block accumulator loop for bucket 112: bucket 100: 70% bucket 102: 60% Sorting block of length 12222 for bucket 92 (Using difference cover) bucket 95: 100% Entering block accumulator loop for bucket 113: bucket 97: 90% bucket 94: 100% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 137: Returning block of 23275 for bucket 91 Reserving size (25350) for bucket 138 bucket 111: 10% Getting block 139 of 204 bucket 107: 70% Getting block 140 of 204 bucket 93: 90% Getting block 141 of 204 bucket 108: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 24010 for bucket 122 (Using difference cover) Returning block of 8770 for bucket 117 Returning block of 8383 for bucket 115 Returning block of 4750 for bucket 119 bucket 125: 90% Sorting block time: 00:00:00 bucket 104: 70% bucket 103: 70% bucket 98: 90% bucket 101: 70% Sorting block time: 00:00:00 Sorting block of length 5516 for bucket 123 (Using difference cover) bucket 124: 90% bucket 130: 60% bucket 131: 60% bucket 134: 40% bucket 135: 40% Returning block of 20830 for bucket 118 Returning block of 20413 for bucket 116 bucket 128: 70% Calculating Z arrays for bucket 114 Sorting block time: 00:00:00 bucket 127: 80% bucket 129: 70% Calculating Z arrays for bucket 115 Calculating Z arrays for bucket 116 bucket 110: 50% bucket 109: 50% Sorting block of length 20769 for bucket 96 (Using difference cover) bucket 132: 60% bucket 126: 90% bucket 133: 60% Sorting block time: 00:00:00 Sorting block of length 24183 for bucket 95 (Using difference cover) Calculating Z arrays for bucket 138 Reserving size (25350) for bucket 139 Reserving size (25350) for bucket 140 Reserving size (25350) for bucket 141 Returning block of 23351 for bucket 120 Returning block of 24908 for bucket 121 bucket 136: 10% Returning block of 24011 for bucket 122 bucket 125: 100% Returning block of 5517 for bucket 123 bucket 124: 100% bucket 128: 80% bucket 131: 70% bucket 134: 50% bucket 135: 50% bucket 130: 70% bucket 127: 90% Sorting block time: 00:00:00 Sorting block of length 21091 for bucket 94 (Using difference cover) bucket 99: 80% Sorting block time: 00:00:00 Returning block of 12223 for bucket 92 bucket 105: 70% bucket 106: 70% bucket 111: 20% bucket 108: 70% bucket 107: 80% bucket 100: 80% bucket 102: 70% bucket 97: 100% bucket 93: 100% bucket 103: 80% bucket 129: 80% bucket 132: 70% bucket 98: 100% bucket 101: 80% bucket 126: 100% bucket 133: 70% Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 138: Calculating Z arrays for bucket 140 Calculating Z arrays for bucket 141 Getting block 142 of 204 Getting block 143 of 204 Getting block 144 of 204 Sorting block of length 9733 for bucket 125 (Using difference cover) Getting block 145 of 204 Getting block 146 of 204 Sorting block of length 23630 for bucket 124 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 137: 10% bucket 136: 20% bucket 128: 90% bucket 127: 100% bucket 134: 60% bucket 131: 80% bucket 135: 60% Entering block accumulator loop for bucket 114: bucket 130: 80% Sorting block of length 17794 for bucket 126 (Using difference cover) Entering block accumulator loop for bucket 139: Entering block accumulator loop for bucket 115: Getting block 117 of 203 Entering block accumulator loop for bucket 116: bucket 104: 80% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 140: Returning block of 20770 for bucket 96 Reserving size (25350) for bucket 142 bucket 109: 60% Entering block accumulator loop for bucket 141: bucket 110: 60% Returning block of 24184 for bucket 95 bucket 112: 10% bucket 113: 10% Returning block of 21092 for bucket 94 Getting block 118 of 203 Sorting block of length 10875 for bucket 97 (Using difference cover) Sorting block of length 23110 for bucket 93 (Using difference cover) bucket 99: 90% bucket 111: 30% Reserving size (25350) for bucket 143 Reserving size (25350) for bucket 144 Reserving size (25350) for bucket 145 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 107: 90% Reserving size (25350) for bucket 146 bucket 105: 80% Returning block of 9734 for bucket 125 bucket 108: 80% bucket 106: 80% bucket 100: 90% Getting block 147 of 204 Getting block 148 of 204 Getting block 149 of 204 Getting block 150 of 204 bucket 132: 80% Returning block of 23631 for bucket 124 bucket 133: 80% Sorting block of length 20057 for bucket 127 (Using difference cover) Returning block of 17795 for bucket 126 Sorting block of length 23631 for bucket 98 (Using difference cover) bucket 102: 80% bucket 103: 90% bucket 101: 90% Sorting block time: 00:00:00 bucket 137: 20% bucket 136: 30% bucket 128: 100% bucket 130: 90% bucket 134: 70% bucket 131: 90% bucket 138: 10% bucket 135: 70% Sorting block time: 00:00:00 Reserving size (25350) for bucket 117 Calculating Z arrays for bucket 142 bucket 129: 90% Calculating Z arrays for bucket 143 Calculating Z arrays for bucket 144 Reserving size (25350) for bucket 118 Getting block 119 of 203 Returning block of 10876 for bucket 97 Returning block of 23111 for bucket 93 bucket 113: 20% bucket 109: 70% bucket 104: 90% bucket 110: 70% bucket 111: 40% bucket 112: 20% bucket 99: 100% Calculating Z arrays for bucket 145 Calculating Z arrays for bucket 146 Reserving size (25350) for bucket 147 Reserving size (25350) for bucket 148 Reserving size (25350) for bucket 149 Reserving size (25350) for bucket 150 Returning block of 20058 for bucket 127 bucket 132: 90% bucket 133: 90% Sorting block of length 15549 for bucket 128 (Using difference cover) bucket 139: 10% bucket 136: 40% bucket 108: 90% bucket 105: 90% bucket 107: 100% bucket 106: 90% bucket 100: 100% Returning block of 23632 for bucket 98 bucket 102: 90% bucket 101: 100% Calculating Z arrays for bucket 117 bucket 103: 100% Calculating Z arrays for bucket 118 Reserving size (25350) for bucket 119 Sorting block of length 24269 for bucket 99 (Using difference cover) bucket 115: 10% bucket 114: 10% bucket 113: 30% bucket 111: 50% bucket 116: 10% Sorting block time: 00:00:00 bucket 137: 30% bucket 138: 20% Entering block accumulator loop for bucket 142: Entering block accumulator loop for bucket 143: Entering block accumulator loop for bucket 144: bucket 131: 100% Sorting block time: 00:00:00 bucket 109: 80% bucket 110: 80% bucket 134: 80% bucket 130: 100% bucket 135: 80% bucket 129: 100% bucket 104: 100% bucket 112: 30% bucket 140: 10% bucket 141: 10% Getting block 151 of 204 Getting block 120 of 203 Getting block 121 of 203 Getting block 122 of 203 Sorting block of length 12955 for bucket 107 (Using difference cover) Sorting block of length 23863 for bucket 100 (Using difference cover) Sorting block of length 20880 for bucket 101 (Using difference cover) Entering block accumulator loop for bucket 117: Sorting block of length 19550 for bucket 103 (Using difference cover) Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 118: Getting block 123 of 203 Getting block 124 of 203 Returning block of 24270 for bucket 99 bucket 106: 100% bucket 108: 100% bucket 102: 100% bucket 105: 100% bucket 113: 40% bucket 115: 20% bucket 114: 20% bucket 111: 60% bucket 116: 20% Sorting block of length 44827 for bucket 104 (Using difference cover) bucket 109: 90% bucket 110: 90% Entering block accumulator loop for bucket 145: Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 146: Calculating Z arrays for bucket 148 Calculating Z arrays for bucket 149 Calculating Z arrays for bucket 150 Getting block 152 of 204 Getting block 153 of 204 bucket 112: 40% Returning block of 15550 for bucket 128 bucket 136: 50% bucket 132: 100% bucket 133: 100% Reserving size (25350) for bucket 120 Reserving size (25350) for bucket 121 Reserving size (25350) for bucket 122 Entering block accumulator loop for bucket 119: Reserving size (25350) for bucket 123 Reserving size (25350) for bucket 124 Getting block 125 of 203 Sorting block of length 16588 for bucket 106 (Using difference cover) Sorting block of length 24076 for bucket 108 Sorting block of length 17027 for bucket 131 (Using difference cover) (Using difference cover) Sorting block of length 10886 for bucket 102 bucket 139: 20% (Using difference cover) Sorting block of length 23305 for bucket 130 (Using difference cover) Sorting block of length 11986 for bucket 129 (Using difference cover) bucket 137: 40% bucket 138: 30% Reserving size (25350) for bucket 151 bucket 134: 90% bucket 135: 90% bucket 141: 20% Sorting block of length 7584 for bucket 105 (Using difference cover) bucket 113: 50% bucket 111: 70% bucket 115: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 140: 20% Entering block accumulator loop for bucket 147: Entering block accumulator loop for bucket 148: Entering block accumulator loop for bucket 149: Reserving size (25350) for bucket 152 Entering block accumulator loop for bucket 150: Reserving size (25350) for bucket 153 Getting block 154 of 204 Sorting block of length 9425 for bucket 132 (Using difference cover) Sorting block of length 25164 for bucket 133 (Using difference cover) bucket 114: 30% bucket 110: 100% bucket 116: 30% Calculating Z arrays for bucket 120 Sorting block time: 00:00:00 bucket 136: 60% bucket 142: 10% bucket 143: 10% Calculating Z arrays for bucket 151 Returning block of 11987 for bucket 129 Returning block of 17028 for bucket 131 Returning block of 23306 for bucket 130 Calculating Z arrays for bucket 121 Calculating Z arrays for bucket 122 Calculating Z arrays for bucket 123 Calculating Z arrays for bucket 124 Reserving size (25350) for bucket 125 bucket 112: 50% bucket 109: 100% Getting block 126 of 203 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 117: 10% bucket 118: 10% Sorting block time: 00:00:00 bucket 144: 10% bucket 139: 30% bucket 137: 50% bucket 138: 40% bucket 141: 30% Calculating Z arrays for bucket 152 Calculating Z arrays for bucket 153 Reserving size (25350) for bucket 154 bucket 134: 100% bucket 135: 100% Returning block of 9426 for bucket 132 Getting block 155 of 204 Entering block accumulator loop for bucket 151: bucket 146: 10% bucket 145: 10% Returning block of 25165 for bucket 133 bucket 140: 30% bucket 136: 70% bucket 142: 20% bucket 143: 20% Entering block accumulator loop for bucket 152: Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 153: Sorting block of length 18090 for bucket 134 (Using difference cover) Sorting block of length 22771 for bucket 135 (Using difference cover) Reserving size (25350) for bucket 155 Sorting block time: 00:00:00 Sorting block of length 23460 for bucket 110 (Using difference cover) Entering block accumulator loop for bucket 120: bucket 113: 60% bucket 111: 80% bucket 115: 40% bucket 114: 40% bucket 116: 40% Entering block accumulator loop for bucket 121: Sorting block time: 00:00:00 Entering block accumulator loop for bucket 122: Entering block accumulator loop for bucket 123: Entering block accumulator loop for bucket 124: Calculating Z arrays for bucket 125 Sorting block of length 22746 for bucket 109 (Using difference cover) Reserving size (25350) for bucket 126 Returning block of 10887 for bucket 102 Returning block of 12956 for bucket 107 Returning block of 19551 for bucket 103 Returning block of 44828 for bucket 104 Sorting block time: 00:00:00 bucket 144: 20% bucket 139: 40% bucket 137: 60% bucket 141: 40% bucket 138: 50% bucket 147: 10% bucket 148: 10% Returning block of 7585 for bucket 105 Returning block of 24077 for bucket 108 Returning block of 23864 for bucket 100 Returning block of 20881 for bucket 101 Returning block of 16589 for bucket 106 bucket 119: 10% bucket 112: 60% bucket 117: 20% bucket 118: 20% Returning block of 23461 for bucket 110 bucket 113: 70% Sorting block time: 00:00:00 Getting block 156 of 204 Getting block 157 of 204 Getting block 158 of 204 Entering block accumulator loop for bucket 154: Calculating Z arrays for bucket 155 bucket 149: 10% bucket 150: 10% bucket 146: 20% bucket 136: 80% bucket 145: 20% Returning block of 22772 for bucket 135 bucket 143: 30% bucket 142: 30% bucket 140: 40% Returning block of 18091 for bucket 134 bucket 137: 70% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 125: bucket 111: 90% Calculating Z arrays for bucket 126 bucket 115: 50% bucket 116: 50% bucket 114: 50% bucket 119: 20% bucket 118: 30% bucket 141: 50% bucket 117: 30% bucket 121: 10% bucket 138: 60% bucket 148: 20% bucket 144: 30% Reserving size (25350) for bucket 156 bucket 147: 20% Reserving size (25350) for bucket 157 Reserving size (25350) for bucket 158 bucket 139: 50% bucket 120: 10% bucket 151: 10% bucket 152: 10% Returning block of 22747 for bucket 109 bucket 113: 80% bucket 112: 70% Getting block 159 of 204 Getting block 160 of 204 Entering block accumulator loop for bucket 155: bucket 153: 10% bucket 149: 20% bucket 136: 90% bucket 146: 30% bucket 150: 20% bucket 137: 80% bucket 143: 40% bucket 145: 30% bucket 142: 40% bucket 140: 50% Calculating Z arrays for bucket 156 Calculating Z arrays for bucket 157 Calculating Z arrays for bucket 158 bucket 122: 10% bucket 141: 60% bucket 123: 10% Entering block accumulator loop for bucket 126: bucket 138: 70% bucket 144: 40% bucket 139: 60% bucket 148: 30% bucket 147: 30% Getting block 127 of 203 Getting block 128 of 203 Getting block 129 of 203 Getting block 130 of 203 Getting block 131 of 203 Getting block 132 of 203 bucket 111: 100% bucket 115: 60% bucket 114: 60% bucket 116: 60% bucket 121: 20% bucket 118: 40% bucket 119: 30% bucket 117: 40% bucket 124: 10% bucket 120: 20% bucket 151: 20% bucket 152: 20% Reserving size (25350) for bucket 159 Reserving size (25350) for bucket 160 Getting block 133 of 203 Getting block 161 of 204 Getting block 134 of 203 Getting block 135 of 203 Getting block 136 of 203 bucket 113: 90% bucket 112: 80% Getting block 162 of 204 Reserving size (25350) for bucket 127 Entering block accumulator loop for bucket 156: Reserving size (25350) for bucket 128 Reserving size (25350) for bucket 129 Entering block accumulator loop for bucket 157: Entering block accumulator loop for bucket 158: bucket 154: 10% bucket 136: 100% bucket 146: 40% bucket 137: 90% bucket 143: 50% bucket 145: 40% bucket 150: 30% bucket 149: 30% bucket 140: 60% bucket 142: 50% bucket 153: 20% bucket 122: 20% bucket 125: 10% bucket 141: 70% bucket 139: 70% bucket 138: 80% bucket 144: 50% bucket 148: 40% bucket 147: 40% Calculating Z arrays for bucket 159 Calculating Z arrays for bucket 160 Reserving size (25350) for bucket 161 Reserving size (25350) for bucket 162 Reserving size (25350) for bucket 130 Reserving size (25350) for bucket 131 Reserving size (25350) for bucket 132 bucket 123: 20% Sorting block of length 21141 for bucket 111 (Using difference cover) bucket 121: 30% bucket 120: 30% bucket 151: 30% bucket 152: 30% Sorting block of length 12150 for bucket 136 (Using difference cover) bucket 155: 10% Reserving size (25350) for bucket 133 bucket 118: 50% Sorting block time: 00:00:00 bucket 115: 70% bucket 114: 70% bucket 119: 40% bucket 117: 50% Sorting block time: 00:00:00 bucket 154: 20% bucket 137: 100% bucket 146: 50% bucket 143: 60% bucket 145: 50% bucket 150: 40% bucket 140: 70% bucket 149: 40% bucket 142: 60% Entering block accumulator loop for bucket 159: Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 160: Reserving size (25350) for bucket 134 Calculating Z arrays for bucket 162 Reserving size (25350) for bucket 135 bucket 153: 30% Reserving size (25350) for bucket 136 Getting block 137 of 203 bucket 116: 70% bucket 141: 80% bucket 139: 80% bucket 138: 90% bucket 144: 60% bucket 147: 50% bucket 148: 50% bucket 156: 10% Calculating Z arrays for bucket 127 Calculating Z arrays for bucket 128 Calculating Z arrays for bucket 129 bucket 126: 10% bucket 112: 90% bucket 113: 100% bucket 124: 20% bucket 125: 20% Calculating Z arrays for bucket 130 Calculating Z arrays for bucket 131 Calculating Z arrays for bucket 132 bucket 122: 30% bucket 121: 40% bucket 120: 40% Returning block of 12151 for bucket 136 bucket 155: 20% bucket 157: 10% bucket 158: 10% bucket 151: 40% bucket 152: 40% Sorting block of length 13486 for bucket 137 (Using difference cover) Sorting block time: 00:00:00 Entering block accumulator loop for bucket 161: Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 162: bucket 123: 30% Returning block of 21142 for bucket 111 bucket 118: 60% bucket 119: 50% bucket 117: 60% bucket 115: 80% bucket 114: 80% bucket 154: 30% bucket 146: 60% bucket 143: 70% bucket 145: 60% bucket 150: 50% bucket 142: 70% bucket 140: 80% bucket 149: 50% bucket 153: 40% bucket 139: 90% Calculating Z arrays for bucket 134 Calculating Z arrays for bucket 135 Calculating Z arrays for bucket 136 Reserving size (25350) for bucket 137 bucket 116: 80% bucket 141: 90% bucket 138: 100% bucket 144: 70% bucket 156: 20% bucket 147: 60% bucket 148: 60% Entering block accumulator loop for bucket 127: Entering block accumulator loop for bucket 128: Entering block accumulator loop for bucket 129: Sorting block of length 19307 for bucket 113 (Using difference cover) bucket 126: 20% bucket 125: 30% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 130: Entering block accumulator loop for bucket 131: Entering block accumulator loop for bucket 132: bucket 112: 100% bucket 121: 50% bucket 122: 40% bucket 120: 50% Returning block of 13487 for bucket 137 Entering block accumulator loop for bucket 133: bucket 123: 40% bucket 157: 20% bucket 124: 30% bucket 155: 30% bucket 117: 70% bucket 152: 50% bucket 118: 70% bucket 151: 50% bucket 119: 60% bucket 159: 10% bucket 160: 10% bucket 115: 90% bucket 114: 90% bucket 154: 40% bucket 158: 20% bucket 146: 70% bucket 145: 70% bucket 143: 80% bucket 150: 60% bucket 139: 100% bucket 142: 80% bucket 140: 90% Entering block accumulator loop for bucket 134: Entering block accumulator loop for bucket 135: Entering block accumulator loop for bucket 136: Calculating Z arrays for bucket 137 bucket 116: 90% Returning block of 19308 for bucket 113 bucket 125: 40% Sorting block of length 22772 for bucket 138 (Using difference cover) bucket 149: 60% bucket 126: 30% bucket 153: 50% bucket 141: 100% bucket 147: 70% Sorting block of length 20285 for bucket 112 (Using difference cover) bucket 122: 50% bucket 121: 60% bucket 120: 60% Sorting block time: 00:00:00 Getting block 163 of 204 bucket 144: 80% bucket 148: 70% bucket 156: 30% bucket 155: 40% bucket 161: 10% bucket 157: 30% bucket 162: 10% bucket 160: 20% bucket 159: 20% bucket 152: 60% Sorting block of length 19098 for bucket 139 (Using difference cover) Sorting block time: 00:00:00 Getting block 138 of 203 bucket 123: 50% bucket 151: 60% bucket 117: 80% bucket 118: 80% bucket 119: 70% bucket 115: 100% bucket 114: 100% Entering block accumulator loop for bucket 137: bucket 124: 40% bucket 125: 50% bucket 127: 10% bucket 128: 10% bucket 116: 100% Returning block of 20286 for bucket 112 bucket 126: 40% bucket 130: 10% bucket 131: 10% bucket 121: 70% bucket 122: 60% Sorting block time: 00:00:00 bucket 154: 50% bucket 146: 80% bucket 145: 80% bucket 143: 90% bucket 150: 70% bucket 140: 100% bucket 142: 90% bucket 158: 30% bucket 120: 70% bucket 129: 10% Sorting block of length 19251 for bucket 141 (Using difference cover) Returning block of 22773 for bucket 138 bucket 149: 70% bucket 147: 80% bucket 132: 10% bucket 133: 10% Reserving size (25350) for bucket 138 Sorting block of length 19111 for bucket 115 (Using difference cover) Sorting block of length 20302 for bucket 114 (Using difference cover) Getting block 139 of 203 bucket 123: 60% bucket 125: 60% bucket 134: 10% bucket 135: 10% bucket 136: 10% bucket 117: 90% Sorting block of length 23513 for bucket 116 (Using difference cover) bucket 127: 20% Sorting block time: 00:00:00 Reserving size (25350) for bucket 163 Getting block 164 of 204 bucket 118: 90% bucket 119: 80% bucket 124: 50% bucket 126: 50% bucket 153: 60% bucket 121: 80% bucket 156: 40% bucket 122: 70% bucket 148: 80% bucket 128: 20% bucket 144: 90% bucket 130: 20% bucket 155: 50% bucket 131: 20% Returning block of 19099 for bucket 139 bucket 161: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 129: 20% bucket 157: 40% bucket 162: 20% bucket 160: 30% bucket 159: 30% bucket 152: 70% Sorting block of length 24789 for bucket 140 (Using difference cover) bucket 151: 70% Calculating Z arrays for bucket 138 Reserving size (25350) for bucket 139 bucket 120: 80% Getting block 140 of 203 bucket 125: 70% bucket 123: 70% bucket 132: 20% bucket 133: 20% bucket 134: 20% bucket 137: 10% bucket 135: 20% bucket 127: 30% bucket 136: 20% bucket 117: 100% Sorting block time: 00:00:00 bucket 154: 60% bucket 146: 90% bucket 145: 90% bucket 143: 100% bucket 158: 40% bucket 142: 100% bucket 150: 80% Returning block of 19252 for bucket 141 bucket 147: 90% bucket 119: 90% bucket 118: 100% Returning block of 19112 for bucket 115 Returning block of 20303 for bucket 114 Returning block of 23514 for bucket 116 bucket 124: 60% bucket 126: 60% bucket 121: 90% bucket 122: 80% bucket 130: 30% bucket 128: 30% bucket 131: 30% Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 138: Reserving size (25350) for bucket 140 bucket 129: 30% Sorting block of length 21736 for bucket 117 (Using difference cover) bucket 125: 80% bucket 123: 80% bucket 120: 90% bucket 134: 30% bucket 133: 30% Calculating Z arrays for bucket 163 Reserving size (25350) for bucket 164 bucket 149: 80% bucket 148: 90% bucket 144: 100% bucket 156: 50% Sorting block time: 00:00:00 bucket 132: 30% bucket 135: 30% bucket 127: 40% bucket 136: 30% bucket 137: 20% bucket 161: 30% Sorting block of length 21705 for bucket 118 (Using difference cover) Entering block accumulator loop for bucket 139: Calculating Z arrays for bucket 140 bucket 126: 70% bucket 130: 40% bucket 153: 70% bucket 155: 60% Returning block of 24790 for bucket 140 bucket 128: 40% bucket 119: 100% bucket 131: 40% Sorting block time: 00:00:00 bucket 121: 100% bucket 122: 90% Returning block of 21737 for bucket 117 bucket 129: 40% bucket 157: 50% bucket 160: 40% bucket 159: 40% bucket 162: 30% bucket 152: 80% Sorting block of length 22056 for bucket 143 (Using difference cover) Sorting block of length 21431 for bucket 142 (Using difference cover) Getting block 165 of 204 bucket 151: 80% bucket 125: 90% bucket 123: 90% bucket 134: 40% bucket 133: 40% bucket 120: 100% Getting block 141 of 203 Getting block 142 of 203 Getting block 143 of 203 Entering block accumulator loop for bucket 140: bucket 127: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 154: 70% bucket 145: 100% bucket 158: 50% bucket 150: 90% bucket 146: 100% bucket 147: 100% Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 163: Getting block 166 of 204 Sorting block of length 19015 for bucket 144 (Using difference cover) bucket 149: 90% bucket 148: 100% bucket 156: 60% bucket 161: 40% Reserving size (25350) for bucket 165 bucket 132: 40% bucket 135: 40% Sorting block of length 8810 for bucket 119 (Using difference cover) bucket 136: 40% Sorting block time: 00:00:00 bucket 155: 70% Returning block of 22057 for bucket 143 Returning block of 21432 for bucket 142 bucket 153: 80% bucket 157: 60% bucket 160: 50% bucket 162: 40% bucket 152: 90% Sorting block of length 10597 for bucket 145 (Using difference cover) bucket 159: 50% bucket 151: 90% Sorting block of length 21556 for bucket 146 (Using difference cover) Getting block 167 of 204 Sorting block of length 17340 for bucket 147 (Using difference cover) Sorting block time: 00:00:00 Returning block of 21706 for bucket 118 Sorting block of length 22459 for bucket 121 (Using difference cover) bucket 137: 30% bucket 124: 70% bucket 126: 80% bucket 130: 50% bucket 138: 10% bucket 122: 100% bucket 131: 50% bucket 128: 50% Sorting block of length 23527 for bucket 120 (Using difference cover) Reserving size (25350) for bucket 141 Entering block accumulator loop for bucket 164: Reserving size (25350) for bucket 166 Sorting block time: 00:00:00 Sorting block of length 17946 for bucket 148 (Using difference cover) Calculating Z arrays for bucket 165 Getting block 168 of 204 Returning block of 19016 for bucket 144 bucket 154: 80% bucket 158: 60% bucket 150: 100% Reserving size (25350) for bucket 167 bucket 149: 100% bucket 161: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 125: 100% bucket 123: 100% bucket 134: 50% Sorting block time: 00:00:00 bucket 156: 70% bucket 155: 80% bucket 157: 70% bucket 160: 60% Reserving size (25350) for bucket 142 bucket 133: 50% Reserving size (25350) for bucket 143 bucket 129: 50% Returning block of 8811 for bucket 119 bucket 127: 60% bucket 139: 10% bucket 136: 50% bucket 135: 50% Getting block 144 of 203 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Calculating Z arrays for bucket 166 bucket 153: 90% bucket 162: 50% bucket 152: 100% bucket 163: 10% Returning block of 10598 for bucket 145 bucket 151: 100% bucket 159: 60% Entering block accumulator loop for bucket 165: Reserving size (25350) for bucket 168 Getting block 169 of 204 Getting block 170 of 204 Sorting block of length 11545 for bucket 150 (Using difference cover) Calculating Z arrays for bucket 167 Sorting block of length 6222 for bucket 122 Sorting block of length 19702 for bucket 149 (Using difference cover) (Using difference cover) Calculating Z arrays for bucket 141 Returning block of 21557 for bucket 146 Returning block of 22460 for bucket 121 bucket 154: 90% bucket 161: 60% Sorting block time: 00:00:00 bucket 124: 80% bucket 137: 40% Returning block of 23528 for bucket 120 Sorting block time: 00:00:00 bucket 158: 70% Returning block of 17341 for bucket 147 Returning block of 17947 for bucket 148 bucket 155: 90% bucket 156: 80% bucket 157: 80% bucket 160: 70% Entering block accumulator loop for bucket 166: Sorting block of length 14385 for bucket 152 (Using difference cover) bucket 132: 50% Sorting block of length 24553 for bucket 151 (Using difference cover) bucket 126: 90% bucket 130: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Calculating Z arrays for bucket 168 Reserving size (25350) for bucket 169 Reserving size (25350) for bucket 170 Entering block accumulator loop for bucket 167: Getting block 171 of 204 bucket 164: 10% Returning block of 11546 for bucket 150 bucket 163: 20% bucket 162: 60% Sorting block time: 00:00:00 bucket 154: 100% bucket 159: 70% bucket 153: 100% bucket 161: 70% Sorting block of length 19735 for bucket 125 (Using difference cover) Sorting block of length 24677 for bucket 123 (Using difference cover) bucket 131: 60% bucket 128: 60% bucket 138: 20% bucket 134: 60% Returning block of 14386 for bucket 152 Returning block of 19703 for bucket 149 bucket 155: 100% bucket 158: 80% bucket 160: 80% bucket 157: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Calculating Z arrays for bucket 142 Calculating Z arrays for bucket 143 Getting block 145 of 203 Reserving size (25350) for bucket 144 bucket 133: 60% bucket 127: 70% bucket 136: 60% bucket 139: 20% Entering block accumulator loop for bucket 141: bucket 140: 10% bucket 135: 60% bucket 156: 90% bucket 165: 10% Calculating Z arrays for bucket 169 Returning block of 6223 for bucket 122 bucket 129: 60% bucket 137: 50% bucket 132: 60% Entering block accumulator loop for bucket 168: Calculating Z arrays for bucket 170 Reserving size (25350) for bucket 171 bucket 124: 90% bucket 126: 100% bucket 130: 70% Getting block 172 of 204 Getting block 173 of 204 Returning block of 24554 for bucket 151 Sorting block of length 24733 for bucket 154 (Using difference cover) Sorting block of length 12779 for bucket 153 (Using difference cover) bucket 162: 70% bucket 164: 20% bucket 163: 30% Getting block 174 of 204 Getting block 175 of 204 Returning block of 19736 for bucket 125 Returning block of 24678 for bucket 123 bucket 131: 70% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 161: 80% bucket 159: 80% Sorting block of length 21565 for bucket 155 (Using difference cover) Entering block accumulator loop for bucket 169: bucket 166: 10% bucket 157: 100% Entering block accumulator loop for bucket 143: Entering block accumulator loop for bucket 142: Reserving size (25350) for bucket 145 Calculating Z arrays for bucket 144 Getting block 146 of 203 bucket 160: 90% bucket 128: 70% bucket 138: 30% bucket 134: 70% bucket 133: 70% bucket 127: 80% bucket 136: 70% Sorting block time: 00:00:00 bucket 158: 90% bucket 165: 20% Getting block 147 of 203 bucket 139: 30% Getting block 148 of 203 bucket 135: 70% bucket 140: 20% bucket 156: 100% Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 170: bucket 167: 10% bucket 129: 70% bucket 137: 60% bucket 132: 70% Sorting block of length 8956 for bucket 126 (Using difference cover) Reserving size (25350) for bucket 172 Reserving size (25350) for bucket 173 Getting block 176 of 204 Reserving size (25350) for bucket 174 Reserving size (25350) for bucket 175 Returning block of 12780 for bucket 153 Returning block of 24734 for bucket 154 Sorting block time: 00:00:00 bucket 124: 100% Getting block 177 of 204 bucket 130: 80% Getting block 178 of 204 Sorting block of length 18659 for bucket 157 (Using difference cover) bucket 162: 80% bucket 164: 30% bucket 163: 40% Returning block of 21566 for bucket 155 bucket 161: 90% bucket 159: 90% Sorting block time: 00:00:01 bucket 160: 100% bucket 158: 100% bucket 165: 30% Calculating Z arrays for bucket 145 Sorting block of length 22798 for bucket 156 Reserving size (25350) for bucket 146 (Using difference cover) Entering block accumulator loop for bucket 171: bucket 166: 20% Sorting block time: 00:00:01 bucket 168: 10% bucket 167: 20% Entering block accumulator loop for bucket 144: bucket 131: 80% bucket 128: 80% bucket 134: 80% bucket 141: 10% bucket 138: 40% bucket 133: 80% bucket 127: 90% bucket 136: 80% Reserving size (25350) for bucket 147 Reserving size (25350) for bucket 148 bucket 139: 40% Calculating Z arrays for bucket 172 Calculating Z arrays for bucket 173 Reserving size (25350) for bucket 176 Calculating Z arrays for bucket 174 Calculating Z arrays for bucket 175 Reserving size (25350) for bucket 177 Reserving size (25350) for bucket 178 Getting block 179 of 204 Returning block of 18660 for bucket 157 bucket 169: 10% bucket 164: 40% bucket 163: 50% Getting block 149 of 203 bucket 135: 80% bucket 140: 30% Returning block of 8957 for bucket 126 bucket 129: 80% bucket 132: 80% Sorting block of length 14401 for bucket 160 (Using difference cover) bucket 159: 100% bucket 162: 90% Sorting block of length 22593 for bucket 158 (Using difference cover) bucket 161: 100% Returning block of 22799 for bucket 156 bucket 165: 40% bucket 170: 10% bucket 166: 30% Sorting block of length 12847 for bucket 124 (Using difference cover) bucket 137: 70% bucket 130: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 168: 20% bucket 167: 30% Sorting block time: 00:00:01 Getting block 150 of 203 Getting block 151 of 203 Entering block accumulator loop for bucket 145: Calculating Z arrays for bucket 146 bucket 142: 10% bucket 143: 10% bucket 128: 90% Entering block accumulator loop for bucket 172: Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 173: Entering block accumulator loop for bucket 174: Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 175: Calculating Z arrays for bucket 178 Reserving size (25350) for bucket 179 Getting block 180 of 204 Getting block 181 of 204 Getting block 182 of 204 bucket 169: 20% bucket 163: 60% bucket 164: 50% Sorting block of length 21276 for bucket 159 (Using difference cover) Sorting block of length 17308 for bucket 161 (Using difference cover) bucket 134: 90% bucket 131: 90% bucket 133: 90% bucket 136: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 14402 for bucket 160 Returning block of 22594 for bucket 158 bucket 162: 100% bucket 165: 50% bucket 170: 20% bucket 171: 10% bucket 166: 40% Calculating Z arrays for bucket 147 Calculating Z arrays for bucket 148 bucket 127: 100% bucket 141: 20% bucket 138: 50% bucket 139: 50% bucket 168: 30% bucket 167: 40% Reserving size (25350) for bucket 149 bucket 135: 90% bucket 132: 90% bucket 140: 40% bucket 129: 90% Returning block of 12848 for bucket 124 Entering block accumulator loop for bucket 176: bucket 130: 100% Entering block accumulator loop for bucket 177: Reserving size (25350) for bucket 150 Calculating Z arrays for bucket 179 Reserving size (25350) for bucket 151 bucket 137: 80% Entering block accumulator loop for bucket 178: Reserving size (25350) for bucket 180 Reserving size (25350) for bucket 181 Reserving size (25350) for bucket 182 Getting block 183 of 204 Getting block 184 of 204 Returning block of 17309 for bucket 161 Returning block of 21277 for bucket 159 Entering block accumulator loop for bucket 146: bucket 128: 100% bucket 144: 10% bucket 142: 20% bucket 143: 20% bucket 163: 70% bucket 169: 30% bucket 164: 60% bucket 134: 100% bucket 131: 100% bucket 133: 100% bucket 136: 100% Entering block accumulator loop for bucket 147: Sorting block of length 22246 for bucket 127 (Using difference cover) Entering block accumulator loop for bucket 148: bucket 139: 60% Sorting block of length 21162 for bucket 162 (Using difference cover) bucket 165: 60% bucket 170: 30% bucket 171: 20% bucket 166: 50% Sorting block time: 00:00:00 Calculating Z arrays for bucket 149 Getting block 152 of 203 bucket 141: 30% bucket 138: 60% bucket 132: 100% bucket 129: 100% Sorting block of length 11020 for bucket 130 (Using difference cover) bucket 135: 100% Sorting block time: 00:00:00 Calculating Z arrays for bucket 150 Calculating Z arrays for bucket 151 bucket 140: 50% Sorting block time: 00:00:00 bucket 168: 40% Sorting block of length 4920 for bucket 128 bucket 167: 50% (Using difference cover) bucket 145: 10% bucket 137: 90% bucket 144: 20% bucket 142: 30% Sorting block time: 00:00:00 Sorting block of length 18922 for bucket 134 (Using difference cover) Sorting block of length 24672 for bucket 131 (Using difference cover) Sorting block of length 14873 for bucket 133 (Using difference cover) Sorting block of length 20803 for bucket 136 (Using difference cover) Entering block accumulator loop for bucket 179: bucket 143: 30% Calculating Z arrays for bucket 180 Calculating Z arrays for bucket 181 Calculating Z arrays for bucket 182 Reserving size (25350) for bucket 183 Returning block of 22247 for bucket 127 Reserving size (25350) for bucket 184 bucket 139: 70% Reserving size (25350) for bucket 152 bucket 172: 10% bucket 173: 10% bucket 174: 10% bucket 175: 10% bucket 169: 40% bucket 164: 70% Entering block accumulator loop for bucket 149: Sorting block of length 20824 for bucket 132 (Using difference cover) Sorting block of length 22708 for bucket 129 (Using difference cover) Sorting block of length 24345 for bucket 135 (Using difference cover) Returning block of 11021 for bucket 130 Entering block accumulator loop for bucket 150: Entering block accumulator loop for bucket 151: Getting block 153 of 203 Returning block of 4921 for bucket 128 bucket 141: 40% bucket 138: 70% bucket 137: 100% bucket 140: 60% bucket 146: 10% bucket 145: 20% bucket 142: 40% Getting block 185 of 204 bucket 144: 30% Getting block 186 of 204 Calculating Z arrays for bucket 152 bucket 163: 80% Returning block of 21163 for bucket 162 bucket 165: 70% bucket 166: 60% bucket 170: 40% bucket 171: 30% bucket 176: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 148: 10% bucket 177: 10% bucket 168: 50% Entering block accumulator loop for bucket 180: Entering block accumulator loop for bucket 181: Calculating Z arrays for bucket 183 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 147: 10% bucket 139: 80% Entering block accumulator loop for bucket 182: Calculating Z arrays for bucket 184 Getting block 187 of 204 Getting block 188 of 204 bucket 167: 60% bucket 143: 40% Reserving size (25350) for bucket 153 bucket 172: 20% Sorting block of length 20252 for bucket 137 (Using difference cover) Entering block accumulator loop for bucket 152: Getting block 154 of 203 bucket 178: 10% bucket 140: 70% bucket 169: 50% bucket 141: 50% bucket 173: 20% bucket 138: 80% bucket 174: 20% Returning block of 20825 for bucket 132 bucket 164: 80% Returning block of 18923 for bucket 134 Returning block of 24346 for bucket 135 Returning block of 22709 for bucket 129 Returning block of 14874 for bucket 133 bucket 144: 40% Reserving size (25350) for bucket 185 Reserving size (25350) for bucket 186 bucket 175: 20% Sorting block time: 00:00:00 bucket 146: 20% bucket 163: 90% bucket 145: 30% bucket 165: 80% Returning block of 24673 for bucket 131 Entering block accumulator loop for bucket 183: Returning block of 20804 for bucket 136 bucket 148: 20% bucket 142: 50% Calculating Z arrays for bucket 153 bucket 147: 20% bucket 149: 10% bucket 150: 10% bucket 166: 70% bucket 176: 20% bucket 171: 40% bucket 170: 50% bucket 168: 60% bucket 179: 10% Getting block 155 of 203 bucket 151: 10% Reserving size (25350) for bucket 154 Getting block 156 of 203 bucket 139: 90% bucket 143: 50% Returning block of 20253 for bucket 137 bucket 141: 60% bucket 140: 80% Entering block accumulator loop for bucket 184: Reserving size (25350) for bucket 187 Reserving size (25350) for bucket 188 bucket 167: 70% bucket 177: 20% Calculating Z arrays for bucket 185 Calculating Z arrays for bucket 186 bucket 144: 50% bucket 138: 90% bucket 146: 30% bucket 145: 40% Entering block accumulator loop for bucket 153: Getting block 189 of 204 bucket 148: 30% bucket 149: 20% bucket 142: 60% bucket 150: 20% bucket 172: 30% bucket 169: 60% bucket 178: 20% bucket 173: 30% bucket 174: 30% bucket 164: 90% Reserving size (25350) for bucket 155 Calculating Z arrays for bucket 154 Reserving size (25350) for bucket 156 Getting block 157 of 203 Getting block 158 of 203 Getting block 159 of 203 Getting block 160 of 203 bucket 147: 30% bucket 163: 100% bucket 165: 90% bucket 180: 10% bucket 181: 10% bucket 175: 30% bucket 179: 20% Calculating Z arrays for bucket 187 Getting block 161 of 203 Getting block 162 of 203 Getting block 163 of 203 bucket 151: 20% bucket 139: 100% bucket 152: 10% bucket 143: 60% bucket 140: 90% bucket 141: 70% bucket 144: 60% bucket 146: 40% bucket 145: 50% bucket 138: 100% bucket 148: 40% bucket 149: 30% bucket 142: 70% bucket 150: 30% Calculating Z arrays for bucket 188 bucket 166: 80% Entering block accumulator loop for bucket 185: Entering block accumulator loop for bucket 186: bucket 168: 70% bucket 176: 30% bucket 171: 50% bucket 170: 60% Reserving size (25350) for bucket 189 bucket 182: 10% bucket 177: 30% bucket 167: 80% bucket 183: 10% Calculating Z arrays for bucket 155 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 154: Reserving size (25350) for bucket 157 Reserving size (25350) for bucket 158 Reserving size (25350) for bucket 159 Reserving size (25350) for bucket 160 bucket 147: 40% bucket 172: 40% bucket 169: 70% bucket 178: 30% bucket 164: 100% bucket 173: 40% bucket 174: 40% Reserving size (25350) for bucket 161 Reserving size (25350) for bucket 162 Reserving size (25350) for bucket 163 Getting block 164 of 203 Sorting block of length 15326 for bucket 139 (Using difference cover) Sorting block of length 25142 for bucket 138 (Using difference cover) bucket 153: 10% bucket 140: 100% bucket 151: 30% bucket 143: 70% bucket 152: 20% bucket 144: 70% bucket 148: 50% Sorting block of length 16301 for bucket 163 (Using difference cover) Entering block accumulator loop for bucket 187: bucket 165: 100% bucket 181: 20% bucket 180: 20% bucket 179: 30% bucket 184: 10% Sorting block time: 00:00:00 bucket 149: 40% bucket 150: 40% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 188: bucket 175: 40% Calculating Z arrays for bucket 189 bucket 176: 40% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 155: bucket 145: 60% bucket 146: 50% bucket 141: 80% bucket 142: 80% bucket 166: 90% bucket 168: 80% bucket 171: 60% bucket 177: 40% bucket 183: 20% bucket 170: 70% bucket 182: 20% bucket 167: 90% Sorting block of length 20268 for bucket 164 (Using difference cover) Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 156: Calculating Z arrays for bucket 158 Calculating Z arrays for bucket 159 Calculating Z arrays for bucket 160 bucket 147: 50% Sorting block time: 00:00:00 bucket 172: 50% bucket 178: 40% bucket 169: 80% bucket 174: 50% bucket 173: 50% Sorting block of length 17602 for bucket 165 (Using difference cover) Calculating Z arrays for bucket 161 Calculating Z arrays for bucket 162 Calculating Z arrays for bucket 163 Reserving size (25350) for bucket 164 Sorting block of length 20456 for bucket 140 (Using difference cover) Returning block of 15327 for bucket 139 Returning block of 25143 for bucket 138 bucket 153: 20% bucket 148: 60% bucket 151: 40% Sorting block time: 00:00:00 Returning block of 16302 for bucket 163 bucket 144: 80% bucket 181: 30% bucket 143: 80% bucket 179: 40% bucket 152: 30% bucket 180: 30% bucket 150: 50% bucket 184: 20% Sorting block time: 00:00:00 bucket 149: 50% bucket 154: 10% bucket 145: 70% bucket 142: 90% bucket 141: 90% bucket 146: 60% Entering block accumulator loop for bucket 189: bucket 176: 50% bucket 185: 10% bucket 186: 10% bucket 175: 50% Entering block accumulator loop for bucket 157: Entering block accumulator loop for bucket 158: Returning block of 20269 for bucket 164 bucket 166: 100% bucket 183: 30% Entering block accumulator loop for bucket 159: bucket 177: 50% bucket 182: 30% bucket 168: 90% bucket 171: 70% bucket 170: 80% bucket 167: 100% Entering block accumulator loop for bucket 160: bucket 147: 60% Returning block of 17603 for bucket 165 bucket 172: 60% bucket 169: 90% bucket 178: 50% bucket 174: 60% bucket 173: 60% bucket 187: 10% Entering block accumulator loop for bucket 161: Entering block accumulator loop for bucket 162: Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 163: Returning block of 20457 for bucket 140 bucket 144: 90% bucket 150: 60% bucket 143: 90% bucket 151: 50% bucket 181: 40% bucket 148: 70% bucket 179: 50% bucket 152: 40% bucket 180: 40% bucket 153: 30% bucket 184: 30% bucket 149: 60% bucket 155: 10% bucket 142: 100% bucket 145: 80% bucket 176: 60% bucket 185: 20% bucket 186: 20% bucket 146: 70% bucket 141: 100% bucket 154: 20% bucket 188: 10% bucket 175: 60% bucket 156: 10% Sorting block of length 24148 for bucket 166 (Using difference cover) Sorting block of length 21938 for bucket 167 (Using difference cover) bucket 183: 40% bucket 182: 40% bucket 147: 70% Getting block 165 of 203 Getting block 166 of 203 Entering block accumulator loop for bucket 164: bucket 144: 100% bucket 150: 70% Sorting block of length 24425 for bucket 142 (Using difference cover) bucket 143: 100% bucket 148: 80% bucket 149: 70% bucket 151: 60% bucket 153: 40% Sorting block of length 23832 for bucket 141 (Using difference cover) bucket 152: 50% bucket 157: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 177: 60% bucket 168: 100% bucket 171: 80% bucket 170: 90% bucket 172: 70% bucket 155: 20% bucket 145: 90% bucket 158: 10% bucket 146: 80% bucket 154: 30% bucket 169: 100% bucket 178: 60% bucket 174: 70% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 159: 10% bucket 156: 20% Reserving size (25350) for bucket 165 Reserving size (25350) for bucket 166 Getting block 167 of 203 Sorting block of length 16817 for bucket 144 (Using difference cover) Sorting block of length 17453 for bucket 143 (Using difference cover) Getting block 190 of 204 bucket 187: 20% bucket 173: 70% bucket 181: 50% bucket 179: 60% bucket 180: 50% bucket 176: 70% bucket 189: 10% bucket 185: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 160: 10% bucket 163: 10% bucket 162: 10% bucket 161: 10% bucket 148: 90% bucket 149: 80% bucket 151: 70% bucket 150: 80% bucket 153: 50% bucket 157: 20% bucket 152: 60% bucket 186: 30% bucket 175: 70% bucket 147: 80% Getting block 191 of 204 Returning block of 24426 for bucket 142 bucket 188: 20% Returning block of 23833 for bucket 141 bucket 158: 20% bucket 154: 40% bucket 146: 90% Calculating Z arrays for bucket 165 bucket 155: 30% Calculating Z arrays for bucket 166 Reserving size (25350) for bucket 167 bucket 145: 100% Returning block of 16818 for bucket 144 Returning block of 17454 for bucket 143 bucket 159: 20% bucket 164: 10% bucket 156: 30% bucket 184: 40% Returning block of 21939 for bucket 167 Returning block of 24149 for bucket 166 bucket 183: 50% bucket 182: 50% Sorting block of length 24921 for bucket 168 (Using difference cover) Getting block 192 of 204 bucket 177: 70% bucket 170: 100% bucket 172: 80% bucket 171: 90% bucket 160: 20% bucket 163: 20% bucket 162: 20% bucket 148: 100% Sorting block time: 00:00:00 Sorting block of length 24778 for bucket 169 bucket 161: 20% (Using difference cover) bucket 149: 90% bucket 174: 80% bucket 153: 60% bucket 178: 70% Sorting block time: 00:00:00 Reserving size (25350) for bucket 190 bucket 179: 70% bucket 181: 60% bucket 180: 60% bucket 187: 30% bucket 173: 80% bucket 189: 20% bucket 185: 40% Reserving size (25350) for bucket 191 bucket 176: 80% bucket 151: 80% bucket 150: 90% bucket 157: 30% Entering block accumulator loop for bucket 165: Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 166: Sorting block of length 13023 for bucket 145 (Using difference cover) bucket 152: 70% Sorting block time: 00:00:00 bucket 158: 30% bucket 154: 50% bucket 155: 40% bucket 186: 40% bucket 188: 30% bucket 175: 80% bucket 146: 100% Reserving size (25350) for bucket 192 bucket 147: 90% bucket 159: 30% bucket 164: 20% bucket 156: 40% Sorting block of length 7700 for bucket 148 (Using difference cover) Sorting block of length 23165 for bucket 170 (Using difference cover) bucket 184: 50% bucket 183: 60% bucket 182: 60% Returning block of 24922 for bucket 168 bucket 177: 80% bucket 172: 90% bucket 171: 100% Returning block of 24779 for bucket 169 Calculating Z arrays for bucket 190 Sorting block time: 00:00:00 bucket 163: 30% bucket 162: 30% Calculating Z arrays for bucket 191 bucket 178: 80% bucket 181: 70% bucket 180: 70% Sorting block time: 00:00:00 bucket 179: 80% bucket 189: 30% bucket 187: 40% bucket 185: 50% bucket 160: 30% bucket 173: 90% bucket 161: 30% Calculating Z arrays for bucket 192 bucket 149: 100% bucket 153: 70% Getting block 193 of 204 bucket 176: 90% Entering block accumulator loop for bucket 167: Returning block of 13024 for bucket 145 bucket 151: 90% bucket 157: 40% bucket 174: 90% bucket 186: 50% bucket 188: 40% bucket 175: 90% Getting block 168 of 203 Getting block 169 of 203 Getting block 170 of 203 bucket 150: 100% Getting block 171 of 203 Sorting block of length 24994 for bucket 146 (Using difference cover) bucket 152: 80% bucket 158: 40% bucket 154: 60% bucket 155: 50% bucket 147: 100% Returning block of 7701 for bucket 148 Getting block 194 of 204 Sorting block of length 28647 for bucket 171 (Using difference cover) Entering block accumulator loop for bucket 190: Entering block accumulator loop for bucket 191: Returning block of 23166 for bucket 170 bucket 184: 60% Sorting block time: 00:00:00 bucket 159: 40% bucket 164: 30% bucket 156: 50% Sorting block of length 23772 for bucket 149 (Using difference cover) bucket 183: 70% bucket 182: 70% bucket 177: 90% bucket 172: 100% Entering block accumulator loop for bucket 192: Reserving size (25350) for bucket 193 bucket 181: 80% bucket 180: 80% bucket 178: 90% bucket 189: 40% Sorting block time: 00:00:00 bucket 163: 40% bucket 162: 40% bucket 160: 40% bucket 161: 40% bucket 165: 10% bucket 153: 80% Sorting block time: 00:00:00 bucket 179: 90% bucket 185: 60% bucket 173: 100% bucket 176: 100% bucket 187: 50% bucket 166: 10% bucket 151: 100% bucket 157: 50% bucket 174: 100% bucket 186: 60% bucket 175: 100% Reserving size (25350) for bucket 194 bucket 188: 50% Sorting block of length 9759 for bucket 172 (Using difference cover) Sorting block time: 00:00:00 Calculating Z arrays for bucket 193 Reserving size (25350) for bucket 168 Reserving size (25350) for bucket 169 Reserving size (25350) for bucket 170 Sorting block of length 24002 for bucket 150 (Using difference cover) Reserving size (25350) for bucket 171 Sorting block of length 21144 for bucket 147 (Using difference cover) Returning block of 24995 for bucket 146 bucket 154: 70% bucket 158: 50% Getting block 195 of 204 Getting block 196 of 204 Returning block of 28648 for bucket 171 bucket 184: 70% bucket 177: 100% bucket 183: 80% bucket 181: 90% bucket 180: 90% bucket 189: 50% bucket 182: 80% Sorting block of length 18142 for bucket 173 (Using difference cover) Sorting block of length 23429 for bucket 176 (Using difference cover) bucket 178: 100% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 155: 60% bucket 152: 90% Returning block of 23773 for bucket 149 bucket 159: 50% bucket 164: 40% bucket 156: 60% Getting block 172 of 203 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 179: 100% bucket 185: 70% bucket 163: 50% bucket 162: 50% bucket 165: 20% bucket 160: 50% Sorting block of length 18615 for bucket 151 (Using difference cover) bucket 161: 50% bucket 167: 10% bucket 153: 90% Sorting block of length 24918 for bucket 174 (Using difference cover) bucket 187: 60% Sorting block of length 11376 for bucket 175 (Using difference cover) Calculating Z arrays for bucket 194 Getting block 197 of 204 Returning block of 9760 for bucket 172 Entering block accumulator loop for bucket 193: bucket 191: 10% Sorting block time: 00:00:00 bucket 166: 20% bucket 157: 60% Calculating Z arrays for bucket 168 Calculating Z arrays for bucket 169 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 186: 70% Calculating Z arrays for bucket 170 bucket 188: 60% Calculating Z arrays for bucket 171 bucket 192: 10% Reserving size (25350) for bucket 195 Reserving size (25350) for bucket 196 Sorting block of length 24864 for bucket 177 (Using difference cover) Sorting block of length 21557 for bucket 178 Getting block 173 of 203 (Using difference cover) Returning block of 21145 for bucket 147 Returning block of 18143 for bucket 173 Returning block of 24003 for bucket 150 bucket 190: 10% bucket 158: 60% Returning block of 23430 for bucket 176 bucket 154: 80% bucket 181: 100% bucket 189: 60% bucket 183: 90% bucket 180: 100% bucket 182: 90% Reserving size (25350) for bucket 172 bucket 155: 70% Returning block of 18616 for bucket 151 bucket 159: 60% bucket 164: 50% bucket 156: 70% bucket 152: 100% bucket 162: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 18514 for bucket 179 bucket 160: 60% (Using difference cover) bucket 163: 60% bucket 184: 80% bucket 165: 30% bucket 185: 80% bucket 167: 20% Reserving size (25350) for bucket 197 bucket 153: 100% Entering block accumulator loop for bucket 194: bucket 161: 60% bucket 157: 70% Sorting block time: 00:00:00 Returning block of 11377 for bucket 175 Returning block of 24919 for bucket 174 bucket 187: 70% bucket 191: 20% bucket 192: 20% bucket 166: 30% Entering block accumulator loop for bucket 168: Entering block accumulator loop for bucket 169: Entering block accumulator loop for bucket 170: Entering block accumulator loop for bucket 171: Reserving size (25350) for bucket 173 Getting block 174 of 203 Calculating Z arrays for bucket 172 Getting block 175 of 203 bucket 158: 70% bucket 154: 90% bucket 155: 80% Calculating Z arrays for bucket 195 Sorting block of length 13191 for bucket 152 Calculating Z arrays for bucket 196 (Using difference cover) bucket 186: 80% bucket 188: 70% Getting block 198 of 204 Sorting block of length 23314 for bucket 181 (Using difference cover) Sorting block of length 25038 for bucket 180 (Using difference cover) Returning block of 24865 for bucket 177 bucket 189: 70% bucket 183: 100% Returning block of 21558 for bucket 178 bucket 182: 100% Calculating Z arrays for bucket 197 Returning block of 18515 for bucket 179 Getting block 199 of 204 bucket 184: 90% bucket 185: 90% Sorting block time: 00:00:00 Sorting block of length 18446 for bucket 153 (Using difference cover) bucket 159: 70% bucket 164: 60% bucket 156: 80% bucket 163: 70% bucket 165: 40% bucket 161: 70% bucket 167: 30% bucket 160: 70% bucket 157: 80% bucket 162: 70% Sorting block time: 00:00:00 bucket 190: 20% bucket 193: 10% bucket 191: 30% bucket 187: 80% bucket 192: 30% Sorting block time: 00:00:00 Calculating Z arrays for bucket 173 Reserving size (25350) for bucket 174 Entering block accumulator loop for bucket 172: Entering block accumulator loop for bucket 195: Reserving size (25350) for bucket 175 Getting block 176 of 203 Returning block of 13192 for bucket 152 bucket 166: 40% bucket 158: 80% bucket 154: 100% bucket 155: 90% Entering block accumulator loop for bucket 196: Reserving size (25350) for bucket 198 Getting block 200 of 204 Getting block 201 of 204 Sorting block of length 9540 for bucket 183 (Using difference cover) Sorting block of length 20483 for bucket 182 (Using difference cover) Reserving size (25350) for bucket 199 Entering block accumulator loop for bucket 197: Getting block 202 of 204 Returning block of 25039 for bucket 180 bucket 186: 90% bucket 189: 80% bucket 188: 80% bucket 184: 100% bucket 185: 100% Getting block 203 of 204 Sorting block time: 00:00:00 bucket 194: 10% bucket 191: 40% Sorting block time: 00:00:00 bucket 193: 20% Getting block 177 of 203 Getting block 178 of 203 Returning block of 18447 for bucket 153 bucket 159: 80% bucket 164: 70% bucket 156: 90% bucket 163: 80% bucket 162: 80% bucket 165: 50% bucket 167: 40% bucket 161: 80% bucket 157: 90% Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 173: bucket 160: 80% bucket 170: 10% Sorting block time: 00:00:00 bucket 192: 40% bucket 171: 10% bucket 187: 90% bucket 168: 10% bucket 169: 10% Calculating Z arrays for bucket 175 Reserving size (25350) for bucket 176 Sorting block of length 22637 for bucket 154 (Using difference cover) bucket 158: 90% bucket 166: 50% bucket 155: 100% Reserving size (25350) for bucket 177 Reserving size (25350) for bucket 178 Calculating Z arrays for bucket 198 Reserving size (25350) for bucket 200 Reserving size (25350) for bucket 201 Getting block 204 of 204 Sorting block time: 00:00:00 bucket 159: 90% bucket 164: 80% Entering block accumulator loop for bucket 174: bucket 162: 90% bucket 163: 90% bucket 156: 100% bucket 172: 10% bucket 161: 90% Calculating Z arrays for bucket 199 Reserving size (25350) for bucket 202 Sorting block of length 17407 for bucket 184 (Using difference cover) Sorting block of length 15446 for bucket 185 (Using difference cover) Reserving size (25350) for bucket 203 Returning block of 23315 for bucket 181 bucket 170: 20% bucket 165: 60% bucket 171: 20% bucket 167: 50% bucket 157: 100% Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 175: Getting block 179 of 203 bucket 160: 90% Sorting block of length 17122 for bucket 155 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 190: 30% Returning block of 9541 for bucket 183 Returning block of 20484 for bucket 182 bucket 189: 90% bucket 186: 100% bucket 188: 90% bucket 194: 20% bucket 191: 50% bucket 193: 30% bucket 192: 50% Calculating Z arrays for bucket 200 Sorting block time: 00:00:00 Calculating Z arrays for bucket 177 Calculating Z arrays for bucket 178 Returning block of 22638 for bucket 154 bucket 168: 20% Entering block accumulator loop for bucket 198: Calculating Z arrays for bucket 201 Reserving size (25350) for bucket 204 bucket 187: 100% bucket 166: 60% bucket 169: 20% bucket 158: 100% Getting block 180 of 203 Sorting block of length 13440 for bucket 156 (Using difference cover) bucket 195: 10% bucket 196: 10% Calculating Z arrays for bucket 202 Sorting block of length 20122 for bucket 157 (Using difference cover) bucket 162: 100% bucket 172: 20% bucket 164: 90% bucket 159: 100% bucket 173: 10% bucket 163: 100% bucket 161: 100% Entering block accumulator loop for bucket 176: Reserving size (25350) for bucket 179 bucket 170: 30% Sorting block time: 00:00:00 bucket 165: 70% bucket 167: 60% bucket 171: 30% Returning block of 17123 for bucket 155 Entering block accumulator loop for bucket 177: Entering block accumulator loop for bucket 178: bucket 160: 100% Sorting block of length 23311 for bucket 158 (Using difference cover) Entering block accumulator loop for bucket 199: Calculating Z arrays for bucket 203 Returning block of 15447 for bucket 185 Returning block of 17408 for bucket 184 Sorting block of length 11939 for bucket 186 (Using difference cover) bucket 197: 10% Entering block accumulator loop for bucket 200: Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (25350) for bucket 180 bucket 168: 30% Sorting block of length 14050 for bucket 162 (Using difference cover) Sorting block of length 19559 for bucket 159 (Using difference cover) Sorting block of length 20821 for bucket 163 (Using difference cover) Sorting block time: 00:00:00 bucket 189: 100% Sorting block of length 20305 for bucket 161 bucket 191: 60% (Using difference cover) Calculating Z arrays for bucket 179 bucket 194: 30% Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 201: Sorting block of length 13542 for bucket 187 (Using difference cover) bucket 193: 40% bucket 188: 100% bucket 190: 40% bucket 192: 60% Returning block of 13441 for bucket 156 bucket 174: 10% bucket 166: 70% Getting block 181 of 203 Sorting block of length 6170 for bucket 160 (Using difference cover) bucket 169: 30% Entering block accumulator loop for bucket 202: Sorting block time: 00:00:00 bucket 195: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 20123 for bucket 157 bucket 172: 30% bucket 175: 10% bucket 170: 40% bucket 164: 100% bucket 173: 20% Returning block of 23312 for bucket 158 Calculating Z arrays for bucket 180 bucket 171: 40% bucket 165: 80% bucket 167: 70% Entering block accumulator loop for bucket 179: bucket 168: 40% Reserving size (25350) for bucket 181 Sorting block time: 00:00:00 bucket 176: 10% Returning block of 20822 for bucket 163 Returning block of 14051 for bucket 162 Returning block of 19560 for bucket 159 Returning block of 6171 for bucket 160 bucket 178: 10% bucket 177: 10% Entering block accumulator loop for bucket 203: bucket 196: 20% Returning block of 11940 for bucket 186 Sorting block of length 13854 for bucket 189 (Using difference cover) Entering block accumulator loop for bucket 204: Sorting block of length 19761 for bucket 188 (Using difference cover) bucket 197: 20% Returning block of 13543 for bucket 187 bucket 191: 70% bucket 194: 40% bucket 198: 10% Getting block 182 of 203 bucket 174: 20% bucket 190: 50% bucket 193: 50% Sorting block of length 24206 for bucket 164 (Using difference cover) Entering block accumulator loop for bucket 180: bucket 166: 80% Calculating Z arrays for bucket 181 bucket 169: 40% Returning block of 20306 for bucket 161 Getting block 183 of 203 bucket 175: 20% bucket 172: 40% bucket 170: 50% bucket 200: 10% bucket 199: 10% Sorting block time: 00:00:00 bucket 165: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 195: 30% bucket 171: 50% bucket 167: 80% Reserving size (25350) for bucket 182 bucket 168: 50% bucket 192: 70% bucket 196: 30% bucket 201: 10% bucket 191: 80% bucket 202: 10% bucket 197: 30% Returning block of 13855 for bucket 189 Returning block of 19762 for bucket 188 bucket 204: 10% bucket 194: 50% bucket 203: 10% bucket 198: 20% bucket 193: 60% bucket 177: 20% bucket 200: 20% bucket 176: 20% bucket 178: 20% Entering block accumulator loop for bucket 181: bucket 199: 20% bucket 190: 60% Reserving size (25350) for bucket 183 Getting block 184 of 203 Getting block 185 of 203 Getting block 186 of 203 Getting block 187 of 203 Getting block 188 of 203 bucket 174: 30% Returning block of 24207 for bucket 164 bucket 179: 10% bucket 166: 90% bucket 169: 50% bucket 175: 30% bucket 172: 50% bucket 170: 60% bucket 173: 30% bucket 195: 40% bucket 201: 20% bucket 191: 90% bucket 196: 40% bucket 202: 20% bucket 197: 40% bucket 204: 20% bucket 203: 20% bucket 200: 30% bucket 198: 30% bucket 165: 100% Calculating Z arrays for bucket 182 bucket 171: 60% bucket 167: 90% bucket 168: 60% bucket 199: 30% bucket 193: 70% bucket 190: 70% Getting block 189 of 203 bucket 176: 30% bucket 177: 30% bucket 180: 10% bucket 178: 30% Calculating Z arrays for bucket 183 bucket 192: 80% bucket 194: 60% bucket 204: 30% bucket 191: 100% bucket 201: 30% bucket 203: 30% Reserving size (25350) for bucket 184 Reserving size (25350) for bucket 185 Reserving size (25350) for bucket 186 Reserving size (25350) for bucket 187 Reserving size (25350) for bucket 188 Getting block 190 of 203 bucket 179: 20% bucket 175: 40% bucket 174: 40% bucket 172: 60% bucket 170: 70% bucket 173: 40% bucket 166: 100% Sorting block of length 14856 for bucket 165 (Using difference cover) Entering block accumulator loop for bucket 182: bucket 169: 60% bucket 195: 50% bucket 171: 70% bucket 202: 30% bucket 167: 100% bucket 197: 50% bucket 168: 70% bucket 196: 50% bucket 200: 40% bucket 198: 40% Sorting block time: 00:00:00 Reserving size (25350) for bucket 189 bucket 199: 40% Sorting block of length 4590 for bucket 191 (Using difference cover) bucket 193: 80% bucket 190: 80% bucket 204: 40% bucket 203: 40% bucket 201: 40% Entering block accumulator loop for bucket 183: bucket 181: 10% bucket 176: 40% bucket 178: 40% bucket 177: 40% bucket 180: 20% Sorting block time: 00:00:00 bucket 192: 90% bucket 194: 70% bucket 200: 50% Calculating Z arrays for bucket 184 Calculating Z arrays for bucket 185 Calculating Z arrays for bucket 186 Calculating Z arrays for bucket 187 Calculating Z arrays for bucket 188 Reserving size (25350) for bucket 190 Getting block 191 of 203 Sorting block of length 13947 for bucket 166 (Using difference cover) Sorting block of length 12867 for bucket 167 (Using difference cover) Returning block of 14857 for bucket 165 bucket 179: 30% bucket 175: 50% bucket 172: 70% bucket 170: 80% bucket 173: 50% bucket 174: 50% bucket 171: 80% bucket 169: 70% bucket 168: 80% bucket 195: 60% bucket 196: 60% bucket 202: 40% bucket 197: 60% bucket 198: 50% Returning block of 4591 for bucket 191 bucket 204: 50% bucket 203: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Calculating Z arrays for bucket 189 bucket 199: 50% bucket 201: 50% bucket 193: 90% bucket 181: 20% bucket 176: 50% bucket 178: 50% bucket 177: 50% bucket 180: 30% bucket 190: 90% bucket 192: 100% Entering block accumulator loop for bucket 184: bucket 200: 60% Entering block accumulator loop for bucket 185: bucket 194: 80% Entering block accumulator loop for bucket 186: Entering block accumulator loop for bucket 187: Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 188: Reserving size (25350) for bucket 191 Returning block of 13948 for bucket 166 Returning block of 12868 for bucket 167 bucket 182: 10% bucket 179: 40% bucket 175: 60% bucket 172: 80% bucket 170: 90% bucket 173: 60% bucket 174: 60% bucket 171: 90% bucket 168: 90% bucket 195: 70% bucket 202: 50% bucket 198: 60% bucket 197: 70% bucket 196: 70% bucket 204: 60% bucket 203: 60% bucket 201: 60% Entering block accumulator loop for bucket 189: bucket 169: 80% bucket 183: 10% bucket 181: 30% bucket 176: 60% bucket 199: 60% bucket 178: 60% bucket 180: 40% bucket 177: 60% Sorting block of length 21963 for bucket 192 (Using difference cover) bucket 193: 100% bucket 190: 100% bucket 204: 70% bucket 200: 70% bucket 203: 70% bucket 202: 60% bucket 196: 80% bucket 198: 70% bucket 197: 80% bucket 201: 70% Sorting block time: 00:00:00 bucket 194: 90% Entering block accumulator loop for bucket 190: Sorting block of length 21424 for bucket 193 (Using difference cover) Sorting block of length 21181 for bucket 190 (Using difference cover) bucket 204: 80% Returning block of 21964 for bucket 192 bucket 195: 80% bucket 203: 80% Calculating Z arrays for bucket 191 Getting block 192 of 203 bucket 182: 20% bucket 175: 70% bucket 179: 50% bucket 172: 90% bucket 170: 100% bucket 173: 70% bucket 174: 70% bucket 171: 100% bucket 168: 100% bucket 169: 90% bucket 181: 40% bucket 183: 20% bucket 178: 70% bucket 176: 70% bucket 177: 70% bucket 180: 50% bucket 185: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 196: 90% bucket 202: 70% bucket 187: 10% bucket 186: 10% bucket 184: 10% Reserving size (25350) for bucket 192 Getting block 193 of 203 Getting block 194 of 203 Entering block accumulator loop for bucket 191: Sorting block of length 11355 for bucket 170 (Using difference cover) bucket 200: 80% Sorting block of length 21388 for bucket 171 bucket 197: 90% (Using difference cover) bucket 198: 80% Sorting block of length 23437 for bucket 168 bucket 201: 80% (Using difference cover) Returning block of 21425 for bucket 193 bucket 204: 90% bucket 188: 10% Returning block of 21182 for bucket 190 bucket 203: 90% bucket 199: 70% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 189: 10% bucket 182: 30% bucket 175: 80% bucket 179: 60% bucket 181: 50% bucket 172: 100% bucket 176: 80% bucket 183: 30% bucket 185: 20% bucket 174: 80% bucket 178: 80% bucket 173: 80% bucket 180: 60% Calculating Z arrays for bucket 192 Reserving size (25350) for bucket 193 Reserving size (25350) for bucket 194 bucket 177: 80% bucket 169: 100% bucket 187: 20% Returning block of 11356 for bucket 170 Returning block of 21389 for bucket 171 bucket 195: 90% Returning block of 23438 for bucket 168 Sorting block of length 13921 for bucket 172 (Using difference cover) bucket 184: 20% bucket 190: 10% Entering block accumulator loop for bucket 192: Calculating Z arrays for bucket 193 Sorting block time: 00:00:00 Calculating Z arrays for bucket 194 bucket 188: 20% bucket 196: 100% bucket 202: 80% bucket 194: 100% bucket 204: 100% bucket 201: 90% bucket 197: 100% bucket 200: 90% bucket 203: 100% bucket 199: 80% bucket 186: 20% Sorting block of length 24932 for bucket 169 (Using difference cover) bucket 189: 20% bucket 195: 100% bucket 182: 40% bucket 198: 90% bucket 181: 60% Sorting block of length 11840 for bucket 196 bucket 175: 90% (Using difference cover) bucket 179: 70% Sorting block of length 23319 for bucket 194 bucket 174: 90% (Using difference cover) bucket 173: 90% Sorting block of length 15248 for bucket 204 bucket 176: 90% (Using difference cover) bucket 178: 90% Sorting block of length 16201 for bucket 197 bucket 191: 10% (Using difference cover) bucket 180: 70% Sorting block of length 17104 for bucket 203 Entering block accumulator loop for bucket 193: (Using difference cover) bucket 185: 30% Sorting block time: 00:00:00 bucket 187: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 201: 100% bucket 202: 90% bucket 177: 90% Returning block of 13922 for bucket 172 Entering block accumulator loop for bucket 194: bucket 183: 40% bucket 190: 20% bucket 184: 30% bucket 188: 30% Getting block 195 of 203 Getting block 196 of 203 Returning block of 24933 for bucket 169 Sorting block time: 00:00:00 bucket 199: 90% Sorting block of length 15523 for bucket 195 (Using difference cover) bucket 200: 100% Sorting block time: 00:00:00 Returning block of 17105 for bucket 203 Returning block of 15249 for bucket 204 Returning block of 16202 for bucket 197 Sorting block of length 22698 for bucket 201 (Using difference cover) Returning block of 23320 for bucket 194 Sorting block of length 13724 for bucket 200 (Using difference cover) Returning block of 11841 for bucket 196 Sorting block time: 00:00:00 Returning block of 15524 for bucket 195 bucket 186: 30% bucket 189: 30% bucket 202: 100% Sorting block of length 9915 for bucket 202 (Using difference cover) bucket 198: 100% Sorting block of length 25231 for bucket 198 (Using difference cover) Sorting block time: 00:00:00 Returning block of 13725 for bucket 200 bucket 199: 100% Sorting block of length 18811 for bucket 199 (Using difference cover) Getting block 197 of 203 bucket 192: 10% bucket 182: 50% bucket 191: 20% bucket 181: 70% bucket 176: 100% bucket 175: 100% bucket 179: 80% bucket 174: 100% bucket 185: 40% bucket 178: 100% bucket 173: 100% bucket 180: 80% Reserving size (25350) for bucket 195 Reserving size (25350) for bucket 196 Sorting block time: 00:00:00 Returning block of 9916 for bucket 202 Sorting block time: 00:00:00 Returning block of 25232 for bucket 198 Sorting block time: 00:00:00 Returning block of 18812 for bucket 199 bucket 187: 40% bucket 177: 100% bucket 193: 10% bucket 184: 40% bucket 183: 50% bucket 188: 40% bucket 190: 30% Reserving size (25350) for bucket 197 Sorting block of length 3721 for bucket 176 (Using difference cover) Sorting block of length 21650 for bucket 175 Sorting block of length 22209 for bucket 174 (Using difference cover) (Using difference cover) Sorting block of length 21627 for bucket 178 (Using difference cover) Sorting block of length 25138 for bucket 173 (Using difference cover) Calculating Z arrays for bucket 195 Calculating Z arrays for bucket 196 bucket 186: 40% bucket 189: 40% bucket 192: 20% bucket 182: 60% bucket 191: 30% bucket 181: 80% bucket 185: 50% bucket 179: 90% bucket 194: 10% Sorting block time: 00:00:00 Returning block of 22699 for bucket 201 Sorting block time: 00:00:00 Getting block 198 of 203 Sorting block of length 24628 for bucket 177 (Using difference cover) Getting block 199 of 203 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 195: Entering block accumulator loop for bucket 196: bucket 180: 90% Returning block of 3722 for bucket 176 Reserving size (25350) for bucket 198 Reserving size (25350) for bucket 199 Entering block accumulator loop for bucket 197: Calculating Z arrays for bucket 198 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 198: Entering block accumulator loop for bucket 199: Getting block 200 of 203 Reserving size (25350) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: Sorting block time: 00:00:00 Returning block of 21651 for bucket 175 bucket 193: 20% Sorting block time: 00:00:00 Returning block of 22210 for bucket 174 bucket 183: 60% bucket 188: 50% bucket 187: 50% bucket 184: 50% bucket 190: 40% Sorting block time: 00:00:00 Returning block of 21628 for bucket 178 Sorting block time: 00:00:00 Returning block of 25139 for bucket 173 bucket 192: 30% bucket 182: 70% bucket 189: 50% bucket 185: 60% bucket 186: 50% bucket 181: 90% bucket 191: 40% bucket 179: 100% Sorting block of length 24316 for bucket 179 (Using difference cover) bucket 194: 20% Getting block 201 of 203 Reserving size (25350) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: Getting block 202 of 203 Reserving size (25350) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: Exited Ebwt loop fchr[A]: 0 fchr[C]: 1210749 fchr[G]: 1210749 fchr[T]: 1897502 fchr[$]: 3785646 Getting block 203 of 203 Reserving size (25350) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: Sorting block time: 00:00:00 Returning block of 24629 for bucket 177 bucket 195: 10% bucket 197: 10% bucket 196: 10% bucket 199: 10% bucket 198: 10% bucket 200: 10% bucket 193: 30% bucket 187: 60% bucket 184: 60% bucket 190: 50% bucket 183: 70% Sorting block time: 00:00:00 Returning block of 24317 for bucket 179 bucket 192: 40% bucket 189: 60% bucket 182: 80% bucket 185: 70% bucket 181: 100% bucket 186: 60% Sorting block of length 19759 for bucket 181 (Using difference cover) bucket 191: 50% bucket 194: 30% bucket 188: 60% bucket 203: 10% bucket 201: 10% bucket 180: 100% Sorting block of length 16298 for bucket 180 (Using difference cover) bucket 195: 20% bucket 197: 20% bucket 196: 20% bucket 202: 10% bucket 199: 20% bucket 198: 20% Sorting block time: 00:00:00 Returning block of 19760 for bucket 181 bucket 200: 20% bucket 193: 40% bucket 184: 70% bucket 190: 60% bucket 192: 50% bucket 203: 20% bucket 183: 80% bucket 189: 70% Sorting block time: 00:00:00 Returning block of 16299 for bucket 180 bucket 186: 70% bucket 187: 70% bucket 182: 90% bucket 185: 80% bucket 191: 60% bucket 188: 70% bucket 194: 40% bucket 201: 20% bucket 195: 30% bucket 197: 30% bucket 202: 20% bucket 196: 30% bucket 203: 30% bucket 199: 30% bucket 198: 30% bucket 193: 50% bucket 200: 30% bucket 192: 60% bucket 190: 70% bucket 184: 80% bucket 189: 80% bucket 183: 90% bucket 186: 80% bucket 182: 100% Sorting block of length 19883 for bucket 182 (Using difference cover) bucket 185: 90% bucket 187: 80% bucket 191: 70% bucket 188: 80% bucket 194: 50% bucket 201: 30% bucket 203: 40% bucket 195: 40% bucket 197: 40% bucket 202: 30% bucket 196: 40% bucket 198: 40% bucket 199: 40% Sorting block time: 00:00:00 Returning block of 19884 for bucket 182 bucket 193: 60% bucket 200: 40% bucket 192: 70% bucket 190: 80% bucket 184: 90% bucket 189: 90% bucket 186: 90% bucket 183: 100% bucket 203: 50% Sorting block of length 22749 for bucket 183 (Using difference cover) bucket 185: 100% Sorting block of length 24041 for bucket 185 (Using difference cover) bucket 187: 90% bucket 188: 90% bucket 191: 80% bucket 194: 60% bucket 201: 40% bucket 195: 50% bucket 197: 50% bucket 202: 40% bucket 196: 50% bucket 198: 50% bucket 199: 50% bucket 203: 60% bucket 200: 50% bucket 193: 70% Sorting block time: 00:00:00 Returning block of 22750 for bucket 183 bucket 192: 80% Sorting block time: 00:00:00 Returning block of 24042 for bucket 185 bucket 190: 90% bucket 184: 100% Sorting block of length 25234 for bucket 184 (Using difference cover) bucket 189: 100% Sorting block of length 19760 for bucket 189 (Using difference cover) bucket 186: 100% Sorting block of length 8099 for bucket 186 (Using difference cover) bucket 187: 100% Sorting block of length 21184 for bucket 187 (Using difference cover) bucket 188: 100% Sorting block of length 12300 for bucket 188 (Using difference cover) bucket 191: 90% bucket 194: 70% bucket 201: 50% bucket 203: 70% Sorting block time: 00:00:00 Returning block of 8100 for bucket 186 bucket 195: 60% bucket 197: 60% bucket 202: 50% bucket 196: 60% bucket 198: 60% bucket 199: 60% Sorting block time: 00:00:00 Returning block of 12301 for bucket 188 bucket 200: 60% bucket 193: 80% Sorting block time: 00:00:00 Returning block of 19761 for bucket 189 bucket 192: 90% Sorting block time: 00:00:00 Returning block of 21185 for bucket 187 bucket 190: 100% Sorting block of length 20684 for bucket 190 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25235 for bucket 184 bucket 191: 100% Sorting block of length 21792 for bucket 191 (Using difference cover) bucket 201: 60% bucket 194: 80% bucket 203: 80% bucket 195: 70% bucket 197: 70% bucket 202: 60% bucket 196: 70% bucket 198: 70% bucket 199: 70% bucket 200: 70% Sorting block time: 00:00:00 Returning block of 20685 for bucket 190 bucket 193: 90% bucket 192: 100% Sorting block of length 11513 for bucket 192 (Using difference cover) bucket 203: 90% Sorting block time: 00:00:00 Returning block of 21793 for bucket 191 bucket 201: 70% bucket 194: 90% Sorting block time: 00:00:00 Returning block of 11514 for bucket 192 bucket 195: 80% bucket 197: 80% bucket 202: 70% bucket 198: 80% bucket 196: 80% bucket 203: 100% Sorting block of length 14882 for bucket 203 (Using difference cover) bucket 199: 80% bucket 200: 80% bucket 193: 100% Sorting block of length 24767 for bucket 193 (Using difference cover) bucket 201: 80% bucket 194: 100% Sorting block of length 21249 for bucket 194 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14883 for bucket 203 bucket 195: 90% bucket 197: 90% bucket 202: 80% bucket 198: 90% bucket 196: 90% bucket 199: 90% bucket 200: 90% Sorting block time: 00:00:00 Returning block of 24768 for bucket 193 Sorting block time: 00:00:00 Returning block of 21250 for bucket 194 bucket 201: 90% bucket 195: 100% Sorting block of length 4625 for bucket 195 (Using difference cover) bucket 197: 100% Sorting block of length 10295 for bucket 197 (Using difference cover) bucket 202: 90% bucket 198: 100% Sorting block of length 18695 for bucket 198 (Using difference cover) bucket 196: 100% Sorting block of length 21530 for bucket 196 (Using difference cover) Sorting block time: 00:00:00 Returning block of 4626 for bucket 195 bucket 200: 100% Sorting block of length 7041 for bucket 200 (Using difference cover) bucket 199: 100% Sorting block of length 25325 for bucket 199 (Using difference cover) Sorting block time: 00:00:00 Returning block of 10296 for bucket 197 bucket 201: 100% Sorting block of length 22310 for bucket 201 (Using difference cover) Sorting block time: 00:00:00 Returning block of 7042 for bucket 200 Sorting block time: 00:00:00 Returning block of 18696 for bucket 198 Sorting block time: 00:00:00 Returning block of 21531 for bucket 196 bucket 202: 100% Sorting block of length 21781 for bucket 202 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25326 for bucket 199 Sorting block time: 00:00:00 Returning block of 22311 for bucket 201 Sorting block time: 00:00:00 Returning block of 21782 for bucket 202 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1897502 fchr[G]: 2570152 fchr[T]: 2570152 fchr[$]: 3785646 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 5461730 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 946416 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 3785646 bwtLen: 3785647 sz: 946412 bwtSz: 946412 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 236603 offsSz: 946412 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 19717 numLines: 19717 ebwtTotLen: 1261888 ebwtTotSz: 1261888 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:03 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 5461730 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 946416 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 3785646 bwtLen: 3785647 sz: 946412 bwtSz: 946412 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 236603 offsSz: 946412 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 19717 numLines: 19717 ebwtTotLen: 1261888 ebwtTotSz: 1261888 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:02 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 33800 Using parameters --bmax 25350 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 25350 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 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 33, merged 133; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 15, merged 17; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 7, merged 5; iterating... Splitting and merging Splitting and merging time: 00:00:01 Split 5, merged 5; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 4; iterating... Avg bucket size: 19022.4 (target: 25349) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 199 Reserving size (25350) for bucket 1 Getting block 2 of 199 Getting block 3 of 199 Getting block 4 of 199 Getting block 5 of 199 Getting block 6 of 199 Getting block 7 of 199 Getting block 8 of 199 Getting block 9 of 199 Getting block 10 of 199 Getting block 11 of 199 Getting block 12 of 199 Getting block 13 of 199 Getting block 14 of 199 Getting block 15 of 199 Getting block 16 of 199 Getting block 17 of 199 Getting block 18 of 199 Getting block 19 of 199 Getting block 20 of 199 Getting block 21 of 199 Getting block 22 of 199 Getting block 23 of 199 Getting block 24 of 199 Getting block 25 of 199 Calculating Z arrays for bucket 1 Reserving size (25350) for bucket 2 Reserving size (25350) for bucket 3 Getting block 26 of 199 Reserving size (25350) for bucket 4 Reserving size (25350) for bucket 5 Reserving size (25350) for bucket 6 Reserving size (25350) for bucket 7 Reserving size (25350) for bucket 8 Reserving size (25350) for bucket 9 Reserving size (25350) for bucket 10 Reserving size (25350) for bucket 11 Reserving size (25350) for bucket 12 Reserving size (25350) for bucket 13 Reserving size (25350) for bucket 14 Reserving size (25350) for bucket 15 Reserving size (25350) for bucket 16 Reserving size (25350) for bucket 17 Reserving size (25350) for bucket 18 Reserving size (25350) for bucket 19 Reserving size (25350) for bucket 20 Reserving size (25350) for bucket 21 Reserving size (25350) for bucket 22 Reserving size (25350) for bucket 23 Reserving size (25350) for bucket 24 Reserving size (25350) for bucket 25 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 3 Reserving size (25350) for bucket 26 Getting block 27 of 199 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 21 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 3: Reserving size (25350) for bucket 27 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: 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 20: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 25: Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 27: bucket 24: 10% bucket 18: 10% bucket 1: 10% bucket 13: 10% bucket 2: 10% bucket 5: 10% bucket 3: 10% bucket 7: 10% bucket 16: 10% bucket 21: 10% bucket 4: 10% bucket 14: 10% bucket 25: 10% bucket 6: 10% bucket 10: 10% bucket 22: 10% bucket 20: 10% bucket 8: 10% bucket 12: 10% bucket 11: 10% bucket 9: 10% bucket 15: 10% bucket 17: 10% bucket 19: 10% bucket 27: 10% bucket 23: 10% bucket 26: 10% bucket 24: 20% bucket 18: 20% bucket 13: 20% bucket 2: 20% bucket 1: 20% bucket 5: 20% bucket 3: 20% bucket 7: 20% bucket 16: 20% bucket 21: 20% bucket 4: 20% bucket 14: 20% bucket 25: 20% bucket 6: 20% bucket 10: 20% bucket 22: 20% bucket 20: 20% bucket 12: 20% bucket 8: 20% bucket 11: 20% bucket 9: 20% bucket 15: 20% bucket 17: 20% bucket 19: 20% bucket 27: 20% bucket 23: 20% bucket 24: 30% bucket 26: 20% bucket 18: 30% bucket 13: 30% bucket 2: 30% bucket 5: 30% bucket 3: 30% bucket 1: 30% bucket 7: 30% bucket 16: 30% bucket 21: 30% bucket 4: 30% bucket 14: 30% bucket 25: 30% bucket 6: 30% bucket 10: 30% bucket 20: 30% bucket 22: 30% bucket 12: 30% bucket 8: 30% bucket 11: 30% bucket 9: 30% bucket 24: 40% bucket 15: 30% bucket 17: 30% bucket 19: 30% bucket 27: 30% bucket 23: 30% bucket 18: 40% bucket 26: 30% bucket 13: 40% bucket 2: 40% bucket 3: 40% bucket 5: 40% bucket 1: 40% bucket 7: 40% bucket 16: 40% bucket 21: 40% bucket 24: 50% bucket 4: 40% bucket 14: 40% bucket 25: 40% bucket 6: 40% bucket 10: 40% bucket 12: 40% bucket 20: 40% bucket 11: 40% bucket 22: 40% bucket 9: 40% bucket 8: 40% bucket 15: 40% bucket 17: 40% bucket 19: 40% bucket 27: 40% bucket 18: 50% bucket 23: 40% bucket 13: 50% bucket 2: 50% bucket 3: 50% bucket 5: 50% bucket 1: 50% bucket 7: 50% bucket 16: 50% bucket 24: 60% bucket 26: 40% bucket 21: 50% bucket 4: 50% bucket 14: 50% bucket 25: 50% bucket 6: 50% bucket 10: 50% bucket 12: 50% bucket 11: 50% bucket 20: 50% bucket 9: 50% bucket 22: 50% bucket 8: 50% bucket 15: 50% bucket 17: 50% bucket 18: 60% bucket 24: 70% bucket 19: 50% bucket 27: 50% bucket 13: 60% bucket 2: 60% bucket 3: 60% bucket 5: 60% bucket 23: 50% bucket 1: 60% bucket 7: 60% bucket 16: 60% bucket 21: 60% bucket 4: 60% bucket 14: 60% bucket 6: 60% bucket 25: 60% bucket 26: 50% bucket 10: 60% bucket 24: 80% bucket 12: 60% bucket 20: 60% bucket 11: 60% bucket 9: 60% bucket 22: 60% bucket 8: 60% bucket 18: 70% bucket 15: 60% bucket 17: 60% bucket 13: 70% bucket 2: 70% bucket 3: 70% bucket 5: 70% bucket 1: 70% bucket 7: 70% bucket 19: 60% bucket 27: 60% bucket 16: 70% bucket 23: 60% bucket 4: 70% bucket 21: 70% bucket 24: 90% bucket 14: 70% bucket 6: 70% bucket 25: 70% bucket 10: 70% bucket 18: 80% bucket 12: 70% bucket 11: 70% bucket 9: 70% bucket 20: 70% bucket 26: 60% bucket 22: 70% bucket 8: 70% bucket 15: 70% bucket 17: 70% bucket 13: 80% bucket 2: 80% bucket 3: 80% bucket 5: 80% bucket 1: 80% bucket 7: 80% bucket 16: 80% bucket 24: 100% Sorting block of length 24228 for bucket 24 (Using difference cover) bucket 19: 70% bucket 27: 70% bucket 23: 70% bucket 21: 80% bucket 4: 80% bucket 14: 80% bucket 6: 80% bucket 18: 90% bucket 25: 80% bucket 10: 80% bucket 12: 80% bucket 11: 80% bucket 9: 80% bucket 20: 80% bucket 22: 80% bucket 8: 80% bucket 13: 90% bucket 2: 90% bucket 3: 90% bucket 1: 90% bucket 5: 90% bucket 15: 80% bucket 17: 80% bucket 26: 70% bucket 7: 90% Sorting block time: 00:00:00 Returning block of 24229 for bucket 24 bucket 16: 90% bucket 19: 80% bucket 27: 80% bucket 4: 90% bucket 21: 90% bucket 23: 80% bucket 18: 100% Sorting block of length 16289 for bucket 18 (Using difference cover) bucket 14: 90% bucket 6: 90% bucket 25: 90% Getting block 28 of 199 Reserving size (25350) for bucket 28 Calculating Z arrays for bucket 28 bucket 10: 90% Entering block accumulator loop for bucket 28: bucket 12: 90% bucket 13: 100% Sorting block of length 13747 for bucket 13 (Using difference cover) bucket 11: 90% bucket 9: 90% bucket 2: 100% Sorting block of length 21615 for bucket 2 (Using difference cover) bucket 3: 100% Sorting block of length 17394 for bucket 3 (Using difference cover) bucket 20: 90% bucket 1: 100% Sorting block of length 12983 for bucket 1 (Using difference cover) bucket 5: 100% Sorting block of length 23870 for bucket 5 (Using difference cover) bucket 8: 90% bucket 22: 90% bucket 7: 100% Sorting block of length 24802 for bucket 7 (Using difference cover) bucket 15: 90% bucket 17: 90% bucket 16: 100% Sorting block of length 10163 for bucket 16 (Using difference cover) bucket 26: 80% Sorting block time: 00:00:00 Returning block of 16290 for bucket 18 bucket 4: 100% Sorting block of length 18089 for bucket 4 (Using difference cover) bucket 19: 90% bucket 27: 90% bucket 21: 100% Sorting block of length 19514 for bucket 21 (Using difference cover) bucket 28: 10% bucket 14: 100% Sorting block of length 24727 for bucket 14 (Using difference cover) bucket 23: 90% Getting block 29 of 199 Reserving size (25350) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 6: 100% Sorting block of length 25122 for bucket 6 (Using difference cover) bucket 25: 100% Sorting block of length 20308 for bucket 25 (Using difference cover) bucket 10: 100% Sorting block of length 9459 for bucket 10 (Using difference cover) Sorting block time: 00:00:00 Returning block of 13748 for bucket 13 bucket 11: 100% Sorting block of length 20135 for bucket 11 (Using difference cover) bucket 9: 100% Sorting block of length 23149 for bucket 9 (Using difference cover) bucket 20: 100% Sorting block of length 20594 for bucket 20 (Using difference cover) Sorting block time: 00:00:00 bucket 12: 100% Returning block of 10164 for bucket 16 Sorting block of length 9351 for bucket 12 (Using difference cover) bucket 8: 100% Sorting block of length 24717 for bucket 8 (Using difference cover) bucket 22: 100% Sorting block of length 17004 for bucket 22 (Using difference cover) Sorting block time: 00:00:00 Returning block of 17395 for bucket 3 Getting block 30 of 199 Reserving size (25350) for bucket 30 Calculating Z arrays for bucket 30 bucket 15: 100% Entering block accumulator loop for bucket 30: Sorting block of length 18285 for bucket 15 (Using difference cover) bucket 17: 100% Sorting block of length 25099 for bucket 17 (Using difference cover) Sorting block time: 00:00:00 Returning block of 21616 for bucket 2 Getting block 31 of 199 Reserving size (25350) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: Sorting block time: 00:00:00 Returning block of 12984 for bucket 1 Getting block 32 of 199 Reserving size (25350) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: bucket 28: 20% bucket 26: 90% bucket 19: 100% Sorting block of length 23328 for bucket 19 (Using difference cover) Getting block 33 of 199 Reserving size (25350) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: Sorting block time: 00:00:00 Returning block of 23871 for bucket 5 Sorting block time: 00:00:00 Returning block of 24803 for bucket 7 Getting block 34 of 199 Reserving size (25350) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: bucket 27: 100% Sorting block of length 7592 for bucket 27 (Using difference cover) bucket 29: 10% Sorting block time: 00:00:00 Returning block of 18090 for bucket 4 bucket 23: 100% Sorting block of length 24025 for bucket 23 (Using difference cover) Getting block 35 of 199 Reserving size (25350) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: Getting block 36 of 199 Reserving size (25350) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Sorting block time: 00:00:00 Returning block of 9460 for bucket 10 bucket 30: 10% bucket 28: 30% bucket 31: 10% Getting block 37 of 199 Reserving size (25350) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: Getting block 38 of 199 Reserving size (25350) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: bucket 32: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 9352 for bucket 12 Sorting block time: 00:00:00 Returning block of 23150 for bucket 9 Returning block of 19515 for bucket 21 bucket 33: 10% bucket 29: 20% Getting block 39 of 199 Reserving size (25350) for bucket 39 bucket 26: 100% Calculating Z arrays for bucket 39 Sorting block of length 18542 for bucket 26 (Using difference cover) Entering block accumulator loop for bucket 39: bucket 34: 10% Getting block 40 of 199 Reserving size (25350) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: Getting block 41 of 199 Reserving size (25350) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: bucket 35: 10% bucket 36: 10% bucket 28: 40% Sorting block time: 00:00:00 Returning block of 7593 for bucket 27 bucket 30: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 25100 for bucket 17 Returning block of 25123 for bucket 6 Sorting block time: 00:00:00 Returning block of 20595 for bucket 20 Returning block of 20136 for bucket 11 bucket 31: 20% Getting block 42 of 199 Reserving size (25350) for bucket 42 Calculating Z arrays for bucket 42 Sorting block time: 00:00:00 Returning block of 20309 for bucket 25 Entering block accumulator loop for bucket 42: Sorting block time: 00:00:00 Returning block of 24728 for bucket 14 Sorting block time: 00:00:00 Returning block of 18286 for bucket 15 Getting block 43 of 199 Reserving size (25350) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: bucket 37: 10% bucket 32: 20% Sorting block time: 00:00:00 Returning block of 24718 for bucket 8 bucket 29: 30% Getting block 44 of 199 Reserving size (25350) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: bucket 33: 20% bucket 38: 10% Sorting block time: 00:00:00 Returning block of 17005 for bucket 22 bucket 34: 20% bucket 39: 10% bucket 28: 50% Getting block 45 of 199 Reserving size (25350) for bucket 45 Calculating Z arrays for bucket 45 bucket 35: 20% Entering block accumulator loop for bucket 45: bucket 40: 10% bucket 41: 10% bucket 36: 20% Sorting block time: 00:00:00 Returning block of 23329 for bucket 19 bucket 31: 30% Sorting block time: 00:00:00 Returning block of 18543 for bucket 26 bucket 30: 30% Sorting block time: 00:00:00 bucket 42: 10% Returning block of 24026 for bucket 23 Getting block 46 of 199 Reserving size (25350) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: bucket 43: 10% Getting block 47 of 199 Reserving size (25350) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 29: 40% Getting block 48 of 199 Reserving size (25350) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Getting block 49 of 199 bucket 32: 30% Reserving size (25350) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: bucket 37: 20% bucket 28: 60% bucket 33: 30% Getting block 50 of 199 Reserving size (25350) for bucket 50 Calculating Z arrays for bucket 50 bucket 44: 10% Entering block accumulator loop for bucket 50: bucket 38: 20% bucket 34: 30% bucket 39: 20% bucket 35: 30% bucket 45: 10% bucket 40: 20% bucket 41: 20% bucket 31: 40% bucket 36: 30% bucket 30: 40% bucket 42: 20% bucket 46: 10% bucket 28: 70% bucket 43: 20% bucket 29: 50% bucket 32: 40% bucket 33: 40% bucket 37: 30% bucket 47: 10% bucket 44: 20% bucket 48: 10% bucket 49: 10% bucket 50: 10% bucket 31: 50% bucket 34: 40% bucket 35: 40% bucket 45: 20% bucket 39: 30% bucket 40: 30% bucket 38: 30% bucket 41: 30% Getting block 51 of 199 Reserving size (25350) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: Getting block 52 of 199 Reserving size (25350) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: Getting block 53 of 199 Reserving size (25350) for bucket 53 Calculating Z arrays for bucket 53 bucket 36: 40% Entering block accumulator loop for bucket 53: bucket 28: 80% Getting block 54 of 199 Reserving size (25350) for bucket 54 Calculating Z arrays for bucket 54 bucket 30: 50% Entering block accumulator loop for bucket 54: bucket 42: 30% bucket 29: 60% bucket 43: 30% bucket 32: 50% bucket 33: 50% bucket 37: 40% bucket 31: 60% bucket 44: 30% bucket 47: 20% bucket 49: 20% bucket 35: 50% bucket 34: 50% bucket 39: 40% bucket 40: 40% bucket 45: 30% bucket 41: 40% bucket 28: 90% bucket 38: 40% bucket 51: 10% bucket 52: 10% bucket 30: 60% bucket 36: 50% bucket 53: 10% bucket 42: 40% bucket 54: 10% bucket 29: 70% bucket 31: 70% bucket 43: 40% bucket 32: 60% bucket 33: 60% bucket 46: 20% bucket 37: 50% bucket 44: 40% bucket 47: 30% bucket 35: 60% bucket 34: 60% bucket 28: 100% Sorting block of length 24630 for bucket 28 (Using difference cover) bucket 49: 30% bucket 39: 50% bucket 40: 50% bucket 45: 40% bucket 41: 50% bucket 30: 70% bucket 38: 50% bucket 36: 60% bucket 31: 80% bucket 51: 20% bucket 52: 20% bucket 42: 50% bucket 29: 80% bucket 54: 20% bucket 53: 20% bucket 32: 70% bucket 43: 50% bucket 33: 70% bucket 37: 60% bucket 44: 50% Sorting block time: 00:00:00 Returning block of 24631 for bucket 28 bucket 46: 30% bucket 48: 20% bucket 34: 70% bucket 35: 70% bucket 47: 40% bucket 40: 60% bucket 39: 60% bucket 45: 50% bucket 49: 40% bucket 41: 60% bucket 31: 90% bucket 50: 20% bucket 30: 80% bucket 36: 70% bucket 38: 60% bucket 29: 90% bucket 42: 60% bucket 51: 30% bucket 52: 30% bucket 32: 80% bucket 54: 30% bucket 33: 80% bucket 53: 30% bucket 43: 60% Getting block 55 of 199 Reserving size (25350) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 37: 70% bucket 44: 60% bucket 48: 30% bucket 46: 40% bucket 34: 80% bucket 35: 80% bucket 31: 100% Sorting block of length 11774 for bucket 31 (Using difference cover) bucket 47: 50% bucket 40: 70% bucket 39: 70% bucket 41: 70% bucket 45: 60% bucket 49: 50% bucket 30: 90% bucket 50: 30% bucket 36: 80% bucket 38: 70% bucket 29: 100% Sorting block time: 00:00:00 Sorting block of length 21103 for bucket 29 (Using difference cover) Returning block of 11775 for bucket 31 bucket 42: 70% bucket 32: 90% bucket 52: 40% bucket 33: 90% bucket 51: 40% bucket 54: 40% bucket 55: 10% bucket 43: 70% bucket 53: 40% bucket 37: 80% bucket 44: 70% bucket 34: 90% bucket 35: 90% bucket 46: 50% bucket 48: 40% bucket 40: 80% bucket 41: 80% bucket 45: 70% bucket 39: 80% bucket 47: 60% bucket 30: 100% Sorting block of length 17604 for bucket 30 (Using difference cover) bucket 49: 60% Getting block 56 of 199 Reserving size (25350) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: Sorting block time: 00:00:00 Returning block of 21104 for bucket 29 bucket 36: 90% bucket 50: 40% bucket 38: 80% Getting block 57 of 199 Reserving size (25350) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 42: 80% bucket 55: 20% bucket 33: 100% Sorting block of length 8213 for bucket 33 (Using difference cover) bucket 32: 100% Sorting block of length 21659 for bucket 32 (Using difference cover) bucket 52: 50% bucket 51: 50% bucket 54: 50% bucket 43: 80% bucket 37: 90% bucket 44: 80% bucket 53: 50% bucket 34: 100% Sorting block of length 23329 for bucket 34 (Using difference cover) bucket 35: 100% Sorting block of length 19946 for bucket 35 (Using difference cover) Sorting block time: 00:00:00 Returning block of 8214 for bucket 33 Sorting block time: 00:00:00 Returning block of 17605 for bucket 30 bucket 48: 50% bucket 46: 60% Getting block 58 of 199 Reserving size (25350) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: bucket 41: 90% bucket 40: 90% bucket 45: 80% bucket 39: 90% Getting block 59 of 199 Reserving size (25350) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 47: 70% bucket 49: 70% bucket 57: 10% bucket 36: 100% Sorting block of length 22417 for bucket 36 (Using difference cover) bucket 55: 30% bucket 50: 50% bucket 56: 10% Sorting block time: 00:00:00 Returning block of 21660 for bucket 32 bucket 42: 90% bucket 38: 90% bucket 54: 60% bucket 52: 60% Sorting block time: 00:00:00 Returning block of 19947 for bucket 35 bucket 51: 60% bucket 37: 100% Sorting block of length 21247 for bucket 37 (Using difference cover) bucket 43: 90% Sorting block time: 00:00:00 Returning block of 23330 for bucket 34 bucket 44: 90% Getting block 60 of 199 Reserving size (25350) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 53: 60% Getting block 61 of 199 Reserving size (25350) for bucket 61 Calculating Z arrays for bucket 61 bucket 41: 100% bucket 46: 70% Sorting block of length 11492 for bucket 41 (Using difference cover) Entering block accumulator loop for bucket 61: bucket 48: 60% Getting block 62 of 199 bucket 40: 100% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (25350) for bucket 62 Sorting block of length 18974 for bucket 40 (Using difference cover) bucket 58: 10% bucket 45: 90% bucket 39: 100% bucket 47: 80% bucket 57: 20% bucket 59: 10% bucket 55: 40% bucket 49: 80% Returning block of 22418 for bucket 36 bucket 56: 20% bucket 42: 100% bucket 38: 100% Returning block of 11493 for bucket 41 Returning block of 21248 for bucket 37 bucket 50: 60% Calculating Z arrays for bucket 62 Sorting block of length 16958 for bucket 39 (Using difference cover) bucket 54: 70% bucket 52: 70% Sorting block of length 18355 for bucket 42 (Using difference cover) Sorting block of length 10363 for bucket 38 (Using difference cover) bucket 43: 100% bucket 51: 70% bucket 44: 100% Entering block accumulator loop for bucket 62: Sorting block of length 16339 for bucket 43 (Using difference cover) Sorting block of length 17568 for bucket 44 (Using difference cover) bucket 60: 10% bucket 53: 70% bucket 46: 80% bucket 48: 70% bucket 61: 10% Getting block 63 of 199 Reserving size (25350) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: Getting block 64 of 199 Reserving size (25350) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: Getting block 65 of 199 Reserving size (25350) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: Sorting block time: 00:00:00 Returning block of 18975 for bucket 40 bucket 57: 30% Sorting block time: 00:00:00 Returning block of 10364 for bucket 38 Getting block 66 of 199 Reserving size (25350) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: bucket 55: 50% bucket 58: 20% bucket 45: 100% Sorting block of length 8115 for bucket 45 (Using difference cover) Getting block 67 of 199 Reserving size (25350) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: bucket 47: 90% Sorting block time: 00:00:00 Returning block of 17569 for bucket 44 bucket 59: 20% bucket 49: 90% Sorting block time: 00:00:00 Returning block of 16959 for bucket 39 Sorting block time: 00:00:00 Returning block of 18356 for bucket 42 bucket 56: 30% bucket 50: 70% Sorting block time: 00:00:00 Returning block of 16340 for bucket 43 Getting block 68 of 199 Reserving size (25350) for bucket 68 Calculating Z arrays for bucket 68 bucket 54: 80% Entering block accumulator loop for bucket 68: Getting block 69 of 199 Reserving size (25350) for bucket 69 Calculating Z arrays for bucket 69 bucket 52: 80% Entering block accumulator loop for bucket 69: bucket 51: 80% bucket 60: 20% bucket 62: 10% Sorting block time: 00:00:00 Returning block of 8116 for bucket 45 bucket 46: 90% bucket 48: 80% bucket 53: 80% bucket 61: 20% Getting block 70 of 199 Reserving size (25350) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: bucket 64: 10% bucket 63: 10% bucket 65: 10% bucket 57: 40% Getting block 71 of 199 Reserving size (25350) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: bucket 55: 60% bucket 58: 30% bucket 66: 10% bucket 47: 100% Sorting block of length 21738 for bucket 47 (Using difference cover) bucket 67: 10% bucket 49: 100% Sorting block of length 23269 for bucket 49 (Using difference cover) bucket 59: 30% bucket 56: 40% bucket 50: 80% bucket 54: 90% bucket 52: 90% bucket 62: 20% bucket 51: 90% bucket 68: 10% bucket 69: 10% bucket 60: 30% bucket 46: 100% Sorting block of length 19105 for bucket 46 (Using difference cover) bucket 48: 90% bucket 57: 50% bucket 61: 30% bucket 53: 90% bucket 70: 10% bucket 64: 20% bucket 65: 20% bucket 55: 70% bucket 63: 20% bucket 71: 10% Sorting block time: 00:00:00 Returning block of 21739 for bucket 47 Getting block 72 of 199 Reserving size (25350) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 58: 40% bucket 66: 20% Getting block 73 of 199 Reserving size (25350) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: Sorting block time: 00:00:00 Returning block of 23270 for bucket 49 Sorting block time: 00:00:00 Returning block of 19106 for bucket 46 bucket 67: 20% bucket 59: 40% bucket 56: 50% bucket 50: 90% Getting block 74 of 199 Reserving size (25350) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: bucket 54: 100% Sorting block of length 23145 for bucket 54 (Using difference cover) bucket 57: 60% bucket 52: 100% Sorting block of length 21313 for bucket 52 (Using difference cover) bucket 62: 30% bucket 51: 100% bucket 60: 40% Sorting block of length 22757 for bucket 51 (Using difference cover) bucket 69: 20% bucket 68: 20% bucket 48: 100% Sorting block of length 22599 for bucket 48 (Using difference cover) bucket 55: 80% bucket 61: 40% bucket 53: 100% Sorting block of length 10298 for bucket 53 (Using difference cover) bucket 64: 30% bucket 70: 20% bucket 65: 30% bucket 63: 30% bucket 58: 50% bucket 71: 20% bucket 72: 10% Sorting block time: 00:00:00 Returning block of 10299 for bucket 53 bucket 66: 30% bucket 73: 10% Getting block 75 of 199 Reserving size (25350) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: Sorting block time: 00:00:00 Returning block of 21314 for bucket 52 bucket 57: 70% bucket 59: 50% bucket 67: 30% Sorting block time: 00:00:00 Returning block of 23146 for bucket 54 bucket 56: 60% bucket 50: 100% Sorting block of length 21800 for bucket 50 (Using difference cover) Getting block 76 of 199 Reserving size (25350) for bucket 76 Sorting block time: 00:00:00 Calculating Z arrays for bucket 76 Returning block of 22758 for bucket 51 Entering block accumulator loop for bucket 76: bucket 55: 90% Getting block 77 of 199 Reserving size (25350) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 74: 10% Getting block 78 of 199 Reserving size (25350) for bucket 78 Sorting block time: 00:00:00 Calculating Z arrays for bucket 78 Returning block of 22600 for bucket 48 Entering block accumulator loop for bucket 78: bucket 62: 40% bucket 60: 50% Getting block 79 of 199 Reserving size (25350) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 69: 30% Getting block 80 of 199 Reserving size (25350) for bucket 80 bucket 68: 30% Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 61: 50% bucket 64: 40% bucket 65: 40% bucket 70: 30% bucket 63: 40% bucket 58: 60% bucket 57: 80% bucket 71: 30% bucket 72: 20% bucket 66: 40% bucket 55: 100% Sorting block of length 22227 for bucket 55 (Using difference cover) bucket 73: 20% bucket 59: 60% Sorting block time: 00:00:00 Returning block of 21801 for bucket 50 bucket 75: 10% bucket 56: 70% bucket 67: 40% bucket 74: 20% Getting block 81 of 199 Reserving size (25350) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 76: 10% bucket 77: 10% bucket 60: 60% bucket 62: 50% bucket 78: 10% bucket 69: 40% bucket 79: 10% bucket 61: 60% bucket 68: 40% bucket 80: 10% bucket 64: 50% bucket 65: 50% bucket 70: 40% bucket 57: 90% Sorting block time: 00:00:00 Returning block of 22228 for bucket 55 bucket 63: 50% bucket 58: 70% bucket 71: 40% bucket 59: 70% bucket 66: 50% bucket 72: 30% bucket 73: 30% bucket 56: 80% bucket 75: 20% bucket 67: 50% bucket 74: 30% bucket 76: 20% bucket 60: 70% bucket 77: 20% bucket 62: 60% Getting block 82 of 199 Reserving size (25350) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 78: 20% bucket 69: 50% bucket 81: 10% bucket 61: 70% bucket 79: 20% bucket 57: 100% Sorting block of length 19517 for bucket 57 (Using difference cover) bucket 68: 50% bucket 64: 60% bucket 80: 20% bucket 65: 60% bucket 70: 50% bucket 58: 80% bucket 63: 60% bucket 59: 80% bucket 66: 60% bucket 71: 50% bucket 56: 90% bucket 73: 40% Sorting block time: 00:00:00 Returning block of 19518 for bucket 57 bucket 72: 40% bucket 75: 30% bucket 67: 60% Getting block 83 of 199 Reserving size (25350) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 74: 40% bucket 62: 70% bucket 60: 80% bucket 76: 30% bucket 77: 30% bucket 69: 60% bucket 82: 10% bucket 78: 30% bucket 61: 80% bucket 81: 20% bucket 79: 30% bucket 68: 60% bucket 64: 70% bucket 65: 70% bucket 80: 30% bucket 70: 60% bucket 58: 90% bucket 63: 70% bucket 59: 90% bucket 66: 70% bucket 56: 100% Sorting block of length 16885 for bucket 56 (Using difference cover) bucket 71: 60% bucket 83: 10% bucket 73: 50% bucket 72: 50% bucket 67: 70% bucket 75: 40% bucket 62: 80% bucket 60: 90% bucket 74: 50% bucket 76: 40% bucket 77: 40% bucket 69: 70% bucket 61: 90% bucket 78: 40% bucket 82: 20% bucket 79: 40% bucket 64: 80% bucket 68: 70% bucket 81: 30% bucket 65: 80% bucket 58: 100% Sorting block of length 11176 for bucket 58 (Using difference cover) bucket 80: 40% Sorting block time: 00:00:00 Returning block of 16886 for bucket 56 bucket 70: 70% bucket 63: 80% Getting block 84 of 199 Reserving size (25350) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 83: 20% bucket 59: 100% Sorting block of length 17768 for bucket 59 (Using difference cover) bucket 66: 80% bucket 71: 70% bucket 73: 60% Sorting block time: 00:00:00 Returning block of 11177 for bucket 58 bucket 72: 60% bucket 67: 80% bucket 75: 50% bucket 60: 100% Sorting block of length 20382 for bucket 60 (Using difference cover) bucket 62: 90% bucket 74: 60% Getting block 85 of 199 Reserving size (25350) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 76: 50% bucket 61: 100% Sorting block of length 25236 for bucket 61 (Using difference cover) bucket 69: 80% bucket 77: 50% bucket 78: 50% bucket 82: 30% bucket 64: 90% bucket 65: 90% bucket 79: 50% bucket 68: 80% Sorting block time: 00:00:00 Returning block of 17769 for bucket 59 bucket 80: 50% bucket 70: 80% Getting block 86 of 199 bucket 81: 40% Reserving size (25350) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 83: 30% bucket 63: 90% bucket 84: 10% Sorting block time: 00:00:00 Returning block of 20383 for bucket 60 bucket 66: 90% bucket 71: 80% bucket 73: 70% Getting block 87 of 199 Reserving size (25350) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 72: 70% bucket 62: 100% Sorting block of length 23955 for bucket 62 (Using difference cover) bucket 75: 60% bucket 67: 90% bucket 74: 70% Sorting block time: 00:00:00 Returning block of 25237 for bucket 61 bucket 69: 90% bucket 85: 10% bucket 77: 60% bucket 78: 60% Getting block 88 of 199 Reserving size (25350) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 64: 100% Sorting block of length 20721 for bucket 64 (Using difference cover) bucket 76: 60% bucket 82: 40% bucket 65: 100% Sorting block of length 10471 for bucket 65 (Using difference cover) bucket 79: 60% bucket 83: 40% bucket 68: 90% bucket 70: 90% bucket 80: 60% bucket 86: 10% bucket 81: 50% Sorting block time: 00:00:00 Returning block of 10472 for bucket 65 bucket 63: 100% Sorting block of length 21312 for bucket 63 (Using difference cover) bucket 66: 100% Sorting block of length 16417 for bucket 66 (Using difference cover) Getting block 89 of 199 Reserving size (25350) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 84: 20% bucket 73: 80% bucket 71: 90% Sorting block time: 00:00:00 Returning block of 23956 for bucket 62 bucket 87: 10% bucket 67: 100% bucket 72: 80% Sorting block of length 15664 for bucket 67 (Using difference cover) bucket 75: 70% bucket 74: 80% Getting block 90 of 199 Reserving size (25350) for bucket 90 Calculating Z arrays for bucket 90 Sorting block time: 00:00:00 Returning block of 20722 for bucket 64 Entering block accumulator loop for bucket 90: bucket 85: 20% bucket 83: 50% bucket 69: 100% Sorting block of length 976 for bucket 69 (Using difference cover) bucket 77: 70% bucket 78: 70% Sorting block time: 00:00:00 Returning block of 977 for bucket 69 Getting block 91 of 199 Reserving size (25350) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 82: 50% bucket 88: 10% bucket 79: 70% bucket 68: 100% Sorting block of length 24689 for bucket 68 (Using difference cover) bucket 76: 70% Sorting block time: 00:00:00 Returning block of 16418 for bucket 66 bucket 70: 100% Sorting block of length 25188 for bucket 70 (Using difference cover) Sorting block time: 00:00:00 Returning block of 21313 for bucket 63 bucket 80: 70% Getting block 92 of 199 Reserving size (25350) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: bucket 86: 20% Sorting block time: 00:00:00 Returning block of 15665 for bucket 67 bucket 81: 60% Getting block 93 of 199 Reserving size (25350) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: Getting block 94 of 199 Reserving size (25350) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: bucket 73: 90% bucket 89: 10% bucket 84: 30% Getting block 95 of 199 Reserving size (25350) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 71: 100% Sorting block of length 12613 for bucket 71 (Using difference cover) bucket 83: 60% bucket 74: 90% bucket 87: 20% bucket 72: 90% bucket 75: 80% Sorting block time: 00:00:00 Returning block of 24690 for bucket 68 bucket 90: 10% bucket 85: 30% bucket 77: 80% bucket 78: 80% bucket 82: 60% bucket 79: 80% bucket 76: 80% Sorting block time: 00:00:00 Returning block of 25189 for bucket 70 bucket 91: 10% bucket 88: 20% Sorting block time: 00:00:00 Returning block of 12614 for bucket 71 bucket 80: 80% Getting block 96 of 199 bucket 86: 30% Reserving size (25350) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 92: 10% bucket 81: 70% Getting block 97 of 199 Reserving size (25350) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: bucket 93: 10% bucket 73: 100% Sorting block of length 23448 for bucket 73 (Using difference cover) bucket 83: 70% bucket 94: 10% bucket 84: 40% bucket 89: 20% bucket 74: 100% Sorting block of length 9734 for bucket 74 (Using difference cover) bucket 75: 90% bucket 72: 100% Sorting block of length 23315 for bucket 72 (Using difference cover) bucket 87: 30% bucket 90: 20% bucket 95: 10% bucket 85: 40% bucket 77: 90% bucket 78: 90% Getting block 98 of 199 Reserving size (25350) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 82: 70% Sorting block time: 00:00:00 Returning block of 9735 for bucket 74 bucket 79: 90% bucket 76: 90% bucket 91: 20% bucket 88: 30% Getting block 99 of 199 Reserving size (25350) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: bucket 80: 90% bucket 83: 80% bucket 86: 40% Sorting block time: 00:00:00 Returning block of 23449 for bucket 73 bucket 92: 20% bucket 96: 10% bucket 97: 10% bucket 93: 20% bucket 84: 50% Sorting block time: 00:00:00 Returning block of 23316 for bucket 72 Getting block 100 of 199 Reserving size (25350) for bucket 100 bucket 81: 80% Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: bucket 89: 30% bucket 94: 20% Getting block 101 of 199 Reserving size (25350) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 75: 100% Sorting block of length 22724 for bucket 75 (Using difference cover) bucket 87: 40% bucket 85: 50% bucket 77: 100% Sorting block of length 24991 for bucket 77 (Using difference cover) bucket 78: 100% Sorting block of length 24110 for bucket 78 (Using difference cover) bucket 90: 30% bucket 95: 20% bucket 98: 10% bucket 79: 100% Sorting block of length 15174 for bucket 79 (Using difference cover) bucket 76: 100% bucket 82: 80% Sorting block of length 25224 for bucket 76 (Using difference cover) bucket 83: 90% bucket 91: 30% bucket 88: 40% bucket 80: 100% Sorting block of length 23910 for bucket 80 (Using difference cover) bucket 99: 10% bucket 86: 50% bucket 92: 30% bucket 97: 20% bucket 96: 20% bucket 84: 60% bucket 93: 30% Sorting block time: 00:00:00 Returning block of 22725 for bucket 75 Sorting block time: 00:00:00 Returning block of 15175 for bucket 79 bucket 81: 90% bucket 101: 10% bucket 100: 10% bucket 89: 40% Getting block 102 of 199 Reserving size (25350) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 94: 30% Getting block 103 of 199 Reserving size (25350) for bucket 103 Calculating Z arrays for bucket 103 Sorting block time: 00:00:00 Returning block of 24111 for bucket 78 Entering block accumulator loop for bucket 103: Sorting block time: 00:00:00 Returning block of 24992 for bucket 77 bucket 85: 60% bucket 87: 50% bucket 90: 40% bucket 83: 100% Sorting block of length 25215 for bucket 83 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25225 for bucket 76 bucket 82: 90% bucket 95: 30% Sorting block time: 00:00:00 Returning block of 23911 for bucket 80 Getting block 104 of 199 Reserving size (25350) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: Getting block 105 of 199 Reserving size (25350) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 91: 40% bucket 98: 20% bucket 88: 50% bucket 99: 20% bucket 86: 60% bucket 92: 40% bucket 84: 70% bucket 101: 20% bucket 96: 30% bucket 97: 30% bucket 93: 40% bucket 81: 100% Sorting block of length 24696 for bucket 81 (Using difference cover) bucket 100: 20% Sorting block time: 00:00:00 Returning block of 25216 for bucket 83 bucket 89: 50% Getting block 106 of 199 Reserving size (25350) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 102: 10% bucket 103: 10% Getting block 107 of 199 Reserving size (25350) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 94: 40% bucket 85: 70% bucket 87: 60% bucket 90: 50% bucket 105: 10% bucket 82: 100% bucket 104: 10% Sorting block of length 22535 for bucket 82 (Using difference cover) bucket 95: 40% bucket 91: 50% bucket 88: 60% bucket 98: 30% bucket 86: 70% bucket 99: 30% bucket 101: 30% Sorting block time: 00:00:00 Returning block of 24697 for bucket 81 bucket 92: 50% bucket 84: 80% Getting block 108 of 199 Reserving size (25350) for bucket 108 Calculating Z arrays for bucket 108 bucket 106: 10% Entering block accumulator loop for bucket 108: bucket 96: 40% bucket 93: 50% bucket 97: 40% bucket 102: 20% bucket 103: 20% bucket 100: 30% bucket 107: 10% bucket 89: 60% bucket 85: 80% Sorting block time: 00:00:00 Returning block of 22536 for bucket 82 bucket 94: 50% bucket 105: 20% bucket 104: 20% bucket 87: 70% bucket 90: 60% bucket 98: 40% Getting block 109 of 199 Reserving size (25350) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 91: 60% bucket 95: 50% bucket 88: 70% bucket 106: 20% Getting block 110 of 199 Reserving size (25350) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 101: 40% bucket 86: 80% bucket 108: 10% bucket 84: 90% bucket 99: 40% bucket 92: 60% bucket 102: 30% bucket 103: 30% bucket 93: 60% bucket 96: 50% bucket 107: 20% bucket 97: 50% bucket 100: 40% bucket 89: 70% bucket 105: 30% bucket 85: 90% bucket 104: 30% bucket 87: 80% bucket 90: 70% bucket 94: 60% bucket 106: 30% bucket 109: 10% bucket 98: 50% bucket 91: 70% bucket 101: 50% bucket 88: 80% bucket 95: 60% bucket 110: 10% bucket 108: 20% bucket 86: 90% bucket 84: 100% Sorting block of length 3467 for bucket 84 (Using difference cover) bucket 102: 40% bucket 92: 70% bucket 103: 40% bucket 107: 30% bucket 99: 50% Sorting block time: 00:00:00 Returning block of 3468 for bucket 84 bucket 105: 40% bucket 93: 70% Getting block 111 of 199 Reserving size (25350) for bucket 111 Calculating Z arrays for bucket 111 bucket 96: 60% Entering block accumulator loop for bucket 111: bucket 104: 40% bucket 100: 50% bucket 97: 60% bucket 89: 80% bucket 85: 100% Sorting block of length 24533 for bucket 85 (Using difference cover) bucket 106: 40% bucket 98: 60% bucket 109: 20% bucket 87: 90% bucket 90: 80% bucket 94: 70% bucket 101: 60% bucket 91: 80% bucket 110: 20% bucket 108: 30% bucket 88: 90% bucket 86: 100% Sorting block of length 24673 for bucket 86 (Using difference cover) bucket 95: 70% bucket 102: 50% bucket 103: 50% bucket 107: 40% bucket 105: 50% bucket 92: 80% bucket 106: 50% bucket 104: 50% Sorting block time: 00:00:00 bucket 111: 10% Returning block of 24534 for bucket 85 bucket 99: 60% bucket 93: 80% bucket 100: 60% bucket 96: 70% Getting block 112 of 199 Reserving size (25350) for bucket 112 Calculating Z arrays for bucket 112 bucket 97: 70% Entering block accumulator loop for bucket 112: bucket 89: 90% bucket 98: 70% bucket 109: 30% bucket 87: 100% Sorting block of length 24306 for bucket 87 (Using difference cover) bucket 101: 70% bucket 90: 90% bucket 94: 80% bucket 110: 30% bucket 108: 40% Sorting block time: 00:00:00 Returning block of 24674 for bucket 86 bucket 91: 90% bucket 88: 100% bucket 106: 60% Sorting block of length 24810 for bucket 88 (Using difference cover) bucket 102: 60% Getting block 113 of 199 Reserving size (25350) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 105: 60% bucket 103: 60% bucket 107: 50% bucket 95: 80% bucket 104: 60% bucket 111: 20% bucket 92: 90% bucket 98: 80% bucket 112: 10% bucket 93: 90% bucket 100: 70% bucket 99: 70% bucket 109: 40% bucket 96: 80% bucket 89: 100% Sorting block of length 16453 for bucket 89 (Using difference cover) bucket 97: 80% Sorting block time: 00:00:00 Returning block of 24307 for bucket 87 bucket 101: 80% Getting block 114 of 199 Reserving size (25350) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 110: 40% bucket 108: 50% bucket 106: 70% bucket 90: 100% Sorting block of length 23138 for bucket 90 (Using difference cover) bucket 94: 90% Sorting block time: 00:00:00 Returning block of 24811 for bucket 88 bucket 91: 100% Sorting block of length 16776 for bucket 91 (Using difference cover) bucket 105: 70% bucket 102: 70% bucket 113: 10% bucket 107: 60% bucket 103: 70% Sorting block time: 00:00:00 bucket 104: 70% Returning block of 16454 for bucket 89 bucket 111: 30% bucket 95: 90% bucket 98: 90% bucket 92: 100% Sorting block of length 16234 for bucket 92 (Using difference cover) bucket 112: 20% bucket 109: 50% bucket 100: 80% Getting block 115 of 199 Reserving size (25350) for bucket 115 Calculating Z arrays for bucket 115 Getting block 116 of 199 Reserving size (25350) for bucket 116 Entering block accumulator loop for bucket 115: Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: bucket 93: 100% Sorting block of length 9996 for bucket 93 (Using difference cover) bucket 96: 90% bucket 99: 80% bucket 106: 80% bucket 101: 90% bucket 97: 90% bucket 114: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 16777 for bucket 91 Returning block of 23139 for bucket 90 bucket 110: 50% bucket 108: 60% Getting block 117 of 199 Reserving size (25350) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: bucket 105: 80% Sorting block time: 00:00:00 Returning block of 9997 for bucket 93 bucket 102: 80% Sorting block time: 00:00:00 Returning block of 16235 for bucket 92 bucket 113: 20% bucket 107: 70% Getting block 118 of 199 Reserving size (25350) for bucket 118 Calculating Z arrays for bucket 118 bucket 94: 100% Entering block accumulator loop for bucket 118: Sorting block of length 22709 for bucket 94 (Using difference cover) bucket 103: 80% Getting block 119 of 199 Reserving size (25350) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: bucket 104: 80% bucket 111: 40% bucket 98: 100% Sorting block of length 13491 for bucket 98 (Using difference cover) bucket 109: 60% bucket 112: 30% bucket 106: 90% bucket 95: 100% Sorting block of length 19153 for bucket 95 (Using difference cover) bucket 116: 10% bucket 115: 10% bucket 100: 90% bucket 101: 100% Sorting block of length 19652 for bucket 101 (Using difference cover) bucket 110: 60% bucket 114: 20% bucket 108: 70% bucket 96: 100% Sorting block of length 10493 for bucket 96 (Using difference cover) Sorting block time: 00:00:00 Returning block of 13492 for bucket 98 bucket 99: 90% bucket 97: 100% Sorting block of length 25205 for bucket 97 (Using difference cover) Getting block 120 of 199 Reserving size (25350) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: Getting block 121 of 199 Reserving size (25350) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 105: 90% bucket 117: 10% Sorting block time: 00:00:00 Returning block of 22710 for bucket 94 bucket 102: 90% bucket 113: 30% bucket 118: 10% bucket 107: 80% bucket 119: 10% Getting block 122 of 199 bucket 103: 90% Reserving size (25350) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: Sorting block time: 00:00:00 Returning block of 10494 for bucket 96 bucket 104: 90% Sorting block time: 00:00:00 Returning block of 19154 for bucket 95 bucket 106: 100% Sorting block of length 21677 for bucket 106 (Using difference cover) bucket 111: 50% bucket 109: 70% Getting block 123 of 199 Reserving size (25350) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: Sorting block time: 00:00:00 Returning block of 19653 for bucket 101 bucket 112: 40% bucket 116: 20% Getting block 124 of 199 Reserving size (25350) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 115: 20% bucket 121: 10% bucket 110: 70% bucket 114: 30% bucket 100: 100% bucket 108: 80% Sorting block of length 21482 for bucket 100 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25206 for bucket 97 bucket 120: 10% bucket 105: 100% Sorting block of length 5919 for bucket 105 (Using difference cover) Getting block 125 of 199 Reserving size (25350) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: bucket 99: 100% Sorting block of length 23878 for bucket 99 (Using difference cover) bucket 117: 20% Sorting block time: 00:00:00 Returning block of 21678 for bucket 106 bucket 118: 20% bucket 102: 100% Sorting block of length 23569 for bucket 102 (Using difference cover) bucket 113: 40% bucket 119: 20% bucket 107: 90% Sorting block time: 00:00:00 Returning block of 5920 for bucket 105 bucket 103: 100% Sorting block of length 22759 for bucket 103 (Using difference cover) bucket 122: 10% Getting block 126 of 199 Reserving size (25350) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: bucket 104: 100% Sorting block of length 21769 for bucket 104 (Using difference cover) Getting block 127 of 199 Reserving size (25350) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 109: 80% bucket 123: 10% bucket 111: 60% bucket 112: 50% bucket 121: 20% Sorting block time: 00:00:00 Returning block of 21483 for bucket 100 bucket 116: 30% bucket 124: 10% bucket 115: 30% Getting block 128 of 199 Reserving size (25350) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: bucket 110: 80% Getting block 129 of 199 Reserving size (25350) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: bucket 108: 90% bucket 114: 40% bucket 120: 20% Sorting block time: 00:00:00 Returning block of 23879 for bucket 99 bucket 118: 30% Getting block 130 of 199 Reserving size (25350) for bucket 130 Calculating Z arrays for bucket 130 Sorting block time: 00:00:00 Returning block of 23570 for bucket 102 Entering block accumulator loop for bucket 130: bucket 126: 10% bucket 119: 30% Sorting block time: 00:00:00 Returning block of 22760 for bucket 103 bucket 125: 10% bucket 117: 30% Sorting block time: 00:00:00 Returning block of 21770 for bucket 104 bucket 113: 50% bucket 107: 100% Sorting block of length 21247 for bucket 107 (Using difference cover) bucket 122: 20% Getting block 131 of 199 Reserving size (25350) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: Getting block 132 of 199 Reserving size (25350) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 127: 10% bucket 121: 30% bucket 123: 20% bucket 109: 90% bucket 111: 70% bucket 112: 60% Getting block 133 of 199 Reserving size (25350) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 116: 40% bucket 124: 20% bucket 110: 90% bucket 128: 10% bucket 115: 40% bucket 120: 30% bucket 108: 100% bucket 129: 10% Sorting block of length 23365 for bucket 108 (Using difference cover) bucket 114: 50% bucket 126: 20% bucket 118: 40% Sorting block time: 00:00:00 Returning block of 21248 for bucket 107 bucket 119: 40% bucket 130: 10% bucket 113: 60% bucket 121: 40% Getting block 134 of 199 Reserving size (25350) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 122: 30% bucket 117: 40% bucket 125: 20% bucket 131: 10% bucket 123: 30% bucket 127: 20% bucket 132: 10% bucket 109: 100% Sorting block of length 20549 for bucket 109 (Using difference cover) bucket 111: 80% bucket 112: 70% bucket 133: 10% bucket 116: 50% bucket 110: 100% Sorting block of length 16653 for bucket 110 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23366 for bucket 108 bucket 124: 30% bucket 120: 40% bucket 128: 20% bucket 114: 60% bucket 129: 20% bucket 126: 30% bucket 115: 50% bucket 118: 50% bucket 121: 50% bucket 119: 50% bucket 130: 20% bucket 122: 40% bucket 113: 70% Sorting block time: 00:00:00 Returning block of 20550 for bucket 109 bucket 134: 10% bucket 117: 50% bucket 125: 30% bucket 123: 40% bucket 131: 20% bucket 127: 30% bucket 132: 20% Sorting block time: 00:00:00 Returning block of 16654 for bucket 110 Getting block 135 of 199 Reserving size (25350) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 111: 90% Getting block 136 of 199 Reserving size (25350) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 112: 80% bucket 126: 40% bucket 116: 60% bucket 120: 50% bucket 121: 60% bucket 124: 40% bucket 133: 20% bucket 128: 30% bucket 114: 70% bucket 129: 30% bucket 115: 60% bucket 118: 60% bucket 119: 60% bucket 130: 30% bucket 122: 50% bucket 113: 80% bucket 123: 50% bucket 117: 60% bucket 125: 40% bucket 134: 20% bucket 131: 30% bucket 127: 40% bucket 132: 30% Getting block 137 of 199 Reserving size (25350) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 111: 100% Sorting block of length 21053 for bucket 111 (Using difference cover) bucket 121: 70% bucket 126: 50% bucket 135: 10% bucket 112: 90% bucket 120: 60% bucket 136: 10% bucket 116: 70% bucket 124: 50% bucket 118: 70% bucket 128: 40% bucket 114: 80% bucket 133: 30% bucket 129: 40% bucket 115: 70% bucket 119: 70% bucket 130: 40% bucket 122: 60% bucket 113: 90% bucket 123: 60% bucket 117: 70% bucket 125: 50% bucket 134: 30% bucket 121: 80% bucket 131: 40% bucket 127: 50% Sorting block time: 00:00:00 Returning block of 21054 for bucket 111 bucket 126: 60% bucket 132: 40% Getting block 138 of 199 Reserving size (25350) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 120: 70% bucket 137: 10% bucket 112: 100% Sorting block of length 23219 for bucket 112 (Using difference cover) bucket 116: 80% bucket 136: 20% bucket 118: 80% bucket 124: 60% bucket 135: 20% bucket 114: 90% bucket 128: 50% bucket 129: 50% bucket 133: 40% bucket 119: 80% bucket 115: 80% bucket 130: 50% bucket 122: 70% bucket 121: 90% bucket 123: 70% bucket 113: 100% Sorting block of length 12885 for bucket 113 (Using difference cover) bucket 126: 70% bucket 117: 80% bucket 125: 60% bucket 127: 60% bucket 131: 50% bucket 134: 40% bucket 132: 50% bucket 120: 80% Sorting block time: 00:00:00 Returning block of 23220 for bucket 112 bucket 138: 10% Sorting block time: 00:00:00 Returning block of 12886 for bucket 113 bucket 118: 90% bucket 137: 20% bucket 116: 90% bucket 124: 70% Getting block 139 of 199 Reserving size (25350) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 136: 30% bucket 119: 90% bucket 114: 100% Sorting block of length 19033 for bucket 114 (Using difference cover) bucket 128: 60% bucket 129: 60% bucket 133: 50% bucket 121: 100% Sorting block of length 22869 for bucket 121 (Using difference cover) bucket 115: 90% Getting block 140 of 199 Reserving size (25350) for bucket 140 Calculating Z arrays for bucket 140 bucket 135: 30% Entering block accumulator loop for bucket 140: bucket 122: 80% bucket 130: 60% bucket 126: 80% bucket 123: 80% bucket 117: 90% bucket 125: 70% bucket 127: 70% bucket 131: 60% bucket 134: 50% bucket 132: 60% bucket 120: 90% Sorting block time: 00:00:00 Returning block of 19034 for bucket 114 bucket 118: 100% Sorting block of length 10954 for bucket 118 (Using difference cover) Sorting block time: 00:00:00 Returning block of 22870 for bucket 121 bucket 116: 100% Sorting block of length 15142 for bucket 116 (Using difference cover) bucket 138: 20% bucket 119: 100% Sorting block of length 23802 for bucket 119 (Using difference cover) Getting block 141 of 199 Reserving size (25350) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 124: 80% bucket 137: 30% bucket 129: 70% bucket 128: 70% bucket 136: 40% bucket 139: 10% bucket 126: 90% bucket 122: 90% bucket 115: 100% Sorting block of length 23454 for bucket 115 (Using difference cover) bucket 133: 60% bucket 130: 70% bucket 140: 10% Sorting block time: 00:00:00 Returning block of 10955 for bucket 118 bucket 123: 90% bucket 135: 40% bucket 117: 100% Sorting block of length 24287 for bucket 117 (Using difference cover) bucket 125: 80% Sorting block time: 00:00:00 Returning block of 15143 for bucket 116 Getting block 142 of 199 Reserving size (25350) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 127: 80% bucket 131: 70% bucket 120: 100% Sorting block of length 20388 for bucket 120 (Using difference cover) Getting block 143 of 199 Reserving size (25350) for bucket 143 Calculating Z arrays for bucket 143 bucket 132: 70% Entering block accumulator loop for bucket 143: bucket 134: 60% Sorting block time: 00:00:00 Returning block of 23803 for bucket 119 bucket 126: 100% Sorting block of length 24957 for bucket 126 (Using difference cover) bucket 124: 90% bucket 138: 30% Sorting block time: 00:00:00 Returning block of 23455 for bucket 115 Getting block 144 of 199 Reserving size (25350) for bucket 144 bucket 141: 10% Calculating Z arrays for bucket 144 bucket 129: 80% Entering block accumulator loop for bucket 144: bucket 128: 80% bucket 122: 100% Sorting block of length 21882 for bucket 122 (Using difference cover) bucket 137: 40% bucket 139: 20% bucket 136: 50% bucket 130: 80% Getting block 145 of 199 Reserving size (25350) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 133: 70% bucket 123: 100% Sorting block of length 14070 for bucket 123 (Using difference cover) bucket 140: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 142: 10% Returning block of 24288 for bucket 117 Returning block of 20389 for bucket 120 bucket 125: 90% bucket 135: 50% bucket 127: 90% Getting block 146 of 199 Reserving size (25350) for bucket 146 Calculating Z arrays for bucket 146 bucket 131: 80% Entering block accumulator loop for bucket 146: Getting block 147 of 199 Reserving size (25350) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 132: 80% bucket 134: 70% Sorting block time: 00:00:00 Returning block of 24958 for bucket 126 bucket 143: 10% Sorting block time: 00:00:00 Returning block of 14071 for bucket 123 bucket 124: 100% Sorting block time: 00:00:00 Sorting block of length 24580 for bucket 124 (Using difference cover) Returning block of 21883 for bucket 122 bucket 129: 90% bucket 128: 90% bucket 141: 20% bucket 144: 10% bucket 130: 90% bucket 138: 40% Getting block 148 of 199 Reserving size (25350) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: Getting block 149 of 199 Reserving size (25350) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: bucket 136: 60% Getting block 150 of 199 Reserving size (25350) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 139: 30% bucket 137: 50% bucket 145: 10% bucket 142: 20% bucket 133: 80% bucket 140: 30% bucket 125: 100% Sorting block of length 24178 for bucket 125 (Using difference cover) bucket 127: 100% Sorting block of length 13471 for bucket 127 (Using difference cover) bucket 146: 10% bucket 132: 90% bucket 131: 90% bucket 147: 10% bucket 134: 80% bucket 135: 60% bucket 143: 20% Sorting block time: 00:00:00 Returning block of 24581 for bucket 124 bucket 129: 100% Sorting block of length 14178 for bucket 129 (Using difference cover) bucket 128: 100% Sorting block of length 16147 for bucket 128 (Using difference cover) Sorting block time: 00:00:00 Returning block of 13472 for bucket 127 bucket 130: 100% Sorting block of length 15898 for bucket 130 (Using difference cover) bucket 149: 10% bucket 144: 20% bucket 142: 30% bucket 148: 10% bucket 141: 30% bucket 138: 50% bucket 136: 70% bucket 133: 90% bucket 139: 40% bucket 145: 20% Getting block 151 of 199 Reserving size (25350) for bucket 151 Calculating Z arrays for bucket 151 bucket 137: 60% Entering block accumulator loop for bucket 151: bucket 150: 10% Getting block 152 of 199 Reserving size (25350) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: Getting block 153 of 199 bucket 140: 40% Reserving size (25350) for bucket 153 Sorting block time: 00:00:00 Calculating Z arrays for bucket 153 Returning block of 24179 for bucket 125 Entering block accumulator loop for bucket 153: bucket 132: 100% Sorting block of length 19584 for bucket 132 (Using difference cover) bucket 131: 100% Sorting block of length 14646 for bucket 131 (Using difference cover) bucket 146: 20% Getting block 154 of 199 Reserving size (25350) for bucket 154 Calculating Z arrays for bucket 154 Sorting block time: 00:00:00 Returning block of 14179 for bucket 129 Entering block accumulator loop for bucket 154: bucket 134: 90% bucket 147: 20% Sorting block time: 00:00:00 Returning block of 16148 for bucket 128 Sorting block time: 00:00:00 Returning block of 15899 for bucket 130 Getting block 155 of 199 Reserving size (25350) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: bucket 135: 70% Getting block 156 of 199 Reserving size (25350) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 149: 20% bucket 143: 30% bucket 142: 40% Getting block 157 of 199 Reserving size (25350) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 148: 20% Sorting block time: 00:00:00 Returning block of 14647 for bucket 131 bucket 141: 40% bucket 144: 30% bucket 138: 60% bucket 133: 100% Sorting block of length 23736 for bucket 133 (Using difference cover) bucket 136: 80% bucket 145: 30% bucket 151: 10% bucket 139: 50% Getting block 158 of 199 Reserving size (25350) for bucket 158 Calculating Z arrays for bucket 158 bucket 152: 10% Entering block accumulator loop for bucket 158: bucket 137: 70% Sorting block time: 00:00:00 Returning block of 19585 for bucket 132 bucket 140: 50% bucket 150: 20% bucket 153: 10% Getting block 159 of 199 Reserving size (25350) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 146: 30% bucket 134: 100% Sorting block of length 23312 for bucket 134 (Using difference cover) bucket 154: 10% bucket 147: 30% bucket 149: 30% bucket 155: 10% bucket 142: 50% bucket 156: 10% bucket 135: 80% bucket 143: 40% bucket 157: 10% bucket 148: 30% bucket 141: 50% bucket 138: 70% Sorting block time: 00:00:00 bucket 144: 40% Returning block of 23737 for bucket 133 bucket 158: 10% bucket 145: 40% bucket 136: 90% bucket 151: 20% bucket 152: 20% bucket 139: 60% bucket 137: 80% bucket 140: 60% Sorting block time: 00:00:00 Returning block of 23313 for bucket 134 Getting block 160 of 199 Reserving size (25350) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 153: 20% bucket 159: 10% bucket 150: 30% Getting block 161 of 199 bucket 146: 40% Reserving size (25350) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 149: 40% bucket 154: 20% bucket 147: 40% bucket 142: 60% bucket 155: 20% bucket 156: 20% bucket 157: 20% bucket 143: 50% bucket 135: 90% bucket 148: 40% bucket 158: 20% bucket 141: 60% bucket 145: 50% bucket 138: 80% bucket 152: 30% bucket 136: 100% Sorting block of length 17198 for bucket 136 (Using difference cover) bucket 151: 30% bucket 144: 50% bucket 139: 70% bucket 137: 90% bucket 140: 70% bucket 159: 20% bucket 149: 50% bucket 153: 30% bucket 160: 10% bucket 161: 10% bucket 142: 70% bucket 146: 50% bucket 150: 40% bucket 154: 30% bucket 147: 50% bucket 155: 30% bucket 156: 30% Sorting block time: 00:00:00 Returning block of 17199 for bucket 136 bucket 157: 30% bucket 143: 60% Getting block 162 of 199 Reserving size (25350) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 148: 50% bucket 158: 30% bucket 135: 100% Sorting block of length 12539 for bucket 135 (Using difference cover) bucket 141: 70% bucket 152: 40% bucket 145: 60% bucket 151: 40% bucket 149: 60% bucket 138: 90% bucket 139: 80% bucket 159: 30% bucket 144: 60% bucket 140: 80% bucket 142: 80% bucket 137: 100% Sorting block of length 24408 for bucket 137 (Using difference cover) bucket 160: 20% bucket 153: 40% bucket 161: 20% bucket 146: 60% bucket 154: 40% bucket 150: 50% Sorting block time: 00:00:00 Returning block of 12540 for bucket 135 bucket 147: 60% bucket 155: 40% Getting block 163 of 199 Reserving size (25350) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: bucket 156: 40% bucket 157: 40% bucket 162: 10% bucket 143: 70% bucket 148: 60% bucket 158: 40% bucket 149: 70% bucket 152: 50% bucket 142: 90% bucket 145: 70% bucket 141: 80% bucket 151: 50% Sorting block time: 00:00:00 Returning block of 24409 for bucket 137 bucket 159: 40% bucket 138: 100% Sorting block of length 12619 for bucket 138 (Using difference cover) bucket 144: 70% bucket 140: 90% bucket 139: 90% bucket 160: 30% bucket 153: 50% Getting block 164 of 199 bucket 161: 30% Reserving size (25350) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 146: 70% bucket 154: 50% bucket 147: 70% bucket 155: 50% bucket 150: 60% bucket 163: 10% Sorting block time: 00:00:00 Returning block of 12620 for bucket 138 bucket 157: 50% bucket 156: 50% Getting block 165 of 199 Reserving size (25350) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 162: 20% bucket 149: 80% bucket 158: 50% bucket 148: 70% bucket 143: 80% bucket 142: 100% Sorting block of length 17981 for bucket 142 (Using difference cover) bucket 152: 60% bucket 145: 80% bucket 151: 60% bucket 159: 50% bucket 141: 90% bucket 140: 100% Sorting block of length 23575 for bucket 140 (Using difference cover) bucket 160: 40% bucket 144: 80% bucket 139: 100% Sorting block of length 22118 for bucket 139 (Using difference cover) bucket 153: 60% bucket 164: 10% bucket 161: 40% bucket 154: 60% Sorting block time: 00:00:00 Returning block of 17982 for bucket 142 bucket 147: 80% bucket 146: 80% bucket 155: 60% Getting block 166 of 199 Reserving size (25350) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 163: 20% bucket 150: 70% bucket 149: 90% bucket 157: 60% bucket 156: 60% bucket 162: 30% bucket 165: 10% bucket 158: 60% bucket 148: 80% bucket 143: 90% bucket 152: 70% Sorting block time: 00:00:00 Returning block of 22119 for bucket 139 Sorting block time: 00:00:00 Returning block of 23576 for bucket 140 bucket 145: 90% bucket 159: 60% bucket 151: 70% bucket 141: 100% Sorting block of length 19885 for bucket 141 (Using difference cover) bucket 160: 50% bucket 144: 90% bucket 153: 70% Getting block 167 of 199 Reserving size (25350) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: bucket 164: 20% bucket 161: 50% Getting block 168 of 199 Reserving size (25350) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 166: 10% bucket 154: 70% bucket 149: 100% Sorting block of length 19165 for bucket 149 (Using difference cover) bucket 147: 90% bucket 155: 70% bucket 163: 30% bucket 157: 70% bucket 146: 90% bucket 162: 40% bucket 150: 80% bucket 156: 70% bucket 158: 70% bucket 165: 20% Sorting block time: 00:00:00 Returning block of 19886 for bucket 141 bucket 148: 90% bucket 143: 100% Sorting block of length 24101 for bucket 143 (Using difference cover) bucket 152: 80% bucket 159: 70% bucket 145: 100% Sorting block of length 11743 for bucket 145 (Using difference cover) bucket 151: 80% Sorting block time: 00:00:00 Returning block of 19166 for bucket 149 bucket 160: 60% bucket 167: 10% bucket 161: 60% bucket 144: 100% bucket 164: 30% Sorting block of length 23033 for bucket 144 (Using difference cover) bucket 153: 80% bucket 168: 10% bucket 166: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 154: 80% Returning block of 11744 for bucket 145 bucket 155: 80% bucket 147: 100% bucket 163: 40% bucket 157: 80% bucket 162: 50% bucket 146: 100% bucket 156: 80% bucket 150: 90% bucket 158: 80% bucket 148: 100% bucket 165: 30% Returning block of 24102 for bucket 143 Getting block 169 of 199 Getting block 170 of 199 bucket 152: 90% Sorting block of length 14340 for bucket 147 Sorting block time: 00:00:00 (Using difference cover) Sorting block of length 16377 for bucket 146 (Using difference cover) bucket 159: 80% Sorting block of length 17747 for bucket 148 (Using difference cover) Reserving size (25350) for bucket 169 Reserving size (25350) for bucket 170 Returning block of 23034 for bucket 144 bucket 151: 90% Calculating Z arrays for bucket 169 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 169: Entering block accumulator loop for bucket 170: bucket 167: 20% Getting block 171 of 199 Reserving size (25350) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 160: 70% bucket 161: 70% bucket 166: 30% bucket 164: 40% bucket 168: 20% bucket 153: 90% Getting block 172 of 199 Reserving size (25350) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: Getting block 173 of 199 Reserving size (25350) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: Sorting block time: 00:00:00 Returning block of 14341 for bucket 147 Sorting block time: 00:00:00 Returning block of 16378 for bucket 146 Sorting block time: 00:00:00 Returning block of 17748 for bucket 148 Getting block 174 of 199 Reserving size (25350) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 170: 10% bucket 157: 90% bucket 162: 60% bucket 155: 90% bucket 158: 90% bucket 154: 90% bucket 163: 50% bucket 166: 40% bucket 156: 90% bucket 169: 10% bucket 167: 30% bucket 152: 100% Sorting block of length 8003 for bucket 152 (Using difference cover) bucket 159: 90% bucket 171: 10% bucket 151: 100% Sorting block of length 23482 for bucket 151 (Using difference cover) Getting block 175 of 199 Reserving size (25350) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 165: 40% bucket 150: 100% Sorting block of length 24440 for bucket 150 (Using difference cover) bucket 161: 80% bucket 168: 30% bucket 164: 50% bucket 153: 100% Sorting block of length 25254 for bucket 153 (Using difference cover) bucket 160: 80% Sorting block time: 00:00:00 Returning block of 8004 for bucket 152 Getting block 176 of 199 Reserving size (25350) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: bucket 173: 10% bucket 172: 10% bucket 170: 20% Getting block 177 of 199 Reserving size (25350) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 174: 10% bucket 166: 50% Sorting block time: 00:00:00 Returning block of 23483 for bucket 151 bucket 158: 100% bucket 162: 70% bucket 157: 100% Sorting block of length 15232 for bucket 158 (Using difference cover) Sorting block of length 21054 for bucket 157 (Using difference cover) bucket 169: 20% bucket 167: 40% bucket 155: 100% Sorting block of length 12286 for bucket 155 (Using difference cover) bucket 163: 60% bucket 154: 100% Sorting block of length 24379 for bucket 154 (Using difference cover) bucket 159: 100% Sorting block of length 17988 for bucket 159 (Using difference cover) bucket 156: 100% bucket 171: 20% Sorting block of length 24621 for bucket 156 (Using difference cover) bucket 175: 10% bucket 161: 90% bucket 168: 40% Sorting block time: 00:00:00 Returning block of 24441 for bucket 150 Sorting block time: 00:00:00 Returning block of 25255 for bucket 153 bucket 165: 50% bucket 164: 60% bucket 160: 90% Getting block 178 of 199 Reserving size (25350) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: bucket 176: 10% bucket 173: 20% bucket 172: 20% Getting block 179 of 199 Reserving size (25350) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 170: 30% Sorting block time: 00:00:00 Returning block of 15233 for bucket 158 Sorting block time: 00:00:00 Returning block of 12287 for bucket 155 bucket 166: 60% Getting block 180 of 199 Reserving size (25350) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 177: 10% bucket 174: 20% Sorting block time: 00:00:00 Returning block of 17989 for bucket 159 Getting block 181 of 199 Reserving size (25350) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: bucket 162: 80% bucket 169: 30% bucket 167: 50% Sorting block time: 00:00:00 Returning block of 21055 for bucket 157 Sorting block time: 00:00:00 Returning block of 24380 for bucket 154 bucket 163: 70% bucket 175: 20% bucket 171: 30% Sorting block time: 00:00:00 Returning block of 24622 for bucket 156 Getting block 182 of 199 Reserving size (25350) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 168: 50% bucket 161: 100% Sorting block of length 16389 for bucket 161 (Using difference cover) Getting block 183 of 199 Reserving size (25350) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: Getting block 184 of 199 Reserving size (25350) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: Getting block 185 of 199 Reserving size (25350) for bucket 185 bucket 164: 70% Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 165: 60% bucket 178: 10% bucket 160: 100% Sorting block of length 16258 for bucket 160 (Using difference cover) bucket 170: 40% bucket 176: 20% bucket 172: 30% bucket 173: 30% bucket 179: 10% bucket 166: 70% Sorting block time: 00:00:00 Returning block of 16390 for bucket 161 bucket 174: 30% bucket 180: 10% bucket 177: 20% Getting block 186 of 199 Reserving size (25350) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: bucket 181: 10% bucket 169: 40% bucket 167: 60% bucket 162: 90% Sorting block time: 00:00:00 Returning block of 16259 for bucket 160 bucket 175: 30% bucket 171: 40% Getting block 187 of 199 bucket 182: 10% bucket 163: 80% Reserving size (25350) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: bucket 168: 60% bucket 183: 10% Getting block 188 of 199 Reserving size (25350) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 184: 10% bucket 185: 10% bucket 170: 50% bucket 164: 80% bucket 178: 20% bucket 176: 30% bucket 165: 70% bucket 172: 40% bucket 173: 40% bucket 166: 80% bucket 179: 20% bucket 174: 40% bucket 180: 20% bucket 186: 10% bucket 177: 30% bucket 181: 20% bucket 169: 50% bucket 167: 70% bucket 162: 100% Sorting block of length 10102 for bucket 162 (Using difference cover) bucket 175: 40% bucket 171: 50% bucket 170: 60% bucket 182: 20% bucket 183: 20% bucket 168: 70% bucket 163: 90% bucket 187: 10% bucket 184: 20% bucket 188: 10% bucket 185: 20% bucket 178: 30% bucket 164: 90% bucket 166: 90% bucket 176: 40% Sorting block time: 00:00:00 Returning block of 10103 for bucket 162 bucket 172: 50% bucket 173: 50% bucket 179: 30% bucket 165: 80% Getting block 189 of 199 Reserving size (25350) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 174: 50% bucket 186: 20% bucket 180: 30% bucket 177: 40% bucket 181: 30% bucket 170: 70% bucket 169: 60% bucket 167: 80% bucket 175: 50% bucket 171: 60% bucket 183: 30% bucket 168: 80% bucket 188: 20% bucket 182: 30% bucket 187: 20% bucket 184: 30% bucket 185: 30% bucket 163: 100% Sorting block of length 23597 for bucket 163 (Using difference cover) bucket 166: 100% Sorting block of length 16091 for bucket 166 (Using difference cover) bucket 178: 40% bucket 176: 50% bucket 164: 100% Sorting block of length 20136 for bucket 164 (Using difference cover) bucket 172: 60% bucket 179: 40% bucket 173: 60% bucket 189: 10% bucket 165: 90% Sorting block time: 00:00:00 Returning block of 16092 for bucket 166 bucket 174: 60% bucket 170: 80% Getting block 190 of 199 Reserving size (25350) for bucket 190 Calculating Z arrays for bucket 190 bucket 186: 30% Entering block accumulator loop for bucket 190: bucket 180: 40% bucket 181: 40% bucket 169: 70% bucket 177: 50% bucket 167: 90% bucket 175: 60% Sorting block time: 00:00:00 Returning block of 23598 for bucket 163 bucket 188: 30% bucket 171: 70% bucket 187: 30% bucket 183: 40% bucket 168: 90% bucket 184: 40% Sorting block time: 00:00:00 Returning block of 20137 for bucket 164 bucket 182: 40% bucket 185: 40% bucket 178: 50% Getting block 191 of 199 Reserving size (25350) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: Getting block 192 of 199 Reserving size (25350) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 176: 60% bucket 172: 70% bucket 189: 20% bucket 173: 70% bucket 179: 50% bucket 170: 90% bucket 190: 10% bucket 165: 100% Sorting block of length 22919 for bucket 165 (Using difference cover) bucket 174: 70% bucket 186: 40% bucket 181: 50% bucket 180: 50% bucket 167: 100% Sorting block of length 12704 for bucket 167 (Using difference cover) bucket 169: 80% bucket 177: 60% bucket 175: 70% bucket 188: 40% bucket 171: 80% bucket 187: 40% bucket 184: 50% bucket 183: 50% bucket 168: 100% Sorting block of length 13328 for bucket 168 (Using difference cover) bucket 185: 50% bucket 182: 50% bucket 191: 10% bucket 178: 60% bucket 192: 10% bucket 176: 70% bucket 172: 80% bucket 189: 30% Sorting block time: 00:00:00 Returning block of 12705 for bucket 167 bucket 170: 100% Sorting block of length 24772 for bucket 170 (Using difference cover) bucket 190: 20% bucket 179: 60% bucket 173: 80% Sorting block time: 00:00:00 Returning block of 22920 for bucket 165 Getting block 193 of 199 Reserving size (25350) 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 13329 for bucket 168 bucket 174: 80% Getting block 194 of 199 Reserving size (25350) for bucket 194 Getting block 195 of 199 Calculating Z arrays for bucket 194 bucket 186: 50% Reserving size (25350) for bucket 195 Entering block accumulator loop for bucket 194: Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 181: 60% bucket 169: 90% bucket 180: 60% bucket 175: 80% bucket 177: 70% bucket 188: 50% bucket 187: 50% bucket 184: 60% bucket 171: 90% bucket 183: 60% bucket 185: 60% bucket 191: 20% bucket 192: 20% bucket 178: 70% bucket 182: 60% Sorting block time: 00:00:00 Returning block of 24773 for bucket 170 bucket 190: 30% bucket 176: 80% bucket 189: 40% bucket 172: 90% Getting block 196 of 199 Reserving size (25350) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 179: 70% bucket 173: 90% bucket 193: 10% bucket 174: 90% bucket 194: 10% bucket 186: 60% bucket 195: 10% bucket 181: 70% bucket 169: 100% Sorting block of length 25285 for bucket 169 (Using difference cover) bucket 175: 90% bucket 188: 60% bucket 184: 70% bucket 171: 100% bucket 177: 80% Sorting block of length 22214 for bucket 171 (Using difference cover) bucket 191: 30% bucket 187: 60% bucket 180: 70% bucket 185: 70% bucket 183: 70% bucket 190: 40% bucket 192: 30% bucket 178: 80% bucket 182: 70% bucket 196: 10% bucket 176: 90% bucket 189: 50% bucket 172: 100% Sorting block of length 12494 for bucket 172 (Using difference cover) bucket 179: 80% bucket 193: 20% bucket 173: 100% Sorting block of length 22700 for bucket 173 (Using difference cover) bucket 195: 20% bucket 194: 20% bucket 174: 100% Sorting block of length 22732 for bucket 174 (Using difference cover) bucket 186: 70% Sorting block time: 00:00:00 Returning block of 25286 for bucket 169 bucket 181: 80% Sorting block time: 00:00:00 Returning block of 12495 for bucket 172 bucket 188: 70% Sorting block time: 00:00:00 bucket 190: 50% Returning block of 22215 for bucket 171 bucket 175: 100% Sorting block of length 24489 for bucket 175 (Using difference cover) bucket 191: 40% bucket 184: 80% bucket 196: 20% bucket 192: 40% bucket 185: 80% bucket 187: 70% bucket 180: 80% bucket 183: 80% bucket 177: 90% bucket 178: 90% Getting block 197 of 199 Reserving size (25350) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: Getting block 198 of 199 Reserving size (25350) for bucket 198 Calculating Z arrays for bucket 198 bucket 182: 80% Entering block accumulator loop for bucket 198: bucket 176: 100% Sorting block of length 15014 for bucket 176 (Using difference cover) bucket 189: 60% Getting block 199 of 199 Reserving size (25350) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: Sorting block time: 00:00:00 Returning block of 22701 for bucket 173 bucket 193: 30% bucket 179: 90% Sorting block time: 00:00:00 Returning block of 22733 for bucket 174 bucket 195: 30% bucket 186: 80% bucket 190: 60% bucket 194: 30% Sorting block time: 00:00:00 Returning block of 15015 for bucket 176 bucket 196: 30% bucket 181: 90% bucket 188: 80% bucket 191: 50% Sorting block time: 00:00:00 Returning block of 24490 for bucket 175 bucket 184: 90% bucket 192: 50% bucket 199: 10% bucket 185: 90% bucket 183: 90% bucket 187: 80% bucket 178: 100% bucket 180: 90% Sorting block of length 25079 for bucket 178 (Using difference cover) bucket 197: 10% bucket 177: 100% Sorting block of length 21795 for bucket 177 (Using difference cover) bucket 198: 10% bucket 182: 90% bucket 189: 70% bucket 193: 40% bucket 179: 100% Sorting block of length 9457 for bucket 179 (Using difference cover) bucket 190: 70% bucket 195: 40% bucket 199: 20% bucket 196: 40% bucket 186: 90% bucket 188: 90% Sorting block time: 00:00:00 Returning block of 9458 for bucket 179 bucket 194: 40% bucket 181: 100% Sorting block of length 25134 for bucket 181 (Using difference cover) bucket 191: 60% bucket 184: 100% bucket 192: 60% Sorting block of length 14430 for bucket 184 (Using difference cover) Sorting block time: 00:00:00 Returning block of 21796 for bucket 177 Sorting block time: 00:00:00 Returning block of 25080 for bucket 178 bucket 185: 100% Sorting block of length 20685 for bucket 185 (Using difference cover) bucket 197: 20% bucket 187: 90% bucket 183: 100% Sorting block of length 19698 for bucket 183 (Using difference cover) bucket 198: 20% bucket 180: 100% Sorting block of length 20090 for bucket 180 (Using difference cover) bucket 182: 100% Sorting block of length 17110 for bucket 182 (Using difference cover) bucket 189: 80% bucket 199: 30% bucket 193: 50% bucket 190: 80% bucket 196: 50% Sorting block time: 00:00:00 Returning block of 14431 for bucket 184 bucket 195: 50% bucket 186: 100% Sorting block of length 21494 for bucket 186 (Using difference cover) bucket 188: 100% Sorting block of length 18955 for bucket 188 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25135 for bucket 181 bucket 191: 70% Sorting block time: 00:00:00 Returning block of 19699 for bucket 183 Sorting block time: 00:00:00 Returning block of 20686 for bucket 185 Sorting block time: 00:00:00 Returning block of 20091 for bucket 180 Sorting block time: 00:00:00 Returning block of 17111 for bucket 182 bucket 192: 70% bucket 194: 50% bucket 197: 30% bucket 199: 40% bucket 198: 30% bucket 187: 100% Sorting block of length 22331 for bucket 187 (Using difference cover) bucket 189: 90% bucket 190: 90% bucket 193: 60% bucket 196: 60% bucket 195: 60% Sorting block time: 00:00:00 Returning block of 18956 for bucket 188 Sorting block time: 00:00:00 Returning block of 21495 for bucket 186 bucket 199: 50% bucket 191: 80% bucket 192: 80% Sorting block time: 00:00:00 Returning block of 22332 for bucket 187 bucket 194: 60% bucket 197: 40% bucket 198: 40% bucket 190: 100% Sorting block of length 18037 for bucket 190 (Using difference cover) bucket 196: 70% bucket 189: 100% Sorting block of length 21260 for bucket 189 (Using difference cover) bucket 193: 70% bucket 199: 60% bucket 195: 70% Sorting block time: 00:00:00 Returning block of 18038 for bucket 190 bucket 191: 90% bucket 192: 90% bucket 197: 50% bucket 198: 50% bucket 194: 70% bucket 196: 80% bucket 199: 70% Sorting block time: 00:00:00 Returning block of 21261 for bucket 189 bucket 193: 80% bucket 195: 80% bucket 199: 80% bucket 191: 100% Sorting block of length 20039 for bucket 191 (Using difference cover) bucket 192: 100% Sorting block of length 10603 for bucket 192 (Using difference cover) bucket 196: 90% bucket 197: 60% bucket 198: 60% bucket 194: 80% Sorting block time: 00:00:00 Returning block of 10604 for bucket 192 bucket 193: 90% bucket 199: 90% bucket 195: 90% Sorting block time: 00:00:00 Returning block of 20040 for bucket 191 bucket 196: 100% Sorting block of length 23492 for bucket 196 (Using difference cover) bucket 197: 70% bucket 198: 70% bucket 194: 90% bucket 199: 100% Sorting block of length 23593 for bucket 199 (Using difference cover) bucket 193: 100% Sorting block of length 7803 for bucket 193 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23493 for bucket 196 bucket 195: 100% Sorting block of length 2237 for bucket 195 (Using difference cover) Sorting block time: 00:00:00 Returning block of 7804 for bucket 193 Sorting block time: 00:00:00 Returning block of 2238 for bucket 195 bucket 197: 80% bucket 198: 80% bucket 194: 100% Sorting block of length 29400 for bucket 194 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23594 for bucket 199 bucket 198: 90% bucket 197: 90% Sorting block time: 00:00:00 Returning block of 29401 for bucket 194 bucket 198: 100% Sorting block of length 10835 for bucket 198 (Using difference cover) bucket 197: 100% Sorting block of length 20904 for bucket 197 (Using difference cover) Sorting block time: 00:00:00 Returning block of 10836 for bucket 198 Sorting block time: 00:00:00 Returning block of 20905 for bucket 197 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1897502 fchr[G]: 2570152 fchr[T]: 2570152 fchr[$]: 3785646 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 5461730 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 946416 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 3785646 bwtLen: 3785647 sz: 946412 bwtSz: 946412 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 236603 offsSz: 946412 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 19717 numLines: 19717 ebwtTotLen: 1261888 ebwtTotSz: 1261888 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:01 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1101:17242:56591_1:N:0:TAGCTT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1104:12397:7545_1:N:0:TAGATT Contig20140 129024 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1106:19204:7206_1:N:0:TAGCTT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1107:14373:56857_1:N:0:TAGCTT Contig20140 129024 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1109:9968:92922_1:N:0:TAGCTT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1110:18595:67306_1:N:0:TAGCTT Contig20625 2 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:3053:43768_1:N:0:TAGCTT Contig18024 1 Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:19105:42611_1:Y:0:TAGCTT Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:17974:17910_1:N:0:TAGCTT Contig18174 105892 Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:12770:71354_1:N:0:TAGCTT Contig19330 108174 Processed 6000000 sequences so far Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1211:13097:89061_1:N:0:TAGCTT Contig20140 129024 Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1309:4071:57849_1:N:0:TAGCTT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1309:19203:58622_1:N:0:TAGCTT Contig19330 108175 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:13455:37227_1:N:0:TAGCTT Contig26138 2 Processed 13000000 sequences so far Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2105:6825:9803_1:Y:0:TAGCTT Contig19330 108174 Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2110:18692:45780_1:N:0:TAGCTT Contig20625 1 Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2112:4943:97595_1:N:0:TAGCTT Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2113:3544:98459_1:N:0:TAGCTT Contig20625 111110 Processed 17000000 sequences so far Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:14976:48201_1:N:0:TAGCTT Contig3 2 Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2304:4169:33681_1:N:0:TAGCTT Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2305:3371:35761_1:N:0:TAGCTT Contig20140 129025 Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2309:15128:63830_1:N:0:TAGCTT Contig20625 1 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1109:11581:81388_1:N:0:TAGCTT Contig0 1 Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1113:4203:75830_1:N:0:TAGCTT Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1113:8033:89949_1:N:0:TAGCTT Contig19826 1 Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1202:19380:59452_1:N:0:TAGCTT Contig19330 108174 Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1203:19781:44000_1:N:0:TAGCTT Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1204:10410:45994_1:N:0:TAGCTT Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1206:3175:9679_1:N:0:TAGCTT Contig20625 1 Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1207:17822:29244_1:N:0:TAGCTT Contig20625 1 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1210:10618:99795_1:N:0:TAGCTT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1213:8686:6994_1:N:0:TAGCTT Contig5 130492 Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1301:6166:26152_1:N:0:TAGCTT Contig19330 108174 Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1301:2970:87662_1:N:0:TAGCTT Contig20625 111110 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1305:10062:77325_1:N:0:TAGCTT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1306:4858:36467_1:N:0:TAGCTT Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1307:6189:35283_1:N:0:TAGCTT Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:16339:42261_1:N:0:TAGCTT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:14213:77255_1:N:0:TAGCTT Contig19330 108174 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:12539:89858_1:N:0:TAGCTT Contig18024 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1312:2246:30042_1:N:0:TAGCTT Contig5 1 Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1312:13318:72803_1:N:0:TAGCTT Contig20140 129024 Processed 39000000 sequences so far Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2103:5549:78583_1:Y:0:TAGCTT Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2104:10610:40292_1:N:0:TTGCTT Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2104:5521:92638_1:N:0:TAGCTT Contig20140 129024 Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2203:21097:45835_1:N:0:TAGCTT Contig18174 105892 Processed 45000000 sequences so far Processed 46000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2210:1827:43539_1:N:0:TAGCTT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2211:7172:43080_1:N:0:TAGCTT Contig18052 116631 Processed 47000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2215:2835:4703_1:N:0:TAGCTT Contig18174 105892 Processed 48000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2303:17032:70977_1:N:0:TAGCTT Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2303:9108:81739_1:N:0:TAGCTT Contig19330 108174 Processed 49000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2306:7355:57531_1:N:0:TAGCTT Contig20625 2 Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1105:2768:64371_1:Y:0:TAGCTT Contig19826 1 Processed 54000000 sequences so far Processed 55000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1112:16883:29009_1:N:0:TAGCTT Contig19646 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1112:13897:86679_1:N:0:TAGCTT Contig19330 108174 Processed 56000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1201:20053:18962_1:N:0:TAGCTT Contig20140 129024 Processed 57000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1205:10408:22059_1:N:0:TAGCTT Contig20140 129023 Processed 58000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1209:2617:76600_1:N:0:TAGCTT Contig26138 1 Processed 59000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1213:6288:2999_1:N:0:TAGCTT Contig19330 108174 Processed 60000000 sequences so far Processed 61000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:4082:30133_1:N:0:TAGCTT Contig19330 108174 Processed 62000000 sequences so far Processed 63000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1309:15936:44487_1:N:0:TAGCTT Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:19767:48413_1:N:0:TAGCTT Contig20140 129024 Processed 64000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:15776:41489_1:N:0:TAGCTT Contig20625 1 Processed 65000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:18053:63576_1:N:0:TAGCTT Contig20625 111110 Processed 66000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2103:17724:95096_1:N:0:TAGCTT Contig18174 105892 Processed 67000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2109:7094:14556_1:N:0:TAGCTT Contig7 109638 Processed 68000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:3424:25262_1:N:0:TAGCTT Contig16668 2 Processed 69000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2115:4586:95395_1:N:0:TAGCTT Contig65 107630 Processed 70000000 sequences so far Processed 71000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2208:17899:93495_1:N:0:TAGCTT Contig19330 108174 Processed 72000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2211:4152:34627_1:N:0:TAGCTT Contig7 109637 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2212:17024:77806_1:N:0:TAGCTT Contig20140 129023 Processed 73000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2214:6000:82149_1:N:0:TAGCTT Contig7 109637 Processed 74000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2303:14089:34346_1:N:0:TAGCTT Contig19330 108174 Processed 75000000 sequences so far Processed 76000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2311:11719:53620_1:N:0:TAGCTT Contig20625 1 Processed 77000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2314:18352:35717_1:N:0:TAGCTT Contig18174 105892 Processed 78000000 sequences so far 78221457 reads; of these: 78221457 (100.00%) were unpaired; of these: 75770246 (96.87%) aligned 0 times 1074788 (1.37%) aligned exactly 1 time 1376423 (1.76%) aligned >1 times 3.13% overall alignment rate 78221457 reads; of these: 78221457 (100.00%) were unpaired; of these: 75750763 (96.84%) aligned 0 times 986993 (1.26%) aligned exactly 1 time 1483701 (1.90%) aligned >1 times 3.16% overall alignment rate 78221457 reads; of these: 78221457 (100.00%) were unpaired; of these: 75673470 (96.74%) aligned 0 times 1075895 (1.3878221457% reads; of these:) aligned exactly 1 time 782214571472092 ( (1.88%) aligned >1 times 3.26% overall alignment rate100.00 %) were unpaired; of these: 75835163 (96.95%) aligned 0 times 1049494 (1.34%) aligned exactly 1 time 1336800 (1.71%) aligned >1 times 3.05% 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: 3147226 Mapping efficiency: 4.0% Sequences with no alignments under any condition: 71822548 Sequences did not map uniquely: 3251683 Sequences which were discarded because genomic sequence could not be extracted: 75 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 763339 ((converted) top strand) CT/GA: 808464 ((converted) bottom strand) GA/CT: 766511 (complementary to (converted) top strand) GA/GA: 808837 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 19635772 Total methylated C's in CpG context: 2906053 Total methylated C's in CHG context: 106168 Total methylated C's in CHH context: 1071747 Total methylated C's in Unknown context: 120 Total unmethylated C's in CpG context: 877521 Total unmethylated C's in CHG context: 3583731 Total unmethylated C's in CHH context: 11090552 Total unmethylated C's in Unknown context: 424 C methylated in CpG context: 76.8% C methylated in CHG context: 2.9% C methylated in CHH context: 8.8% C methylated in Unknown context (CN or CHN): 22.1% Bismark completed in 0d 0h 38m 54s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/olurida-bs/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1106:3878:83791_1:N:0:AGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:9538:52843_1:N:0:GGCTAC Contig18024 2 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1112:15396:12193_1:N:0:GGCTAC Contig20625 1 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1203:16269:11564_1:N:0:GGCTAC Contig20140 129024 Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:19759:13604_1:N:0:GGCTAC Contig19330 108174 Processed 7000000 sequences so far Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1313:6512:40990_1:N:0:GGCTAC Contig20625 1 Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2101:19283:94525_1:N:0:GGCTAC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2102:12415:54563_1:N:0:AGCTAC Contig20625 1 Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2105:2687:38041_1:N:0:GGCTAC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2107:5163:48941_1:N:0:GGCTAC Contig20625 1 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2111:8482:44852_1:N:0:GGCTAC Contig18024 2 Processed 12000000 sequences so far Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2205:19625:71775_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2206:11027:74326_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2207:2691:64906_1:Y:0:GGCTAC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:17936:81757_1:N:0:GGCTAC Contig18024 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:12960:98287_1:N:0:GGCTAC Contig20625 1 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2213:4024:31991_1:N:0:GGCTAC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2215:17238:26031_1:N:0:GGCTAC Contig16668 2 Processed 15000000 sequences so far Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2305:14034:28546_1:N:0:GGCTAC Contig19330 108174 Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2310:15732:39481_1:N:0:GGCTAC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2311:8943:81889_1:N:0:GGCTAC Contig19330 108174 Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1101:7501:83207_1:N:0:GGCTCC Contig20140 1 Processed 19000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1104:10649:97368_1:N:0:GGCTAC Contig20625 2 Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1111:6831:50175_1:N:0:GGCTAC Contig84 102773 Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:10438:78321_1:N:0:GGCTAC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1201:12577:8515_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:3853:34279_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1203:3863:33956_1:N:0:GGCTAC Contig18174 105891 Processed 22000000 sequences so far Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1210:14738:41914_1:N:0:GGCTAC Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1210:9772:98552_1:N:0:GGCTAC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1213:13170:43875_1:N:0:GGCTAC Contig18174 105892 Processed 24000000 sequences so far Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1308:5742:30821_1:N:0:GGCTAC Contig20625 1 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2207:2705:55638_1:N:0:AGCTAC Contig20625 1 Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2209:1594:83271_1:N:0:GGCTAC Contig18052 116631 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2215:8216:12487_1:N:0:GGCTAC Contig19330 108176 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2301:4658:81010_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2302:6533:49525_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2302:8699:76715_1:N:0:GGCTAC Contig19330 108174 Processed 34000000 sequences so far Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2314:6931:94543_1:N:0:GGCTAC Contig19330 108175 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1104:16554:12250_1:N:0:GGCTAC Contig20625 1 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1105:5316:46430_1:N:0:GGCTAC Contig5 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1105:8110:85521_1:Y:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1108:14093:14761_1:N:0:GGCTAC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1108:16893:81184_1:N:0:GGCTAC Contig3 141627 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1109:10694:44846_1:N:0:GGCTAC Contig20625 1 Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:4733:36697_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:7473:62469_1:N:0:GGCTAC Contig19646 1 Processed 42000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1214:4409:59178_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1301:3983:9857_1:N:0:GGCTAC Contig20625 1 Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1316:2346:20960_1:N:0:GGCTAC Contig20625 1 Processed 46000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2104:13826:24829_1:N:0:GGCTAC Contig19330 108176 Processed 47000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2109:16827:42716_1:N:0:GGCTAC Contig20625 1 Processed 48000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2202:9507:5178_1:N:0:AGCTAC Contig19646 1 Processed 49000000 sequences so far Processed 50000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2210:12700:6815_1:N:0:AGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2210:16997:97235_1:N:0:GGCTAC Contig19330 108177 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2212:14760:66069_1:N:0:GGCTAC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2213:1656:67963_1:N:0:GGCTAC Contig20140 129024 Processed 51000000 sequences so far Processed 52000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2307:6657:60258_1:N:0:GGCTAC Contig16668 1 Processed 53000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2309:11497:19994_1:N:0:GGCTAC Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:15571:47089_1:Y:0:GGCTAC Contig19646 1 Processed 54000000 sequences so far 54458572 reads; of these: 54458572 (54458572100.00 reads; of these:% ) were unpaired; of these: 54458572 (52376921 (96.18%) aligned 0 times100.00 % ) were unpaired; of these:972460 ( 1.7952907484% () aligned exactly 1 time97.15 % ) aligned 0 times1109191 ( 2.04773429% () aligned >1 times1.42 %3.82) aligned exactly 1 time% overall alignment rate 777659 (1.43%) aligned >1 times 2.85% overall alignment rate 54458572 reads; of these: 54458572 (100.00%) were unpaired; of these: 52941845 (97.21%) aligned 0 times 738138 (1.36%) aligned exactly 1 time 778589 (1.43%) aligned >1 times 2.79% overall alignment rate 54458572 reads; of these: 54458572 (100.00%) were unpaired; of these: 52455711 (96.32%) aligned 0 times 904372 (1.66%) aligned exactly 1 time 1098489 (2.02%) aligned >1 times 3.68% 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: 2533316 Mapping efficiency: 4.7% Sequences with no alignments under any condition: 49708344 Sequences did not map uniquely: 2216912 Sequences which were discarded because genomic sequence could not be extracted: 60 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 526236 ((converted) top strand) CT/GA: 570358 ((converted) bottom strand) GA/CT: 693851 (complementary to (converted) top strand) GA/GA: 742811 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 15943045 Total methylated C's in CpG context: 3143225 Total methylated C's in CHG context: 96153 Total methylated C's in CHH context: 702171 Total methylated C's in Unknown context: 141 Total unmethylated C's in CpG context: 717521 Total unmethylated C's in CHG context: 2746405 Total unmethylated C's in CHH context: 8537570 Total unmethylated C's in Unknown context: 281 C methylated in CpG context: 81.4% C methylated in CHG context: 3.4% C methylated in CHH context: 7.6% C methylated in Unknown context (CN or CHN): 33.4% Bismark completed in 0d 0h 27m 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1102:6692:66182_1:Y:0:CTTGTA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1104:7121:44571_1:N:0:CTTGTA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1104:6225:64692_1:N:0:CTTGTA Contig84 102773 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:19449:52880_1:N:0:CTTGTA Contig19330 108174 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1114:4787:7619_1:N:0:CTTGTA Contig0 1 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1203:16611:97928_1:N:0:CTTGTA Contig26138 1 Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1205:6074:54985_1:N:0:CTTGTA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1206:18089:39266_1:N:0:CTTGTA Contig18174 105892 Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1212:7944:19664_1:N:0:CTTGTA Contig18174 105892 Processed 6000000 sequences so far Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1303:5456:61868_1:N:0:CTTGTA Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1306:10392:73347_1:N:0:CTTGTA Contig0 1 Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:4071:76677_1:N:0:CTTGTA Contig3 141636 Processed 9000000 sequences so far Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2101:12118:80832_1:N:0:CTTGTA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2102:3224:9291_1:N:0:CTTGTA Contig0 1 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2109:5653:67027_1:N:0:CTTGTA Contig20625 1 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2113:19694:44853_1:N:0:CTTGTA Contig26138 1 Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2203:1186:9363_1:N:0:CTTGTA Contig20140 129025 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2204:10250:20221_1:N:0:CTTGTA Contig18052 116630 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2204:19503:86571_1:N:0:CTTGTA Contig20625 111120 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2206:9427:2591_1:N:0:CTTGTA Contig0 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2206:7889:76421_1:N:0:CTTGTA Contig20625 1 Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2212:8492:26498_1:N:0:CTTGTA Contig20140 129024 Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2216:21287:71613_1:Y:0:CTTGTA Contig0 1 Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2307:1246:28336_1:N:0:CTTGTA Contig18174 105892 Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2311:3219:9542_1:N:0:CTTGTA Contig20625 1 Processed 19000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:11017:75216_1:N:0:CTTGTA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2314:14316:41898_1:N:0:CTTGTA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2314:5546:96460_1:N:0:CTTGTA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2315:8731:41097_1:N:0:CTTGTA Contig19267 115726 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2316:17499:27252_1:N:0:CTTGTA Contig23978 1 Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:16508:2190_1:N:0:CTTGTA Contig20625 1 Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1106:7244:56652_1:N:0:CTTGTA Contig20625 2 Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:14342:64013_1:N:0:CTTGTA Contig18024 109269 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:16510:69012_1:N:0:CTTGTA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:19867:5100_1:N:0:CTTGTA Contig19826 1 Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:17716:73668_1:N:0:CTTGTA Contig9 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1203:9274:47009_1:N:0:CTTGTA Contig20140 129024 Processed 24000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1205:14426:48617_1:N:0:CTTGTA Contig18174 105892 Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:19698:65849_1:N:0:CTTGTA Contig19267 115726 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:8119:48266_1:N:0:CTTGTA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:12368:67120_1:N:0:CTTGTA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1213:17406:21250_1:N:0:CTTGTA Contig23978 1 Processed 26000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1214:8331:82717_1:N:0:CTTGTA Contig20140 129024 Processed 27000000 sequences so far Processed 28000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:2247:56592_1:N:0:CTTGTA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:13396:77538_1:N:0:CTTGTA Contig18174 105892 Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:2328:58331_1:Y:0:CTTGTA Contig18174 105893 Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2103:11567:33992_1:N:0:CTTGTA Contig20625 1 Processed 31000000 sequences so far Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2111:14070:42147_1:N:0:CTTGTA Contig3 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2112:5953:78628_1:Y:0:CTTGTA Contig18024 109269 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2116:6928:33517_1:N:0:CTTGTA Contig18174 105892 Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2206:9770:7568_1:Y:0:CTTGTA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2207:15200:72468_1:N:0:CTTGTA Contig9 1 Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2211:13813:40475_1:N:0:CTTGTA Contig18174 105892 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2215:17183:13893_1:N:0:CTTGTA Contig18174 105897 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2215:12961:36914_1:N:0:CTTGTA Contig19330 108174 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2306:1311:35512_1:N:0:CTTGTA Contig18174 105893 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2307:1227:93260_1:N:0:CTTGTA Contig20625 2 Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2308:4697:93231_1:N:0:CTTGTA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2311:19982:29243_1:N:0:CTTGTA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:1501:46702_1:N:0:CTTGTA Contig19330 108174 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:18738:45491_1:Y:0:CTTGTA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:4063:98423_1:N:0:CTTGTA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1204:14478:12198_1:N:0:CTTGTA Contig16668 1 Processed 44000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1208:8839:70664_1:N:0:CTTGTA Contig19826 1 Processed 45000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1211:15134:88788_1:N:0:CTTGTA Contig19330 108174 Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1311:13773:96267_1:N:0:CTTGTA Contig3 141626 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1313:10685:24880_1:N:0:CTTGTA Contig5 130492 Processed 49000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:10456:10960_1:N:0:CTTGTA Contig16668 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1315:20005:81089_1:N:0:CTTGTA Contig5 130492 Processed 50000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2105:4748:96719_1:N:0:CTTGTA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2106:14869:93548_1:N:0:CTTGTA Contig20625 111110 Processed 51000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2108:3406:2331_1:N:0:CTTGTA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2108:21133:39441_1:Y:0:CTTGTA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2109:1946:64351_1:Y:0:CTTGTA Contig3 1 Processed 52000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2113:14061:53994_1:N:0:CTTGTA Contig26138 1 Processed 53000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2204:9398:60173_1:N:0:CTTGTA Contig20140 129023 Processed 54000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2208:13750:60500_1:N:0:CTTGTA Contig18174 105891 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2210:6619:70592_1:N:0:CTTGAA Contig16668 2 Processed 55000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2212:12724:44897_1:N:0:CTTGTA Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2213:5731:83021_1:N:0:CTTGTA Contig18174 105892 Processed 56000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:1385:3970_1:N:0:CTTGTA Contig19330 108174 Processed 57000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2309:8208:10787_1:N:0:CTTGTA Contig0 1 Processed 58000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2313:14394:88612_1:N:0:CTTGTA Contig19646 1 Processed 59000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2315:11336:67308_1:N:0:CTTGTA Contig20140 129023 59459431 reads; of these: 59459431 (100.00%) were unpaired; of these: 57005958 (95.87%) aligned 0 times 1024885 (1.72%) aligned exactly 1 time 1428588 (2.40%) aligned >1 times 4.13% overall alignment rate 59459431 reads; of these: 59459431 (100.00%) were unpaired; of these: 56910709 (95.71%) aligned 0 times 1102941 (1.85%59459431) aligned exactly 1 time reads; of these: 144578159459431 ( (2.43%) aligned >1 times 4.29% overall alignment rate100.00 %) were unpaired; of these: 57657333 (96.97%) aligned 0 times 816955 (1.37%) aligned exactly 1 time 985143 (1.66%) aligned >1 times 3.03% overall alignment rate 59459431 reads; of these: 59459431 (100.00%) were unpaired; of these: 57614545 (96.90%) aligned 0 times 830197 (1.40%) aligned exactly 1 time 1014689 (1.71%) aligned >1 times 3.10% 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: 2728328 Mapping efficiency: 4.6% Sequences with no alignments under any condition: 53907751 Sequences did not map uniquely: 2823352 Sequences which were discarded because genomic sequence could not be extracted: 84 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 555991 ((converted) top strand) CT/GA: 602078 ((converted) bottom strand) GA/CT: 756652 (complementary to (converted) top strand) GA/GA: 813523 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 16759013 Total methylated C's in CpG context: 1970106 Total methylated C's in CHG context: 81593 Total methylated C's in CHH context: 852411 Total methylated C's in Unknown context: 54 Total unmethylated C's in CpG context: 816317 Total unmethylated C's in CHG context: 3000835 Total unmethylated C's in CHH context: 10037751 Total unmethylated C's in Unknown context: 490 C methylated in CpG context: 70.7% C methylated in CHG context: 2.6% C methylated in CHH context: 7.8% C methylated in Unknown context (CN or CHN): 9.9% Bismark completed in 0d 0h 30m 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 GGTAAGTTTTGTTTTATTAATATGTTGTTGT FBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 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/v082/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 GGTAAGTTTTGTTTTATTAATATGTTGTTGT FBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 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/v082/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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1102:10249:43758_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1102:5577:90140_1:N:0:AGTCAA Contig18174 105892 Processed 1000000 sequences so far Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:8322:65967_1:N:0:AGTCAA Contig0 2 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1114:17031:72979_1:Y:0:AGTCAA Contig26138 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:15214:39115_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:13416:73048_1:N:0:AGTCAA Contig2 1 Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1203:3281:98289_1:N:0:AGTCAA Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:10177:16312_1:N:0:AGTCAA Contig18024 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:20648:34837_1:N:0:AGTCAA Contig20625 1 Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1208:3986:88842_1:N:0:AGTCAA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1209:4923:58877_1:N:0:AGTCAA Contig23978 1 Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1212:18342:17431_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1212:12751:89314_1:N:0:AGTCAA Contig2 1 Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1301:3286:26038_1:N:0:AGTCAA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1301:2690:62156_1:Y:0:AGTCAA Contig20140 129025 Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1305:12281:42618_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1306:6777:11350_1:N:0:AGTCAA Contig20625 2 Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1309:5770:9287_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1312:5772:76185_1:N:0:AGTCAA Contig20625 1 Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:19668:31188_1:N:0:AGTCAA Contig20140 129024 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2102:5572:74479_1:N:0:AGTCAA Contig468 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2105:8134:60896_1:N:0:AGTCAA Contig20140 129025 Processed 12000000 sequences so far Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2114:13468:4482_1:N:0:AGTCAA Contig20625 2 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2116:6389:22754_1:N:0:AGTCAA Contig19826 1 Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2204:12810:72478_1:N:0:AGTCAA Contig5 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2204:16912:76992_1:N:0:AGTCAA Contig19646 2 Processed 16000000 sequences so far Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2215:15740:55290_1:N:0:AGTCAA Contig20140 129025 Processed 18000000 sequences so far Processed 19000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2307:7128:3672_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2309:18922:84958_1:N:0:AGTCAA Contig18052 116632 Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2311:17664:82896_1:N:0:AGTCAA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2314:2692:51385_1:N:0:AGTCAA Contig20625 1 Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1102:17768:56368_1:N:0:AGTCAA Contig20625 111110 Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1104:15443:81003_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1104:10046:93362_1:N:0:AATCAA Contig9 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1105:17771:79161_1:N:0:AGTCAA Contig0 1 Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1109:13959:87458_1:N:0:AGTCAA Contig16668 1 Processed 24000000 sequences so far Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1202:11061:78538_1:N:0:AGTCAA Contig20625 1 Processed 26000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1205:17214:68798_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1206:21039:3930_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1206:14009:73383_1:N:0:AGTCAA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1208:9599:48348_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1209:15384:65779_1:N:0:AGTCAA Contig20625 1 Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1211:12510:75311_1:Y:0:AGTCAA Contig17050 2 Processed 28000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1215:16297:47168_1:N:0:AGTCAA Contig19330 108174 Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1303:8059:64333_1:N:0:AGTCAA Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1303:17309:81607_1:N:0:AGTCAA Contig19330 108174 Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1307:14159:45718_1:N:0:AGTCAA Contig19330 108176 Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1311:16039:61182_1:N:0:AGTCAA Contig20625 111110 Processed 32000000 sequences so far Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2106:2914:3482_1:Y:0:AGTCAA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2106:9572:19074_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2106:11307:50850_1:N:0:AGTCAA Contig20625 1 Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2112:6104:37480_1:N:0:AGTCAA Contig20625 2 Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2212:18813:57522_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2212:3080:62298_1:N:0:AGTCAA Contig16668 2 Processed 39000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2301:10481:82028_1:N:0:AGTCAA Contig19330 108174 Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2305:17220:57565_1:N:0:AGTCAA Contig19646 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2305:6003:73845_1:N:0:AGTCAA Contig20625 1 Processed 41000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2310:13394:78961_1:N:0:AGTCAA Contig19330 108174 Processed 42000000 sequences so far Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:15121:98913_1:N:0:AGTCAA Contig16668 2 Processed 44000000 sequences so far Processed 45000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:10966:25045_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1113:17294:23693_1:Y:0:AGTCAA Contig19646 1 Processed 46000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1201:8503:52581_1:N:0:AGTCAA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1202:18857:28163_1:N:0:AGTCAA Contig18052 116631 Processed 47000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1204:19953:58053_1:N:0:AGTCAA Contig7 109637 Processed 48000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1209:14821:95928_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1211:4109:18041_1:N:0:AGTCAA Contig19267 115726 Processed 49000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:14077:12451_1:N:0:AGTCAA Contig65 107630 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1213:15374:32679_1:N:0:AGTCAA Contig7 109638 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1213:12538:54699_1:N:0:AGTCAA Contig5 130492 Processed 50000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1302:4798:92252_1:N:0:AGTCAA Contig20625 1 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2112:4856:83743_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:6833:85134_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2114:18699:34645_1:N:0:AGTCAA Contig20140 129023 Processed 57000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2202:16705:23483_1:N:0:AGTCAA Contig20625 1 Processed 58000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2206:10212:19529_1:N:0:AGTCAA Contig0 1 Processed 59000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2212:2507:100177_1:N:0:AGTCAA Contig20625 1 Processed 60000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2213:3380:35324_1:N:0:AGTCAA Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2301:8708:35961_1:N:0:AGTCAA Contig20625 1 Processed 61000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2305:8874:78993_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2306:17424:21251_1:N:0:AGTCAA Contig20625 1 Processed 62000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2308:7047:38239_1:N:0:AGTCAA Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2308:11594:42547_1:N:0:AGTCAA Contig19330 108174 Processed 63000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2311:8074:9649_1:N:0:AGTCAA Contig18174 105892 Processed 64000000 sequences so far 64352550 reads; of these: 64352550 (100.00%) were unpaired; of these: 61671890 (95.83%) aligned 0 times 1110685 (1.73%) aligned exactly 1 time 1569975 (2.44%) aligned >1 times 4.17% overall alignment rate 64352550 reads; of these: 64352550 (100.00%) were unpaired; of these: 62320498 (96.84%) aligned 0 times 922540 (1.43%) aligned exactly 1 time 1109512 (1.72%) aligned >1 times 3.16% overall alignment rate 64352550 reads; of these: 64352550 (100.00%) were unpaired; of these: 61567954 (95.67%) aligned 0 times 1199776 (1.86%) aligned exactly 1 time 1584820 (2.46%) aligned >1 times 4.33% overall alignment rate 64352550 reads; of these: 64352550 (100.00%) were unpaired; of these: 62375890 (96.93%) aligned 0 times 891953 (1.39%) aligned exactly 1 time 1084707 (1.69%) aligned >1 times 3.07% 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: 3006813 Mapping efficiency: 4.7% Sequences with no alignments under any condition: 58253464 Sequences did not map uniquely: 3092273 Sequences which were discarded because genomic sequence could not be extracted: 83 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 613488 ((converted) top strand) CT/GA: 669500 ((converted) bottom strand) GA/CT: 827743 (complementary to (converted) top strand) GA/GA: 895999 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 18725396 Total methylated C's in CpG context: 3032628 Total methylated C's in CHG context: 105154 Total methylated C's in CHH context: 863947 Total methylated C's in Unknown context: 102 Total unmethylated C's in CpG context: 833340 Total unmethylated C's in CHG context: 3335556 Total unmethylated C's in CHH context: 10554771 Total unmethylated C's in Unknown context: 418 C methylated in CpG context: 78.4% C methylated in CHG context: 3.1% C methylated in CHH context: 7.6% C methylated in Unknown context (CN or CHN): 19.6% Bismark completed in 0d 0h 33m 9s ==================== 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1103:6504:97324_1:N:0:AGTTCC Contig19330 108174 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1105:10246:2385_1:Y:0:AGTTCC Contig19330 108183 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:19998:19709_1:N:0:AGTTCC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:6662:35962_1:N:0:AGTTCC Contig20625 1 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:1697:76154_1:N:0:AGTTCC Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1109:8282:91520_1:Y:0:AGTTCC Contig20625 1 Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1205:16370:77819_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1206:17082:4114_1:N:0:AGTTCC Contig20625 1 Processed 7000000 sequences so far Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1211:2887:95205_1:N:0:AGTTCC Contig19330 108175 Processed 9000000 sequences so far Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:1368:83545_1:N:0:AGTTCC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1304:17116:6451_1:N:0:AGTTCC Contig20140 129025 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:1:1310:4686:92921_1:N:0:AGTTCC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1311:18389:16313_1:N:0:AGTTCC Contig9 1 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1314:15492:48846_1:N:0:GGTTCC Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1314:20332:98396_1:N:0:AGTTCC Contig20625 1 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2201:9994:56175_1:N:0:AGTTCC Contig19826 1 Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:12702:90148_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:18690:14767_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:6318:35193_1:N:0:AGTTCC Contig20140 129024 Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2212:2758:70243_1:N:0:AGTTCC Contig16668 2 Processed 24000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2216:12846:4440_1:N:0:AGTTCC Contig19330 108175 Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2304:12345:73104_1:N:0:AGTTCC Contig19330 108175 Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2314:12069:51210_1:N:0:AGTTCC Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2314:2363:74948_1:N:0:AGTTCC Contig20625 1 Processed 29000000 sequences so far Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1103:6730:92368_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1103:5246:98159_1:N:0:AGTTCC Contig19646 1 Processed 31000000 sequences so far Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:18849:86219_1:Y:0:AGTTCC Contig19330 108174 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1113:20719:3110_1:Y:0:AGTTCC Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:17765:10301_1:N:0:AGTTCC Contig20625 1 Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1116:13093:7264_1:Y:0:ACTTCC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1202:15821:81654_1:N:0:AGTTCC Contig16668 2 Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1205:18730:57881_1:N:0:AGTTCC Contig20625 1 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1208:9607:93288_1:N:0:AGTTCC Contig5 2 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1211:18700:86672_1:N:0:AGTTCC Contig3 141626 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:21035:11664_1:N:0:ATTTCC Contig9 1 Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1215:18308:58903_1:N:0:AGTTCC Contig20625 1 Processed 39000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1216:15720:9871_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1301:1708:3882_1:N:0:AGTTCC Contig20625 1 Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:14908:88002_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1304:2700:38213_1:N:0:AGTTCC Contig5 2 Processed 41000000 sequences so far Processed 42000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:19636:30817_1:N:0:AGTTCC Contig19826 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1312:21177:70426_1:N:0:AGTTCC Contig3 141626 Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:10405:53576_1:N:0:AGTTCC Contig19826 2 Processed 44000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2101:16653:83763_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2102:2637:97086_1:N:0:AGTTCC Contig20140 129024 Processed 45000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2104:13247:42084_1:N:0:AGTTCC Contig18174 105891 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2104:20506:81718_1:N:0:AGTTCC Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2105:19437:33320_1:N:0:AGTTCC Contig19330 108174 Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:18774:76185_1:N:0:AGTTCC Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2114:5472:79408_1:N:0:AGTTCC Contig20140 129024 Processed 49000000 sequences so far Processed 50000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2204:4274:36303_1:N:0:AGTTCC Contig19330 108175 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2207:4475:7581_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2207:14039:23349_1:N:0:AGTTCC Contig20625 1 Processed 51000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2208:5588:71672_1:N:0:AGTTCC Contig18052 116631 Processed 52000000 sequences so far Processed 53000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2215:7124:87829_1:N:0:AGTTCC Contig20625 1 Processed 54000000 sequences so far Processed 55000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2306:13257:16317_1:N:0:AGTTCC Contig20625 1 Processed 56000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2311:16778:14595_1:N:0:AGTTCC Contig20625 1 Processed 57000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:15908:3593_1:N:0:AGTTCC Contig20625 1 Processed 58000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2315:5723:30368_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2315:15475:88372_1:N:0:AGTTCC Contig18052 116632 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2315:10269:91251_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2316:6652:38760_1:N:0:AGTTCC Contig20140 129024 Processed 59000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1104:16690:56996_1:N:0:AGTTCC Contig19646 1 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1208:13578:91107_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1212:10597:6270_1:N:0:AGTTCC Contig84 102773 Processed 67000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1213:18677:56728_1:N:0:AGTTCC Contig18052 116631 Processed 68000000 sequences so far Processed 69000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1304:7604:61747_1:N:0:AGTTCC Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1305:2392:9037_1:N:0:AGTTCC Contig20625 1 Processed 70000000 sequences so far Processed 71000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1310:14393:93118_1:N:0:AGTTCC Contig19330 108174 Processed 72000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:1428:10253_1:N:0:AGTTCC Contig16668 101411 Processed 73000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1316:20398:82445_1:Y:0:AGTTCC Contig18174 105893 Processed 74000000 sequences so far Processed 75000000 sequences so far Processed 76000000 sequences so far Processed 77000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2115:18994:87011_1:N:0:AGTTCC Contig0 1 Processed 78000000 sequences so far Processed 79000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2206:7537:14898_1:N:0:AGTTCC Contig20140 129023 Processed 80000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2208:17549:87424_1:N:0:AGTTCC Contig16668 2 Processed 81000000 sequences so far Processed 82000000 sequences so far Processed 83000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:5771:56680_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:4111:57352_1:N:0:AGTTCC Contig20625 1 Processed 84000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2306:2390:7465_1:N:0:AGTTCC Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2306:12999:42957_1:N:0:AGTTCC Contig20625 1 Processed 85000000 sequences so far Processed 86000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2313:7225:11507_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2314:18345:8456_1:Y:0:AGTTCC Contig26138 1 Processed 87000000 sequences so far 87834637 reads; of these: 87834637 (100.00%) were unpaired; of these: 85028725 (96.81%) aligned 0 times 1340342 (1.53%) aligned exactly 1 time 1465570 (1.67%) aligned >1 times 3.19% overall alignment rate 87834637 reads; of these: 87834637 (100.00%) were unpaired; of these: 84260365 (8783463795.93 reads; of these:% ) aligned 0 times 87834637 (1562526 (1.78%) aligned exactly 1 time 100.00 %2011746) were unpaired; of these: ( 2.29 %84098850) aligned >1 times ( 95.754.07%%) aligned 0 times overall alignment rate 1686192 (1.92%) aligned exactly 1 time 2049595 (2.33%) aligned >1 times 4.25% overall alignment rate 87834637 reads; of these: 87834637 (100.00%) were unpaired; of these: 85094647 (96.88%) aligned 0 times 1302802 (1.48%) aligned exactly 1 time 1437188 (1.64%) aligned >1 times 3.12% 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: 4288182 Mapping efficiency: 4.9% Sequences with no alignments under any condition: 79466280 Sequences did not map uniquely: 4080175 Sequences which were discarded because genomic sequence could not be extracted: 80 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 892242 ((converted) top strand) CT/GA: 966032 ((converted) bottom strand) GA/CT: 1163049 (complementary to (converted) top strand) GA/GA: 1266779 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 26352415 Total methylated C's in CpG context: 4467852 Total methylated C's in CHG context: 149314 Total methylated C's in CHH context: 1095506 Total methylated C's in Unknown context: 120 Total unmethylated C's in CpG context: 1161113 Total unmethylated C's in CHG context: 4546966 Total unmethylated C's in CHH context: 14931664 Total unmethylated C's in Unknown context: 508 C methylated in CpG context: 79.4% C methylated in CHG context: 3.2% C methylated in CHH context: 6.8% C methylated in Unknown context (CN or CHN): 19.1% Bismark completed in 0d 0h 45m 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1117:2111_1:Y:0:ATGNCA 4 * 0 0 * * 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1105:5744:30400_1:N:0:ATGTCA Contig19330 108183 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:7766:39576_1:N:0:ATGTCA Contig18174 105892 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1111:11504:51345_1:N:0:ATGTCA Contig20625 111109 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1112:13458:83201_1:N:0:ATGTCA Contig20625 111110 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:3212:25625_1:N:0:ATGTCA Contig18024 2 Processed 4000000 sequences so far Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1208:19592:65685_1:N:0:ATGTCA Contig5 130493 Processed 6000000 sequences so far Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1215:8114:68558_1:N:0:ATGTCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1216:21166:38955_1:N:0:ATGTCA Contig19330 108174 Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1306:19061:38185_1:N:0:ATGTCA Contig84 102773 Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1307:20770:42150_1:Y:0:ATGTCA Contig0 1 Processed 10000000 sequences so far Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1315:6641:23060_1:Y:0:ATGTCA Contig23978 1 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2103:10970:84223_1:N:0:ATGTCA Contig19330 108174 Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2107:11673:84243_1:N:0:ATGTCA Contig18174 105892 Processed 14000000 sequences so far Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2116:17526:79688_1:N:0:ATGTCA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2203:12845:30505_1:N:0:ATGTCA Contig84 102772 Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2301:20321:40696_1:N:0:ATGTCA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2304:11835:45186_1:N:0:ATGTCA Contig5 130492 Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2306:9528:56506_1:N:0:ATGTCA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2307:19124:54700_1:N:0:ATGTCA Contig19330 108174 Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2310:13360:30054_1:N:0:ATGTCA Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:2182:57041_1:N:0:ATGTCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:7805:75295_1:N:0:ATGTCA Contig19330 108174 Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1109:3980:10001_1:N:0:ATGTCA Contig19330 108174 Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1111:1411:21055_1:N:0:ATGTCA Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:20445:29718_1:N:0:ATGTCA Contig19330 108174 Processed 26000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:5414:48788_1:N:0:ATGTCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:15007:43698_1:N:0:ATGTCA Contig20625 1 Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:10433:46793_1:N:0:ATGTCA Contig5 130492 Processed 28000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1211:9765:19824_1:N:0:ATGTCA Contig18174 105892 Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1212:6405:43273_1:N:0:ATGTCA Contig19330 108174 Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1215:15747:78373_1:N:0:ATGTCA Contig20625 1 Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1304:7891:25847_1:N:0:ATGTCA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1306:16125:33684_1:N:0:ATGTCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1306:13769:100305_1:N:0:ATGTCN Contig18174 105892 Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1315:3140:96489_1:Y:0:ATGTCA Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2101:9636:96610_1:N:0:ATGTCA Contig0 1 Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2104:11825:41358_1:Y:0:ATGTCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2108:19037:71605_1:N:0:ATGTCA Contig20140 129024 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2110:1257:44366_1:N:0:ATGTCA Contig18052 116631 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2116:11796:41809_1:N:0:ATGTCA Contig18174 105892 Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2214:19213:95810_1:Y:0:ATGTCA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2301:8302:9414_1:N:0:ATGTCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2301:13367:32117_1:N:0:ATGTCA Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2301:3366:94844_1:N:0:ATGTCA Contig18174 105892 Processed 42000000 sequences so far Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2307:16640:56194_1:N:0:ATGTCA Contig19330 108175 Processed 44000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2313:20957:33264_1:Y:0:ATGTCA Contig19330 108175 Processed 45000000 sequences so far Processed 46000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1104:16161:81319_1:N:0:ATGTCA Contig19330 108174 Processed 47000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1110:5846:80654_1:N:0:ATGTCA Contig20625 1 Processed 48000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1114:18960:91368_1:N:0:ATGTCA Contig84 102773 Processed 49000000 sequences so far Processed 50000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1204:11354:77441_1:N:0:ATGTCA Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1206:7571:93868_1:N:0:ATGTCA Contig19330 108174 Processed 51000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:15100:41433_1:N:0:ATGTCA Contig19330 108174 Processed 52000000 sequences so far Processed 53000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1301:10289:83185_1:N:0:ATGTCA Contig20140 129025 Processed 54000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1306:1931:57709_1:N:0:ATGTCA Contig19330 108174 Processed 55000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1309:9104:59952_1:N:0:ATGTCA Contig20140 129023 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2203:19140:32372_1:N:0:ATGTCA Contig7 109638 Processed 62000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2208:20353:18784_1:N:0:ATGTCA Contig20625 1 Processed 63000000 sequences so far Processed 64000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2216:11907:54896_1:N:0:ATGTCA Contig18174 105892 Processed 65000000 sequences so far Processed 66000000 sequences so far Processed 67000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:5563:72679_1:N:0:ATGTCA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2316:13821:47853_1:N:0:ATGTCA Contig20625 111109 67984205 reads; of these: 67984205 (100.00%) were unpaired; of these: 65188361 (95.89%) aligned 0 times 1238628 (1.82%) aligned exactly 1 time 1557216 (2.29%) aligned >1 times 4.11% overall alignment rate 67984205 reads; of these: 67984205 (100.00%) were unpaired; of these: 65879843 (96.90%) aligned 0 times 983754 (1.45%) aligned exactly 1 time 1120608 (1.65%) aligned >1 times 3.10% overall alignment rate 67984205 reads; of these: 67984205 (100.00%) were unpaired; of these: 65931719 (96.98%) aligned 0 times 951538 (1.40%) aligned exactly 1 time 1100948 (1.62%) aligned >1 times 3.02% overall alignment rate 67984205 reads; of these: 67984205 (100.00%) were unpaired; of these: 65295305 (96.04%) aligned 0 times 1146259 (1.69%) aligned exactly 1 time 1542641 (2.27%) aligned >1 times 3.96% 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: 3168995 Mapping efficiency: 4.7% Sequences with no alignments under any condition: 61719035 Sequences did not map uniquely: 3096175 Sequences which were discarded because genomic sequence could not be extracted: 60 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 659615 ((converted) top strand) CT/GA: 718002 ((converted) bottom strand) GA/CT: 858524 (complementary to (converted) top strand) GA/GA: 932794 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 19698902 Total methylated C's in CpG context: 3595616 Total methylated C's in CHG context: 120168 Total methylated C's in CHH context: 904169 Total methylated C's in Unknown context: 115 Total unmethylated C's in CpG context: 814267 Total unmethylated C's in CHG context: 3500880 Total unmethylated C's in CHH context: 10763802 Total unmethylated C's in Unknown context: 368 C methylated in CpG context: 81.5% C methylated in CHG context: 3.3% C methylated in CHH context: 7.7% C methylated in Unknown context (CN or CHN): 23.8% Bismark completed in 0d 0h 34m 45s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/olurida-bs/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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/v082/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/v082/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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1101:7715:5348_1:Y:0:CCGTCC Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1104:3872:85526_1:N:0:CCGTCC Contig19330 108175 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1108:19355:45574_1:N:0:CCGTCC Contig20625 1 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1109:16930:20856_1:N:0:CCGTCC Contig89 100254 Processed 3000000 sequences so far Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:15767:56847_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:13985:63994_1:N:0:CCGTCC Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:5608:96035_1:Y:0:CCGTCC Contig19330 108179 Processed 5000000 sequences so far Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1211:6623:28944_1:N:0:CCGTCC Contig19330 108174 Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1304:5796:40412_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1305:17422:47662_1:N:0:CCGTCC Contig19330 108176 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1306:13132:34588_1:N:0:CCGTCC Contig20625 1 Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1309:2716:13523_1:N:0:CCGTCC Contig19330 108174 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1312:17024:24948_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1312:18435:32831_1:N:0:CCGTCC Contig3 141626 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2101:15293:53013_1:N:0:CCGTCC Contig20140 129024 Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2103:14601:62957_1:Y:0:CCGTCC Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2104:16055:19256_1:N:0:CCGTCC Contig20625 1 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2107:13455:14386_1:N:0:CCGTCC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2108:2641:6811_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2110:2922:39420_1:N:0:CCGTCC Contig19330 108174 Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2111:2133:73304_1:N:0:CCGTCC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2112:8280:64256_1:N:0:CCGTCC Contig18174 105892 Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2116:18610:5571_1:N:0:CCGTCC Contig20625 1 Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2206:18790:3175_1:N:0:CCGTCC Contig23978 1 Processed 18000000 sequences so far Processed 19000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2210:3492:86531_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2213:14212:61624_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2214:9294:16849_1:N:0:CCGTCC Contig18174 105892 Processed 20000000 sequences so far Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:17656:47675_1:N:0:CCGTCC Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2305:14960:60064_1:N:0:CCGTCC Contig20140 129024 Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2308:8664:37641_1:N:0:CCGTCC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2308:3212:53444_1:N:0:CCGTCC Contig20625 1 Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1103:5595:17864_1:N:0:CCATCC Contig20625 2 Processed 26000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:10808:8392_1:N:0:CCGTCC Contig18174 105892 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:1:1201:6963:59676_1:N:0:CCGTCC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1203:2734:30354_1:N:0:CCGTCC Contig20625 1 Processed 30000000 sequences so far Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1208:16994:88920_1:N:0:CCGTCC Contig3 141626 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1212:8688:51518_1:N:0:CCGTCC Contig19330 108174 Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1213:15941:93903_1:N:0:CCGTCC Contig18174 105892 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:16375:18976_1:N:0:CCGTCC Contig5 130492 Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1313:12044:80518_1:N:0:CCGTCC Contig19330 108174 Processed 37000000 sequences so far Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2104:8799:34041_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2104:4692:52056_1:N:0:CCGTCC Contig20625 111109 Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2202:3590:76591_1:N:0:CCGTCC Contig19330 108174 Processed 42000000 sequences so far Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2207:14804:31998_1:N:0:CCGTCC Contig5 130491 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2207:2803:49392_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:20747:25921_1:N:0:CCGTCC Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:20962:43128_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:12402:43901_1:N:0:CCGTCC Contig20625 1 Processed 44000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2212:18877:99135_1:N:0:CCGTCC Contig20625 1 Processed 45000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2216:8220:16429_1:N:0:CCGTCC Contig20625 1 Processed 46000000 sequences so far Processed 47000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2310:7020:20565_1:N:0:CCGTCC Contig19330 108174 Processed 48000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2313:15163:73550_1:N:0:CCGTCC Contig19330 108174 Processed 49000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1101:4716:69673_1:N:0:CCGTCC Contig19330 108174 Processed 50000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:16221:23183_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:8262:43832_1:N:0:CCGTCC Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:3961:95833_1:N:0:CCGTCC Contig18174 105900 Processed 51000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1106:1668:90710_1:N:0:CCGTCC Contig20140 129024 Processed 52000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1112:9303:52753_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1113:7240:28744_1:N:0:CCGTCC Contig20625 1 Processed 53000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:19765:65128_1:N:0:TCGTCC Contig20140 129025 Processed 54000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1203:15093:98825_1:N:0:CCGTCC Contig18174 105892 Processed 55000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1205:9939:41920_1:N:0:CCGTCC Contig20625 1 Processed 56000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:1404:3106_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:12692:68883_1:N:0:CCGTCC Contig5 130492 Processed 57000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1215:20504:95518_1:N:0:CCGTCC Contig18174 105892 Processed 58000000 sequences so far Processed 59000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1307:19943:59227_1:N:0:CCGTCC Contig20625 2 Processed 60000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:13556:28291_1:N:0:CCGTCC Contig20625 1 Processed 61000000 sequences so far Processed 62000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2103:20638:66370_1:N:0:CCGTCC Contig20625 1 Processed 63000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2106:3353:13177_1:N:0:CCGTCC Contig20625 1 Processed 64000000 sequences so far Processed 65000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:16681:88643_1:N:0:CCGTCC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2115:5189:36691_1:N:0:CCGTCC Contig20625 1 Processed 66000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2116:10033:89717_1:Y:0:CCGTCT Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2202:8055:78879_1:N:0:CCGTCC Contig20625 1 Processed 67000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2204:19048:92601_1:N:0:CCGTCC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2205:6832:44105_1:N:0:CCGTCC Contig18174 105892 Processed 68000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2211:18244:22219_1:N:0:CCGTCC Contig20625 111110 Processed 69000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2213:11313:12689_1:N:0:CCGTCC Contig19330 108174 Processed 70000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2301:10010:66694_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2302:14466:18680_1:N:0:CCGTCC Contig20140 129025 Processed 71000000 sequences so far Processed 72000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2307:5009:99379_1:N:0:CCGTCC Contig84 102774 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2309:21136:39385_1:N:0:CCGTCC Contig18024 2 Processed 73000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:14770:92333_1:N:0:CCGTCC Contig19330 108174 Processed 74000000 sequences so far 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 71582846 (96.04%) aligned 0 times 1349018 (1.81%) aligned exactly 1 time 1599192 (2.15%) aligned >1 times 3.96% overall alignment rate 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 72260935 (96.95%) aligned 0 times 1090315 (1.46%) aligned exactly 1 time 1179806 (1.58%) aligned >1 times 3.05% overall alignment rate 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 72209622 (96.89%) aligned 0 times 1127008 (1.51%) aligned exactly 1 time 1194426 (1.60%) aligned >1 times 3.11% overall alignment rate 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 71693649 (96.19%) aligned 0 times 1257299 (1.69%) aligned exactly 1 time 1580108 (2.12%) aligned >1 times 3.81% 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: 3532069 Mapping efficiency: 4.7% Sequences with no alignments under any condition: 67728813 Sequences did not map uniquely: 3270174 Sequences which were discarded because genomic sequence could not be extracted: 82 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 758833 ((converted) top strand) CT/GA: 816847 ((converted) bottom strand) GA/CT: 940596 (complementary to (converted) top strand) GA/GA: 1015711 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 21835046 Total methylated C's in CpG context: 4019431 Total methylated C's in CHG context: 128117 Total methylated C's in CHH context: 950616 Total methylated C's in Unknown context: 97 Total unmethylated C's in CpG context: 986573 Total unmethylated C's in CHG context: 3784804 Total unmethylated C's in CHH context: 11965505 Total unmethylated C's in Unknown context: 373 C methylated in CpG context: 80.3% C methylated in CHG context: 3.3% C methylated in CHH context: 7.4% C methylated in Unknown context (CN or CHN): 20.6% Bismark completed in 0d 0h 38m 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:19565:25996_1:N:0:GTCCGC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1116:11642:31135_1:N:0:GTCCGC Contig19330 108174 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1209:2607:7059_1:N:0:GTCCGC Contig17050 1 Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:6333:6640_1:N:0:GTCCGC Contig18174 105892 Processed 5000000 sequences so far Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1313:4123:95805_1:N:0:GTCCGC Contig20625 1 Processed 7000000 sequences so far Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2110:15369:93313_1:N:0:GTCCGC Contig16668 101411 Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2115:6776:80777_1:N:0:GTCCGC Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2116:17706:79731_1:N:0:GTCCGC Contig20625 1 Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2211:1933:59853_1:N:0:GTCCGC Contig7 109638 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2215:6984:20434_1:N:0:GTCCGC Contig20625 2 Processed 12000000 sequences so far Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2311:5426:23726_1:N:0:GTCCGC Contig20140 129025 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1105:10414:73454_1:N:0:GTCCGC Contig20625 1 Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:18636:16050_1:Y:0:ATCCGC Contig0 1 Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1114:8299:10821_1:N:0:GTCCGC Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1115:18509:26048_1:N:0:GTCCGC Contig23978 1 Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1209:14229:7242_1:N:0:GTCCGC Contig23978 2 Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1213:16507:34918_1:N:0:GTCCGC Contig18174 105892 Processed 19000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1302:7872:52565_1:N:0:GTCCGC Contig19826 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1306:16669:16593_1:N:0:ATCCGC Contig20625 1 Processed 20000000 sequences so far Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2103:12419:4991_1:N:0:GTCCGC Contig20625 1 Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2111:11809:4892_1:N:0:ATCCGC Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2111:19033:85289_1:Y:0:GTCCGC Contig19330 108174 Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2215:17683:87194_1:N:0:ATCCGC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2301:8473:84749_1:N:0:GTCCGC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2302:20333:21938_1:N:0:GTCCGC Contig20625 1 Processed 26000000 sequences so far Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2313:7263:55650_1:N:0:GTCCGC Contig84 1 Processed 28000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2316:8735:83687_1:Y:0:GTCCGC Contig16668 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1101:5169:64610_1:N:0:GTCCGC Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1101:14063:73454_1:N:0:GTCCGC Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1107:15957:6375_1:N:0:GTCCGC Contig18174 105892 Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:11702:34876_1:N:0:GTCCGC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:4155:65924_1:N:0:GTCCGC Contig20140 129024 Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1202:12382:15203_1:N:0:GTCCGC Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1203:19217:38055_1:N:0:GTCCGC Contig19826 1 Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:13243:57486_1:N:0:GTCCGC Contig19330 108174 Processed 32000000 sequences so far Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:11257:9892_1:N:0:GTCCGC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1306:10690:94542_1:N:0:GTCCGC Contig19330 108174 Processed 34000000 sequences so far Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:7467:83052_1:N:0:GTCCGC Contig16668 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2104:13190:73051_1:N:0:GTCCGC Contig468 2 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2109:14336:27688_1:N:0:ATCCGC Contig18174 105892 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2114:21015:100130_1:N:0:GTCCGC Contig19330 108175 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2201:11392:40198_1:N:0:GTCCGC Contig18174 105892 Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2206:2193:50651_1:Y:0:GTCCGC Contig0 1 Processed 39000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2215:1338:95508_1:N:0:GTCCGC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2216:6325:84974_1:N:0:GTCCGC Contig65 107630 Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2308:6882:78130_1:Y:0:GTCCGT Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2309:19974:3544_1:N:0:GTCCGC Contig5 130492 Processed 41000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2313:5720:54875_1:N:0:GTCCGC Contig18174 105892 Processed 42000000 sequences so far 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 40409777 (96.05%) aligned 0 times 686426 (1.63%) aligned exactly 1 time 974343 (2.32%) aligned >1 times 3.95% overall alignment rate 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 40811778 (97.01%) aligned 0 times 558490 (1.33%) aligned exactly 1 time 700278 (1.66%) aligned >1 times 2.99% overall alignment rate 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 40783529 (96.94%) aligned 0 times 573525 (1.36%) aligned exactly 1 time 713492 (1.70%) aligned >1 times 3.06% overall alignment rate 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 40350365 (95.91%) aligned 0 times 738696 (1.76%) aligned exactly 1 time 981485 (2.33%) aligned >1 times 4.09% 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: 1869213 Mapping efficiency: 4.4% Sequences with no alignments under any condition: 38251437 Sequences did not map uniquely: 1949896 Sequences which were discarded because genomic sequence could not be extracted: 48 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 390250 ((converted) top strand) CT/GA: 416810 ((converted) bottom strand) GA/CT: 512015 (complementary to (converted) top strand) GA/GA: 550090 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 11616286 Total methylated C's in CpG context: 1919141 Total methylated C's in CHG context: 67905 Total methylated C's in CHH context: 604313 Total methylated C's in Unknown context: 124 Total unmethylated C's in CpG context: 498929 Total unmethylated C's in CHG context: 2161381 Total unmethylated C's in CHH context: 6364617 Total unmethylated C's in Unknown context: 258 C methylated in CpG context: 79.4% C methylated in CHG context: 3.0% C methylated in CHH context: 8.7% C methylated in Unknown context (CN or CHN): 32.5% Bismark completed in 0d 0h 21m 30s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/olurida-bs/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1101:8422:43552_1:N:0:GTGAAA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1101:15451:70477_1:N:0:GTGAAA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1105:14982:25107_1:N:0:GTGAAA Contig19330 108174 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1106:13308:65324_1:N:0:GTGAAA Contig19330 108173 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:3700:4514_1:N:0:GTGAAA Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:5105:89213_1:N:0:GTGAAA Contig65 107630 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1109:6326:14304_1:N:0:GTGAAA Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1111:10224:15919_1:N:0:GTGAAA Contig20625 2 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1113:21233:14461_1:N:0:GTGAAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:18845:17382_1:N:0:GTGAAA Contig18024 109271 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:2697:80361_1:Y:0:GTGAAA Contig26138 2 Processed 3000000 sequences so far Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1208:7607:72155_1:N:0:GTGAAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1210:10548:54144_1:N:0:GTGAAA Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1210:7519:64795_1:N:0:GTGAAA Contig20625 111110 Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1212:4869:27313_1:N:0:GTGAAA Contig19267 115726 Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:8315:4448_1:N:0:GTGAAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1303:18190:73630_1:N:0:GTGAAA Contig19330 108174 Processed 7000000 sequences so far Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1311:6947:76570_1:N:0:GTGAAA Contig18174 105892 Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1315:12563:40522_1:N:0:GTGAAA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1315:15193:76799_1:N:0:GTGAAA Contig16668 101411 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2102:5494:52274_1:N:0:GTGAAA Contig19646 1 Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2109:16551:32050_1:N:0:GTGAAA Contig19330 108174 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2112:19621:70789_1:N:0:GTGAAA Contig18174 105892 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2116:5010:52585_1:N:0:GTGAAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2202:10521:30207_1:N:0:GTGAAA Contig16668 1 Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2205:16392:98391_1:N:0:GTGAAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2206:14619:24313_1:N:0:GTGAAA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:5412:7422_1:N:0:GTGAAA Contig23978 1 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2214:2688:38673_1:N:0:GTGAAA Contig20625 1 Processed 15000000 sequences so far Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2309:11916:15368_1:N:0:GTGAAA Contig20625 111110 Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2309:18171:95963_1:N:0:GTGAAA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:14065:18109_1:N:0:GTGAAA Contig0 1 Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2315:9312:71091_1:N:0:GTGAAA Contig20625 111109 Processed 19000000 sequences so far Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:10332:84037_1:N:0:GTGAAT Contig18174 105892 Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1114:9260:27091_1:N:0:ATGAAA Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1115:3506:62643_1:N:0:GTGAAA Contig5 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:6333:66596_1:N:0:ATGAAA Contig19330 108174 Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1203:11702:79699_1:N:0:GTGAAA Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:8018:30517_1:N:0:GTGAAA Contig3 141626 Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1303:5703:39956_1:N:0:GTGAAA Contig19330 108173 Processed 26000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1308:11676:46712_1:N:0:GTGAAA Contig5 130491 Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:5018:48312_1:N:0:GTGAAA Contig16668 101411 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:10500:78908_1:N:0:GTGAAT Contig5 2 Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2114:17617:48645_1:N:0:GTGAAA Contig18174 105892 Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:13750:2232_1:N:0:GTGAAA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:7479:3040_1:N:0:GTGAAA Contig19267 115726 Processed 32000000 sequences so far Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2213:9499:89042_1:N:0:GTGAAA Contig18174 105892 Processed 34000000 sequences so far Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2312:5355:34377_1:N:0:GTGAAA Contig16668 101411 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2313:1560:86771_1:N:0:GTGAAT Contig0 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2314:4609:15320_1:N:0:GTGAAA Contig19330 108174 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1107:5390:27752_1:N:0:GTGAAA Contig18174 105892 Processed 38000000 sequences so far Processed 39000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:5281:49984_1:N:0:GTGAAA Contig18174 105892 Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1202:10345:99248_1:N:0:GTGAAA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1203:12453:6957_1:N:0:GTGAAA Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1204:11759:12246_1:N:0:GTGAAA Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1204:11547:28835_1:N:0:GTGAAA Contig19646 1 Processed 41000000 sequences so far Processed 42000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1214:19720:47934_1:N:0:GTGAAA Contig20625 1 Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1301:10560:94623_1:N:0:GTGAAA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:10631:82051_1:N:0:GTGAAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:4970:84369_1:N:0:GTGAAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1306:8803:21056_1:N:0:GTGAAA Contig20625 111110 Processed 44000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1306:5142:97166_1:N:0:GTGAAA Contig19330 108173 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1308:13938:42620_1:N:0:GTGAAA Contig26138 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:11436:36437_1:N:0:GTGAAA Contig20140 129025 Processed 45000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1311:10819:94782_1:N:0:GTGAAA Contig19330 108174 Processed 46000000 sequences so far Processed 47000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2111:8016:28345_1:N:0:GTGAAA Contig18174 105892 Processed 48000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:15477:40064_1:N:0:GTGAAA Contig20140 129023 Processed 49000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2201:3767:96893_1:N:0:GTGAAA Contig26138 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2202:13033:9177_1:N:0:GTGAAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2202:4959:12328_1:N:0:GTGAAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2206:3540:15711_1:N:0:GTGAAA Contig20625 111110 Processed 50000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2208:10728:73345_1:N:0:GTGAAA Contig20625 111110 Processed 51000000 sequences so far Processed 52000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2305:8838:27193_1:Y:0:GTGAAA Contig20140 129023 Processed 53000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2310:17277:99490_1:N:0:GTGAAA Contig18174 105892 Processed 54000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:12604:60551_1:N:0:GTGAAA Contig20625 1 Processed 55000000 sequences so far 55048106 reads; of these: 55048106 (100.00%) were unpaired; of these: 53329830 (96.88%) aligned 0 times 749599 (1.36%) aligned exactly 1 time 968677 (1.76%) aligned >1 times 3.12% overall alignment rate 55048106 reads; of these: 55048106 (100.00%) were unpaired; of these: 52547151 (95.46%) aligned 0 times 1047255 (1.90%) aligned exactly 1 time 1453700 (2.64%) aligned >1 times 4.54% overall alignment rate 55048106 reads; of these: 55048106 (100.00%) were unpaired; of these: 53368965 (96.95%) aligned 0 times 741543 (1.35%) aligned exactly 1 time 937598 (1.70%) aligned >1 times 3.05% overall alignment rate 55048106 reads; of these: 55048106 (100.00%) were unpaired; of these: 52627594 (95.60%) aligned 0 times 986425 (1.79%) aligned exactly 1 time 1434087 (2.61%) aligned >1 times 4.40% 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: 2536705 Mapping efficiency: 4.6% Sequences with no alignments under any condition: 49739989 Sequences did not map uniquely: 2771412 Sequences which were discarded because genomic sequence could not be extracted: 75 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 501017 ((converted) top strand) CT/GA: 539128 ((converted) bottom strand) GA/CT: 728586 (complementary to (converted) top strand) GA/GA: 767899 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 15638469 Total methylated C's in CpG context: 2023305 Total methylated C's in CHG context: 79670 Total methylated C's in CHH context: 767014 Total methylated C's in Unknown context: 64 Total unmethylated C's in CpG context: 710544 Total unmethylated C's in CHG context: 2845824 Total unmethylated C's in CHH context: 9212112 Total unmethylated C's in Unknown context: 425 C methylated in CpG context: 74.0% C methylated in CHG context: 2.7% C methylated in CHH context: 7.7% C methylated in Unknown context (CN or CHN): 13.1% Bismark completed in 0d 0h 28m 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1447:2175_1:N:0:ATCACG 4 * 0 0 * * 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1103:16534:5633_1:N:0:ATCACG Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1103:12131:65981_1:N:0:ATCACG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1105:6630:96074_1:N:0:ATCACG Contig26138 2 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1112:13880:76614_1:N:0:ATCACG Contig20140 129024 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1114:2189:53720_1:N:0:ATCACG Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1201:13018:86049_1:N:0:ATCACG Contig20140 129025 Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1215:2426:62329_1:N:0:ATCACG Contig19330 108175 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1304:4911:66919_1:N:0:ATCACG Contig20625 1 Processed 6000000 sequences so far Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1312:13910:17074_1:Y:0:ATCACG Contig17050 2 Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2101:19631:79270_1:N:0:ATCACG Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2101:15013:99907_1:N:0:ATCACG Contig20140 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2107:16470:23357_1:N:0:ATCACG Contig19330 108174 Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2112:9753:66320_1:N:0:ATCACG Contig0 2 Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2203:17395:32246_1:N:0:ATCACG Contig20625 1 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2204:10353:45978_1:N:0:ATCACG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:17170:20650_1:N:0:ATCACG Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:14197:23035_1:Y:0:ATCACG Contig18174 105892 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2214:6307:42608_1:N:0:ATCACG Contig23978 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2216:6223:14433_1:N:0:ATCACG Contig18174 105892 Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2304:14427:33417_1:N:0:ATCACG Contig16668 2 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:8420:10635_1:N:0:ATCACG Contig19330 108175 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:2:1110:3922:42139_1:N:0:ATCACG Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:15193:7498_1:N:0:ATCACG Contig0 1 Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1115:6006:51596_1:N:0:ACCACG Contig20625 1 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1316:2672:68648_1:Y:0:ATCACG Contig3 141626 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2103:12381:57653_1:N:0:ATCACG Contig18052 116632 Processed 24000000 sequences so far Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2111:16766:28653_1:N:0:ATCACG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2113:16857:68720_1:N:0:ATCACG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2114:1203:40869_1:N:0:ATCACG Contig5 130492 Processed 26000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:7505:68488_1:N:0:ATCACG Contig19330 108176 Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2209:2437:6347_1:N:0:ATCACG Contig20625 2 Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2310:8475:94666_1:N:0:ATCACG Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2314:13235:86099_1:N:0:ATCACG Contig16668 2 Processed 31000000 sequences so far Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1106:10605:45383_1:N:0:ATCACG Contig20625 1 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1112:12687:78124_1:N:0:ATCACG Contig3 141626 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1114:9163:87394_1:N:0:ATCACG Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1114:6194:97506_1:N:0:ATCACG Contig20625 111110 Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1206:12094:82039_1:N:0:ATCACG Contig0 1 Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1208:14765:72184_1:Y:0:ATCACG Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:11654:90808_1:N:0:ATCACG Contig3 141626 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1302:4350:53545_1:N:0:ATCACG Contig3 141627 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1304:9918:42970_1:N:0:ATCACG Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1307:13370:90658_1:N:0:ATCACG Contig18174 105892 Processed 38000000 sequences so far Processed 39000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2102:4549:88245_1:N:0:ATCACG Contig20625 111110 Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2111:17826:52177_1:Y:0:ATCACG Contig23978 2 Processed 41000000 sequences so far Processed 42000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2209:2882:26175_1:N:0:ATCACG Contig16668 2 Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2209:9490:48932_1:N:0:ATCACG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2212:12187:58104_1:N:0:ATCACG Contig18052 116631 Processed 44000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2301:12341:32938_1:N:0:ATCACG Contig16668 101411 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2303:13062:41907_1:N:0:ATCACG Contig26138 101632 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2305:8257:11825_1:N:0:ATCACG Contig18174 105892 Processed 45000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2306:7276:25813_1:N:0:ATCACG Contig20625 111109 Processed 46000000 sequences so far 46792286 reads; of these: 46792286 (100.00%) were unpaired; of these: 44865986 (95.88%) aligned 0 times 791898 (1.69%) aligned exactly 1 time 1134402 (2.42%) aligned >1 times 4.12% overall alignment rate 46792286 reads; of these: 46792286 (100.00%) were unpaired; of these: 45328964 (96.87%) aligned 0 times 654344 (1.40%) aligned exactly 1 time 808978 (1.73%) aligned >1 times 3.13% overall alignment rate 46792286 reads; of these: 46792286 (100.00%) were unpaired; of these: 45366166 (96.95%) aligned 0 times 636822 (1.36%) aligned exactly 1 time 789298 (1.69%) aligned >1 times 3.05% overall alignment rate 46792286 reads; of these: 46792286 (100.00%) were unpaired; of these: 44793151 (95.73%) aligned 0 times 848214 (1.81%) aligned exactly 1 time 1150921 (2.46%) aligned >1 times 4.27% 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: 2117445 Mapping efficiency: 4.5% Sequences with no alignments under any condition: 42430582 Sequences did not map uniquely: 2244259 Sequences which were discarded because genomic sequence could not be extracted: 52 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 432543 ((converted) top strand) CT/GA: 474012 ((converted) bottom strand) GA/CT: 585370 (complementary to (converted) top strand) GA/GA: 625468 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 13077617 Total methylated C's in CpG context: 1860212 Total methylated C's in CHG context: 70565 Total methylated C's in CHH context: 647883 Total methylated C's in Unknown context: 68 Total unmethylated C's in CpG context: 609554 Total unmethylated C's in CHG context: 2297560 Total unmethylated C's in CHH context: 7591843 Total unmethylated C's in Unknown context: 342 C methylated in CpG context: 75.3% C methylated in CHG context: 3.0% C methylated in CHH context: 7.9% C methylated in Unknown context (CN or CHN): 16.6% Bismark completed in 0d 0h 24m 0s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/olurida-bs/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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/v082/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 AATGTAATGATGTTAAATATGTATTAGAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 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/v082/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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1103:18163:37429_1:N:0:CGATGT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1106:14878:6807_1:N:0:CGATGT Contig19330 108174 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:19798:94735_1:N:0:CGATGT Contig19267 115726 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1114:18086:6024_1:N:0:CGATGT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:2843:95821_1:N:0:CGATGT Contig19330 108175 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1208:2036:69459_1:N:0:CGATGT Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1209:7386:15832_1:N:0:CGATGT Contig19330 108174 Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1209:16561:91683_1:N:0:CGATGT Contig0 1 Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1303:13285:79795_1:N:0:CGATGT Contig20140 129024 Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1307:10585:85454_1:N:0:CGATGT Contig16668 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1311:3680:63174_1:N:0:CGATGC Contig0 1 Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2113:12176:86584_1:N:0:CGATGT Contig18052 116632 Processed 10000000 sequences so far Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2205:5198:53831_1:N:0:CGATGT Contig20625 2 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2211:20909:61714_1:N:0:CGATGT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2213:17716:82736_1:N:0:CGATGT Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2216:3825:90184_1:N:0:CGATGT Contig20140 129025 Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2302:13585:21094_1:N:0:CGATGT Contig7 109638 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2302:20893:72574_1:N:0:CGATGT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2303:6553:38778_1:Y:0:CGATGT Contig19330 108175 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2307:11499:3432_1:Y:0:CCATGT Contig26138 2 Processed 14000000 sequences so far Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2316:19872:73946_1:N:0:CGATGT Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1103:9054:61002_1:N:0:CGATGT Contig18052 116632 Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1107:17192:66875_1:N:0:CGATGT Contig18174 105892 Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:9877:86412_1:N:0:CGATGT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1115:17029:48906_1:N:0:CGATGT Contig23978 2 Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:7705:7662_1:N:0:CGATGT Contig9 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:6579:93765_1:N:0:CGATGT Contig20625 1 Processed 19000000 sequences so far Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1213:13224:50878_1:N:0:CGATGT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1303:14321:16030_1:N:0:CGATGT Contig5 1 Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1309:9339:28039_1:N:0:CGATGT Contig20140 129024 Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1310:5023:52509_1:N:0:CGATGT Contig23978 1 Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1315:17846:61549_1:N:0:CGATGT Contig3 141626 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2102:5527:4801_1:N:0:CGATGT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2104:12383:31117_1:N:0:CGATGT Contig3 141626 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2104:4738:34575_1:N:0:CGATGT Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2104:4168:69539_1:N:0:CGATGT Contig0 1 Processed 24000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2109:6740:82940_1:N:0:CGATGT Contig20625 1 Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2113:6022:21315_1:N:0:CGATGT Contig18174 105892 Processed 26000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:6564:10329_1:N:0:CGTTGT Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:15561:58047_1:N:0:CGATGT Contig3 141627 Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2209:7470:83035_1:N:0:CGATGT Contig19330 108175 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2212:16563:69280_1:N:0:CGATGT Contig26138 1 Processed 28000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:18548:58057_1:N:0:CGATGT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2304:11495:50419_1:N:0:CGATGT Contig3 1 Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2307:16861:95644_1:N:0:CGATGT Contig0 1 Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2315:20385:59832_1:N:0:CGATGT Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:20515:49490_1:N:0:CGATAT Contig20625 1 Processed 31000000 sequences so far Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:15686:72509_1:N:0:CGATGT Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1114:8541:6362_1:N:0:CGATGT Contig18174 105892 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1204:14153:20011_1:N:0:CGATGT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1204:3262:88311_1:N:0:CGATGT Contig20140 129025 Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1206:7392:75710_1:N:0:CGATGT Contig19330 108175 Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:7233:61763_1:N:0:CGATGT Contig0 1 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:6044:73666_1:N:0:CGATGT Contig18052 116632 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1305:16860:3157_1:N:0:CGATGT Contig18024 2 Processed 37000000 sequences so far Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1316:14917:65787_1:N:0:CGATGT Contig19330 108174 Processed 39000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2106:19824:34720_1:N:0:CGATGT Contig18024 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2107:16122:20504_1:N:0:CGATGT Contig20625 1 Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2112:5890:33464_1:N:0:CGATGT Contig18174 105892 Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2214:1955:15013_1:Y:0:CGATGT Contig16668 2 Processed 44000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2307:2764:48912_1:N:0:CGATGT Contig20140 129024 Processed 45000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2315:13918:25422_1:N:0:CGATGT Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2315:1434:47852_1:N:0:CGATGT Contig20625 1 Processed 46000000 sequences so far 46105140 reads; of these: 46105140 (46105140100.00 reads; of these:% ) were unpaired; of these: 46105140 (44733268 (97.02%) aligned 0 times 609624 (1.32%) aligned exactly 1 time 100.00 %762248) were unpaired; of these: ( 1.65 %44705477) aligned >1 times ( 96.962.98%%) aligned 0 times overall alignment rate 620042 (1.34%) aligned exactly 1 time 779621 (1.69%) aligned >1 times 3.04% overall alignment rate 46105140 reads; of these: 46105140 (100.00%) were unpaired; of these: 44201005 (95.87%) aligned 0 times 789464 (1.71%) aligned exactly 1 time 1114671 (2.42%) aligned >1 times 4.13% overall alignment rate 46105140 reads; of these: 46105140 (100.00%) were unpaired; of these: 44138412 (95.73%) aligned 0 times 836708 (1.81%) aligned exactly 1 time 1130020 (2.45%) aligned >1 times 4.27% 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: 2050964 Mapping efficiency: 4.4% Sequences with no alignments under any condition: 41863391 Sequences did not map uniquely: 2190785 Sequences which were discarded because genomic sequence could not be extracted: 63 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 413480 ((converted) top strand) CT/GA: 445517 ((converted) bottom strand) GA/CT: 579519 (complementary to (converted) top strand) GA/GA: 612385 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 12647847 Total methylated C's in CpG context: 1678932 Total methylated C's in CHG context: 69149 Total methylated C's in CHH context: 679879 Total methylated C's in Unknown context: 82 Total unmethylated C's in CpG context: 579763 Total unmethylated C's in CHG context: 2266089 Total unmethylated C's in CHH context: 7374035 Total unmethylated C's in Unknown context: 359 C methylated in CpG context: 74.3% C methylated in CHG context: 3.0% C methylated in CHH context: 8.4% C methylated in Unknown context (CN or CHN): 18.6% Bismark completed in 0d 0h 23m 40s ==================== 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1105:14953:38138_1:N:0:TTAGGC Contig18174 105893 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1106:10441:63859_1:N:0:TTAGGC Contig19330 108174 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:11859:17344_1:Y:0:TTATGC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1111:4628:7534_1:N:0:TTAGGC Contig20625 1 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1114:4061:95506_1:Y:0:TTAGGA Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1116:11034:5119_1:N:0:TTAGGC Contig20140 129025 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1207:7692:16584_1:N:0:TTAGGC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1207:17428:63236_1:N:0:TTAGGC Contig20625 1 Processed 4000000 sequences so far Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1215:16303:27171_1:N:0:TTAGGC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1301:13904:10639_1:N:0:TTAGGC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1303:18998:23790_1:N:0:TTAGGC Contig20625 1 Processed 6000000 sequences so far Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1314:13755:55713_1:N:0:TTAGGC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1314:13551:87290_1:N:0:TTAGGC Contig16668 101411 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1315:14393:9707_1:Y:0:TTAGGC Contig20625 2 Processed 8000000 sequences so far Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2105:11905:74714_1:N:0:TTAGGC Contig16668 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2107:7038:13012_1:N:0:TTAGGC Contig3 141626 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2110:17798:23071_1:N:0:TTAGGC Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2110:20528:49968_1:N:0:TTAGGC Contig84 102773 Processed 10000000 sequences so far Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2202:7780:9880_1:N:0:TTAGGC Contig20625 2 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:5308:95683_1:N:0:TTAGGC Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2210:19717:89117_1:N:0:TTAGGC Contig19646 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2211:12032:22503_1:N:0:TTAGGC Contig20625 1 Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2215:3853:78271_1:N:0:TTAGGC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2301:14242:96288_1:N:0:TTAGGC Contig20140 129024 Processed 14000000 sequences so far Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:6173:88617_1:N:0:TTAGGC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2313:19059:7902_1:N:0:TTAGGC Contig9 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2315:16980:20048_1:Y:0:TTAGGC Contig0 1 Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2316:14310:18590_1:N:0:TTAGGC Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1102:15377:69915_1:N:0:TTAGGC Contig20625 1 Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1109:15101:81801_1:N:0:TTAGGC Contig19646 1 Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:5444:4826_1:N:0:TTAGGC Contig23978 1 Processed 19000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:6665:14329_1:N:0:TTAGGC Contig16668 1 Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1208:6280:37952_1:N:0:TTAGGC Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1210:15884:32881_1:N:0:TTAGGC Contig23978 2 Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1213:18040:43800_1:N:0:TTAGGC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1301:18208:84132_1:N:0:TTAGGC Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1302:11723:86060_1:N:0:TTAGGC Contig20140 129025 Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1307:12748:36113_1:N:0:TTAGGC Contig0 2 Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1311:11299:69815_1:N:0:TTAGGC Contig84 102773 Processed 24000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2102:4715:27465_1:N:0:TTAGGC Contig20140 129025 Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2106:13237:17883_1:N:0:TTAGGC Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2107:14166:95980_1:N:0:TTAGGC Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2108:9592:35691_1:N:0:TTAGGC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2110:19769:42778_1:N:0:TTAGGC Contig18174 105892 Processed 26000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2113:19699:60147_1:N:0:TTAGGC Contig9 1 Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2202:11212:75381_1:N:0:TTAGGC Contig20140 129025 Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2309:18142:65189_1:Y:0:TTAGGC Contig19646 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2310:8926:30794_1:N:0:TTAGGC Contig18174 105892 Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1101:17248:71079_1:N:0:TTAGGC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:2991:3382_1:N:0:TTAGGC Contig20625 2 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1105:12847:85993_1:N:0:TTAGGC Contig19826 2 Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1114:16371:99720_1:N:0:TTAGGC Contig19330 108181 Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1206:16637:14170_1:N:0:TTAGGC Contig9 1 Processed 36000000 sequences so far Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1213:8726:10959_1:N:0:TTAGGC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1213:11928:22421_1:Y:0:TTAGGC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1216:6225:52794_1:N:0:TTAGGC Contig19330 108176 Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:4230:44170_1:N:0:TTAGGC Contig19330 108176 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1305:12731:94405_1:N:0:TTAGGC Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1307:2391:12215_1:N:0:TTAGGC Contig20625 1 Processed 39000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:6492:49312_1:N:0:TTAGGC Contig20625 1 Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1316:17083:23193_1:N:0:TTAGGC Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2102:3272:71803_1:N:0:TTAGAC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2102:18166:91929_1:N:0:TTAGGC Contig23978 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2103:9927:66806_1:N:0:TTAGGC Contig19826 1 Processed 41000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2106:2937:76134_1:N:0:TTAGGC Contig19826 1 Processed 42000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2111:3994:98125_1:N:0:TTAGGC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2115:17429:71106_1:N:0:TTAGGC Contig19826 1 Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2206:8041:27866_1:N:0:TTAGGC Contig18174 105892 Processed 44000000 sequences so far Processed 45000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2215:7014:63608_1:N:0:TTAGGC Contig7 109642 Processed 46000000 sequences so far Processed 47000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2313:13154:30543_1:N:0:TTAGGC Contig0 1 Processed 48000000 sequences so far 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 46926855 (97.00%) aligned 0 times 661559 (1.37%) aligned exactly 1 time 788315 (1.63%) aligned >1 times 3.00% overall alignment rate 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 46959732 (97.07%) aligned 0 times 644084 (1.33%) aligned exactly 1 time 772913 (1.60%) aligned >1 times 2.93% overall alignment rate 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 46352150 (95.81%) aligned 0 times 872144 (1.80%) aligned exactly 1 time 1152435 (2.38%) aligned >1 times 4.19% overall alignment rate 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 46424749 (95.97%) aligned 0 times 812501 (1.68%) aligned exactly 1 time 1139479 (2.36%) aligned >1 times 4.03% 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: 2160248 Mapping efficiency: 4.5% Sequences with no alignments under any condition: 43980854 Sequences did not map uniquely: 2235627 Sequences which were discarded because genomic sequence could not be extracted: 70 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 439520 ((converted) top strand) CT/GA: 477578 ((converted) bottom strand) GA/CT: 602057 (complementary to (converted) top strand) GA/GA: 641023 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 13230157 Total methylated C's in CpG context: 1864732 Total methylated C's in CHG context: 69400 Total methylated C's in CHH context: 642023 Total methylated C's in Unknown context: 54 Total unmethylated C's in CpG context: 595943 Total unmethylated C's in CHG context: 2273419 Total unmethylated C's in CHH context: 7784640 Total unmethylated C's in Unknown context: 344 C methylated in CpG context: 75.8% C methylated in CHG context: 3.0% C methylated in CHH context: 7.6% C methylated in Unknown context (CN or CHN): 13.6% Bismark completed in 0d 0h 24m 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1102:12762:55159_1:N:0:TGACCA Contig19826 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1102:10346:77907_1:N:0:TGACCA Contig23978 1 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:17636:86747_1:N:0:TGACCA Contig20625 1 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1203:13938:3051_1:Y:0:TGACCA Contig20625 111110 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1205:4416:11571_1:N:0:TGACCA Contig19330 108174 Processed 4000000 sequences so far Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:2563:78548_1:Y:0:TGACCA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1304:14011:45459_1:N:0:TGACCA Contig3 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1305:5786:12261_1:N:0:TGACCA Contig18174 105892 Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1306:11122:69126_1:N:0:TGACCA Contig18174 105891 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1307:8586:14334_1:N:0:TGACCA Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1309:4884:99258_1:N:0:TGACCA Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1312:12992:21990_1:Y:0:TGACCA Contig16668 2 Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2101:7403:47959_1:Y:0:TGACCA Contig9 1 Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2103:19319:57405_1:N:0:TGACCA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2104:12040:99353_1:N:0:TGACCA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2105:9339:31518_1:N:0:TGACCA Contig20625 1 Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2110:10601:73899_1:Y:0:TGACCA Contig3 141628 Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2116:9285:49006_1:N:0:TGACCA Contig26138 101632 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2203:6567:43514_1:N:0:TGACCA Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2206:17292:45208_1:Y:0:TGACCA Contig19330 108174 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:5728:10479_1:N:0:TGACCA Contig20625 1 Processed 12000000 sequences so far Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2308:7548:84999_1:N:0:TGACCA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2309:14438:62565_1:N:0:TGACCA Contig19330 108174 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2310:18348:27173_1:N:0:TGACCA Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:3649:21741_1:N:0:TGACCA Contig23978 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2315:16866:20805_1:N:0:TGACCA Contig18174 105892 Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1102:15528:4957_1:N:0:TGACCA Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1104:9563:80995_1:N:0:TGACCA Contig18174 105892 Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1109:16760:5232_1:N:0:AGACCA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1111:13633:12656_1:N:0:TGACCA Contig16668 101411 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:20250:16853_1:N:0:TGACCA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:13597:100021_1:N:0:TGACCA Contig84 102773 Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:17884:36100_1:N:0:TGACCA Contig18174 105892 Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:8483:26193_1:N:0:TGACCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:14838:51651_1:N:0:TGACCA Contig23978 2 Processed 19000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1215:8282:45879_1:Y:0:TGACCA Contig20625 1 Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1302:2196:29258_1:N:0:TGACCA Contig20625 1 Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1307:16204:94945_1:N:0:TGACCA Contig18174 105892 Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1313:7722:90530_1:N:0:TGACCA Contig3 141626 Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2105:5941:51186_1:N:0:TGACCA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2105:12849:93799_1:N:0:TGACCA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2106:7761:35650_1:N:0:TGACCA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2106:15688:61849_1:Y:0:TGACCT Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2107:20597:36073_1:N:0:TGACCA Contig19267 115726 Processed 24000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2110:2685:98347_1:Y:0:TGACCA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2111:12852:19882_1:N:0:TGACCA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2111:18995:22053_1:N:0:TGACCA Contig16668 2 Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2202:9620:29031_1:N:0:TGACCA Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2202:19188:62655_1:N:0:TGACCA Contig16668 101411 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2202:7426:65955_1:N:0:TGACCA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:15874:18636_1:N:0:TGACCA Contig0 2 Processed 26000000 sequences so far Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:12280:27794_1:Y:0:TGACCA Contig16668 2 Processed 28000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2305:17538:18994_1:N:0:TGACCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2307:12122:55431_1:N:0:CGACCA Contig20140 129025 Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2314:5566:81432_1:N:0:TGACCA Contig20140 129023 Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1104:16458:74198_1:N:0:TGACCA Contig16668 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1105:18985:99338_1:N:0:TGACCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1106:8822:29930_1:N:0:TGACCA Contig20140 129024 Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1108:19111:68013_1:N:0:TGACCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1113:19897:17352_1:N:0:TGACCA Contig19646 1 Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1202:11914:30219_1:N:0:TGACCA Contig5 130492 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1209:14836:77361_1:N:0:TGACCA Contig20625 2 Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1215:3963:72662_1:N:0:TGACCA Contig0 1 Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1301:2446:98861_1:N:0:TGACCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1302:6388:86991_1:N:0:TGACCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:17160:82903_1:N:0:TGACCA Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1305:16357:45292_1:N:0:TGACCA Contig18174 105892 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1312:16035:22195_1:N:0:TGACCA Contig20625 1 Processed 37000000 sequences so far Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2109:13280:57128_1:N:0:TGACCA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2110:4136:38164_1:N:0:TGACCA Contig0 1 Processed 39000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2116:14695:53645_1:Y:0:TGACCA Contig18174 105892 Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2202:12883:86800_1:N:0:TGACCA Contig19330 108184 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2204:20290:77816_1:N:0:TGACCA Contig0 1 Processed 41000000 sequences so far Processed 42000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2304:18979:3558_1:N:0:TGACCA Contig26138 1 Processed 43000000 sequences so far Processed 44000000 sequences so far 44905078 reads; of these: 44905078 (100.00%) were unpaired; of these: 43004112 (95.77%) aligned 0 times 811331 (1.81%) aligned exactly 1 time 1089635 (2.43%) aligned >1 times 4.23% overall alignment rate 44905078 reads; of these: 44905078 (100.00%) were unpaired; of these: 43064110 (95.90%) aligned 0 times 760924 (1.69%) aligned exactly 1 time 1080044 (2.41%) aligned >1 times 4.10% overall alignment rate 44905078 reads; of these: 44905078 (100.00%) were unpaired; of these: 43577306 (97.04%) aligned 0 times 597245 (1.33%) aligned exactly 1 time 730527 (1.63%) aligned >1 times 2.96% overall alignment rate 44905078 reads; of these: 44905078 (100.00%) were unpaired; of these: 43548424 (96.98%) aligned 0 times 609112 (1.36%) aligned exactly 1 time 747542 (1.66%) aligned >1 times 3.02% 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: 2010139 Mapping efficiency: 4.5% Sequences with no alignments under any condition: 40784777 Sequences did not map uniquely: 2110162 Sequences which were discarded because genomic sequence could not be extracted: 74 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 407301 ((converted) top strand) CT/GA: 439778 ((converted) bottom strand) GA/CT: 568615 (complementary to (converted) top strand) GA/GA: 594371 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 12404965 Total methylated C's in CpG context: 1806777 Total methylated C's in CHG context: 69275 Total methylated C's in CHH context: 620239 Total methylated C's in Unknown context: 50 Total unmethylated C's in CpG context: 510473 Total unmethylated C's in CHG context: 2191210 Total unmethylated C's in CHH context: 7206991 Total unmethylated C's in Unknown context: 290 C methylated in CpG context: 78.0% C methylated in CHG context: 3.1% C methylated in CHH context: 7.9% C methylated in Unknown context (CN or CHN): 14.7% Bismark completed in 0d 0h 23m 2s ==================== 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1101:9627:82262_1:N:0:ACAGTG Contig20625 1 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:10291:69608_1:N:0:ACAGTG Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1110:15053:47598_1:N:0:ACAGTG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1111:2796:72052_1:Y:0:ACAGTG Contig16668 1 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1113:18238:5910_1:N:0:ACAGTG Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1201:4738:72940_1:N:0:ACAGTG Contig9 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1201:4724:72953_1:N:0:ACAGTG Contig9 1 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1204:8197:79912_1:N:0:ACAGTG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1206:8248:84514_1:N:0:ACAGTG Contig19330 108174 Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1210:18006:65523_1:N:0:ACAGTG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1212:3025:46139_1:N:0:ACAGTG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1213:9005:24062_1:N:0:ACAGTG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1213:2370:97269_1:N:0:ACAGTG Contig18174 105892 Processed 5000000 sequences so far Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1305:5389:50043_1:N:0:ACAGTG Contig20140 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1307:16038:26443_1:N:0:ACAGTG Contig19330 108174 Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1311:1477:47704_1:N:0:ACAGTG Contig20625 1 Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2102:19610:58093_1:N:0:ACAGTG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2105:1997:46322_1:N:0:ACAGTG Contig18174 105892 Processed 9000000 sequences so far Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2201:13417:51824_1:N:0:ACAGTG Contig18174 105892 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2205:16087:63977_1:N:0:ACAGTG Contig468 111853 Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2306:11613:84702_1:N:0:ACAGTG Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2308:12828:16278_1:N:0:ACAGTG Contig19330 108175 Processed 15000000 sequences so far Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1104:12149:19162_1:N:0:ACAGTG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1106:21180:41958_1:Y:0:ACAGTG Contig19646 1 Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1107:18020:92544_1:N:0:ACAGTG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1110:2479:97900_1:N:0:ACAGTG Contig18024 2 Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1113:10890:76166_1:N:0:ACAGTG Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1113:21059:87099_1:N:0:ACAGTG Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:14098:24525_1:N:0:ACAGTG Contig16668 1 Processed 19000000 sequences so far Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1212:1732:69517_1:N:0:ACAGTG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1214:1513:11433_1:N:0:ACAGTG Contig18174 105892 Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1302:1198:33413_1:N:0:ACAGTG Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1302:13477:46519_1:N:0:ACAGTG Contig19330 108174 Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1307:8604:8728_1:N:0:ACAGTG Contig19330 108174 Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1311:9501:71787_1:N:0:ACAGTG Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:19139:41663_1:N:0:ACAGTG Contig84 102773 Processed 24000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2104:10791:8429_1:N:0:ACAGTG Contig18174 105892 Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2210:1838:25721_1:N:0:ACAGTG Contig65 107630 Processed 28000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2211:7093:96605_1:N:0:ACAGTG Contig0 1 Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2302:14811:3344_1:N:0:ACAGTG Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2302:6463:21360_1:N:0:ACAGTG Contig9 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:8468:22527_1:N:0:ACAGTG Contig18024 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2304:18385:47615_1:N:0:ACAGTG Contig20140 129024 Processed 30000000 sequences so far Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2314:19440:23083_1:N:0:ACAGTG Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1101:14418:17204_1:N:0:ACAGTG Contig18174 105892 Processed 32000000 sequences so far Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1110:11320:77484_1:Y:0:ACTGTG Contig9 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1114:20072:72907_1:N:0:ACAGTG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1114:7032:85562_1:N:0:ACAGTG Contig18174 105892 Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1202:3866:66862_1:N:0:ACAGTG Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1203:2441:31848_1:N:0:ACAGTG Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1203:1560:62918_1:N:0:ACAGTG Contig19330 108174 Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1207:4718:36260_1:N:0:ACAGTG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:15499:92562_1:N:0:ACAGTG Contig18174 105892 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:15997:39740_1:N:0:ACAGTG Contig19330 108174 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1301:15645:41639_1:N:0:ACAGTG Contig18024 2 Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1309:14731:64280_1:N:0:ACAGTG Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:6743:3706_1:N:0:ACAGTG Contig16668 2 Processed 39000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:1719:80662_1:N:0:ACAGTG Contig19330 108174 Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2103:9645:28741_1:N:0:ACAGTG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2103:12539:42678_1:N:0:ACAGTG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2104:20076:91748_1:N:0:ACAGTG Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2106:5125:64320_1:N:0:ACAGTG Contig3 141635 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2108:19769:15816_1:N:0:ACAGTG Contig20625 111111 Processed 41000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:17255:6167_1:N:0:ACAGTG Contig9 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2114:6781:21623_1:N:0:ACAGTG Contig26138 1 Processed 42000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2115:5941:82722_1:N:0:ACAGTG Contig20625 2 Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2207:20404:92037_1:N:0:ACAGTG Contig3 141635 Processed 44000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2216:18106:26453_1:N:0:ACAGTG Contig20140 129024 Processed 45000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2302:1769:28002_1:N:0:ACAGTG Contig18174 105891 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2303:19304:82574_1:N:0:ACAGTG Contig3 141627 Processed 46000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2309:18145:56126_1:N:0:ACAGTG Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2313:14829:24148_1:N:0:CCAGTG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2313:10313:99415_1:N:0:ACAGTG Contig20625 1 Processed 47000000 sequences so far 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 45901698 (96.84%) aligned 0 times 642579 (1.36%) aligned exactly 1 time 857459 (1.81%) aligned >1 times 3.16% overall alignment rate 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 45933063 (96.90%) aligned 0 times 632678 (1.33%) aligned exactly 1 time 835995 (1.76%) aligned >1 times 3.10% overall alignment rate 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 45355695 (95.68%) aligned 0 times 838553 (1.77%) aligned exactly 1 time 1207488 (2.55%) aligned >1 times 4.32% overall alignment rate 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 45414258 (95.81%) aligned 0 times 791308 (1.67%) aligned exactly 1 time 1196170 (2.52%) aligned >1 times 4.19% 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: 2079533 Mapping efficiency: 4.4% Sequences with no alignments under any condition: 42966736 Sequences did not map uniquely: 2355467 Sequences which were discarded because genomic sequence could not be extracted: 73 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 426898 ((converted) top strand) CT/GA: 463069 ((converted) bottom strand) GA/CT: 580972 (complementary to (converted) top strand) GA/GA: 608521 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 12804963 Total methylated C's in CpG context: 1404189 Total methylated C's in CHG context: 61962 Total methylated C's in CHH context: 717589 Total methylated C's in Unknown context: 50 Total unmethylated C's in CpG context: 670203 Total unmethylated C's in CHG context: 2249103 Total unmethylated C's in CHH context: 7701917 Total unmethylated C's in Unknown context: 461 C methylated in CpG context: 67.7% C methylated in CHG context: 2.7% C methylated in CHH context: 8.5% C methylated in Unknown context (CN or CHN): 9.8% Bismark completed in 0d 0h 24m 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1103:19566:31030_1:N:0:GCCAAT Contig16668 2 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:10261:32509_1:N:0:GCCAAT Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:13875:86436_1:N:0:GCCAAT Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1112:20046:53395_1:N:0:GCCAAT Contig19826 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1112:1695:59634_1:N:0:GCCAAT Contig18174 105892 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1202:9110:31324_1:N:0:GCCAAT Contig16668 2 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1205:16523:58320_1:N:0:GCCAAT Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1207:20556:33924_1:N:0:GCCAAT Contig19330 108174 Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1209:16965:50412_1:N:0:ACCAAT Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1213:18318:72064_1:Y:0:GCCAAT Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1213:13882:86031_1:N:0:GCCAAT Contig18174 105892 Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1301:15545:65374_1:N:0:GCCAAT Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1304:8653:39342_1:N:0:GCCAAT Contig18174 105892 Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:10694:60816_1:N:0:GCCAAT Contig18174 105891 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:14284:86085_1:N:0:GCCAAT Contig20625 2 Processed 7000000 sequences so far Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2101:6090:36151_1:N:0:GCCAAT Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2103:11873:80751_1:N:0:GCCAAT Contig26138 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2106:21311:17006_1:Y:0:GCCAAT Contig5 130493 Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2109:4436:46904_1:N:0:GCCAAT Contig18174 105892 Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2115:17720:76231_1:N:0:GCCAAT Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2116:14533:2445_1:N:0:GCCAAT Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2116:1921:64363_1:N:0:GCCAAT Contig26138 1 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:8973:63498_1:N:0:GCCAAT Contig20140 129024 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2216:15670:87024_1:Y:0:GCCTAT Contig18174 105892 Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2306:8832:51104_1:N:0:GCCAAT Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2307:12314:14413_1:N:0:GCCAAT Contig20625 1 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2308:7789:34740_1:N:0:GCCAAT Contig16668 2 Processed 15000000 sequences so far Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1106:10975:76809_1:N:0:GCCAAT Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1108:19516:4364_1:Y:0:GCCAAT Contig16668 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1109:20743:39950_1:N:0:GCCAAT Contig19826 2 Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1111:10580:45701_1:N:0:GCCAAT Contig18174 105892 Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1205:11383:80655_1:N:0:GCCAAT Contig18174 105892 Processed 19000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:14049:7392_1:Y:0:GCCAAT Contig26138 1 Processed 20000000 sequences so far Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1306:18074:88774_1:N:0:GCCAAT Contig19330 108175 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1307:4286:94032_1:N:0:GCCAAT Contig20625 2 Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1312:2617:55991_1:N:0:GCCAAT Contig5 130492 Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:16623:94869_1:Y:0:GCCAAT Contig3 141626 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2102:11679:11129_1:Y:0:GCTAAT Contig18024 109269 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2104:18136:14001_1:N:0:GCCAAT Contig20625 1 Processed 24000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2105:5520:33029_1:N:0:GCCAAT Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2106:18653:76470_1:N:0:GCCAAT Contig20140 129024 Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2113:13862:14261_1:N:0:GCCAAT Contig19826 1 Processed 26000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:4133:62868_1:N:0:GCCAAT Contig18174 105892 Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2210:1327:75619_1:N:0:GCCAAT Contig18174 105892 Processed 28000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2216:8840:33364_1:N:0:GCCAAT Contig18174 105892 Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2308:15787:17110_1:N:0:GCCAAT Contig19826 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2308:14278:53366_1:N:0:GCCAAT Contig20625 111110 Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2311:19948:96786_1:N:0:GCCAAT Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2312:15121:71857_1:N:0:GCCAAT Contig20625 1 Processed 31000000 sequences so far Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1108:7003:91251_1:N:0:ACCAAT Contig17876 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1112:18394:75340_1:N:0:GCCAAT Contig20140 129024 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:6270:51260_1:N:0:GCCAAT Contig16668 2 Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1206:15793:19137_1:N:0:GCCAAT Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1206:6147:52622_1:N:0:GCCAAT Contig9 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1209:8959:8826_1:N:0:GCCAAT Contig18174 105892 Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1307:12420:22119_1:N:0:GCCAAT Contig3 141627 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1307:5181:85899_1:N:0:GCCAAT Contig23978 1 Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1312:16872:49753_1:N:0:GCCAAT Contig19826 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1313:7805:98158_1:N:0:GCCAAT Contig0 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2101:17866:22288_1:N:0:GCCAAT Contig18174 105892 Processed 39000000 sequences so far Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:7178:9875_1:Y:0:GCCTAT Contig16668 101411 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:5295:90199_1:N:0:GCCAAT Contig20625 1 Processed 41000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2114:10418:68658_1:N:0:GCCAAT Contig18174 105891 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2201:11036:76057_1:N:0:GCCAAT Contig7 109638 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2203:13593:72214_1:N:0:GCCAAT Contig18174 105892 Processed 42000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2211:8173:3640_1:N:0:GCCAAT Contig18174 105892 Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2215:7337:80230_1:N:0:GCCAAT Contig20625 1 Processed 44000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2302:12385:51273_1:N:0:GCCAAT Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2304:11255:24141_1:N:0:GCCAAT Contig5 2 Processed 45000000 sequences so far Processed 46000000 sequences so far 46455148 reads; of these: 46455148 (100.00%) were unpaired; of these: 45064006 (97.01%) aligned 0 times 600256 (1.29%) aligned exactly 1 time 790886 (1.70%) aligned >1 times 2.99% overall alignment rate 46455148 reads; of these: 46455148 (100.00%) were unpaired; of these: 44419827 (95.62%) aligned 0 times 826900 (1.78%) aligned exactly 1 time 1208421 (2.60%) aligned >1 times 4.38% overall alignment rate 46455148 reads; of these: 46455148 (100.00%) were unpaired; of these: 44476913 (95.74%) aligned 0 times 775732 (1.67%) aligned exactly 1 time 1202503 (2.59%) aligned >1 times 4.26% overall alignment rate 46455148 reads; of these: 46455148 (100.00%) were unpaired; of these: 45035533 (96.94%) aligned 0 times 606689 (1.31%) aligned exactly 1 time 812926 (1.75%) aligned >1 times 3.06% 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: 2013278 Mapping efficiency: 4.3% Sequences with no alignments under any condition: 42132594 Sequences did not map uniquely: 2309276 Sequences which were discarded because genomic sequence could not be extracted: 69 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 403589 ((converted) top strand) CT/GA: 436356 ((converted) bottom strand) GA/CT: 576906 (complementary to (converted) top strand) GA/GA: 596358 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 12294135 Total methylated C's in CpG context: 1280460 Total methylated C's in CHG context: 56701 Total methylated C's in CHH context: 642287 Total methylated C's in Unknown context: 42 Total unmethylated C's in CpG context: 536403 Total unmethylated C's in CHG context: 2079296 Total unmethylated C's in CHH context: 7698988 Total unmethylated C's in Unknown context: 457 C methylated in CpG context: 70.5% C methylated in CHG context: 2.7% C methylated in CHH context: 7.7% C methylated in Unknown context (CN or CHN): 8.4% Bismark completed in 0d 0h 23m 54s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/olurida-bs/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1323:2170_1:N:0:CAGATC 4 * 0 0 * * 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:7364:11568_1:N:0:CAGATC Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1110:21070:37591_1:N:0:CAGATC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1111:16167:38728_1:N:0:CAGATC Contig19826 1 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1201:7517:98944_1:N:0:CAGATC Contig23978 2 Processed 3000000 sequences so far Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1209:15073:36225_1:N:0:CAGATC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1211:17534:8668_1:N:0:CAGATC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1212:5001:4983_1:N:0:CAGATC Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1212:19518:35254_1:N:0:CAGATC Contig16668 2 Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1311:11740:17719_1:N:0:CAGATC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1311:19824:52313_1:Y:0:CAGATC Contig26138 1 Processed 8000000 sequences so far Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2105:4857:75284_1:N:0:CAGATC Contig20140 129024 Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2110:7095:72136_1:N:0:CAGATC Contig18174 105892 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2202:7757:89840_1:N:0:CAGATC Contig23978 2 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2207:15520:90842_1:N:0:CAGATC Contig5 2 Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2211:13564:70951_1:N:0:CAGATC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2213:5099:55594_1:N:0:CAGATC Contig20625 111109 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2215:18247:36644_1:N:0:CAGATC Contig18174 105892 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2304:19596:19296_1:N:0:CAGATC Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2305:20118:80844_1:N:0:CAGATC Contig19646 1 Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2308:12044:29017_1:N:0:CAGATC Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:10563:57490_1:N:0:CAGATC Contig18174 105892 Processed 16000000 sequences so far Processed 17000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1106:4266:79239_1:N:0:CAGATC Contig84 102773 Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:10073:41497_1:N:0:CAGATC Contig19330 108174 Processed 19000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1114:3429:94072_1:N:0:CAGATC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1203:12508:34672_1:N:0:CAGATC Contig18174 105892 Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:17612:55151_1:N:0:CAGATC Contig20625 1 Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1212:12048:20408_1:Y:0:CAGATC Contig19330 108174 Processed 22000000 sequences so far Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1310:7789:59233_1:N:0:CAGATC Contig9 1 Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2108:8686:92744_1:N:0:CAGATC Contig9 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2111:16122:7407_1:N:0:CAGATC Contig18174 105892 Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2202:11676:38874_1:N:0:CAGATC Contig20625 1 Processed 28000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2207:5741:67353_1:N:0:CAGATC Contig19330 108174 Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2304:11804:97688_1:N:0:CAGATC Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2305:15448:22924_1:N:0:CAGATC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2309:14748:31996_1:N:0:CAGATC Contig23978 1 Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2310:3248:12347_1:N:0:CAGATC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2311:8631:44713_1:N:0:CAGATT Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2313:3247:40649_1:N:0:CAGATC Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2315:7153:61382_1:N:0:CAGATC Contig0 1 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:17377:29914_1:N:0:CAGATC Contig5 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:13472:68913_1:N:0:CAGATC Contig16668 1 Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1207:11349:43112_1:N:0:CAGATC Contig18174 105892 Processed 38000000 sequences so far Processed 39000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1302:7415:67653_1:N:0:CAGATC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:7351:60075_1:N:0:CAGATC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1307:9561:54868_1:N:0:CAGATC Contig5 130492 Processed 40000000 sequences so far Processed 41000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1314:9525:49867_1:N:0:CAGATC Contig19330 108175 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:8207:18633_1:N:0:CAGATC Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2101:20591:8946_1:N:0:CGGATC Contig19330 108174 Processed 42000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2103:13317:59540_1:N:0:CAGATC Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2107:17648:32291_1:N:0:CAGATC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2109:8648:40277_1:N:0:CAGATC Contig20140 129023 Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2114:17193:59899_1:N:0:CAGATC Contig20140 129025 Processed 44000000 sequences so far Processed 45000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2208:7280:13554_1:N:0:CAGATC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2210:18137:86753_1:N:0:CAGATC Contig19826 1 Processed 46000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2211:20768:56440_1:Y:0:CAGATC Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2212:5630:49992_1:Y:0:CAGATC Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2213:16987:86657_1:N:0:CAGATT Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2216:2914:21304_1:N:0:CAGATC Contig20625 111110 Processed 47000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2306:1307:30031_1:N:0:CAGATC Contig19330 108174 Processed 48000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2309:7511:18831_1:N:0:CAGATC Contig0 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2309:16656:29042_1:N:0:CAGATC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2309:9059:52480_1:N:0:CAGATC Contig7 109637 Processed 49000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2314:3466:98555_1:N:0:CAGATC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2316:2589:9601_1:N:0:CAGATC Contig20625 1 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 48157619 (96.84%) aligned 0 times 705653 (1.42%) aligned exactly 1 time 866841 (1.74%) aligned >1 times 3.16% overall alignment rate 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 48194539 (96.91%) aligned 0 times 688542 (1.38%) aligned exactly 1 time 847032 (1.70%) aligned >1 times 3.09% overall alignment rate 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 47701725 (95.92%) aligned 0 times 837741 (1.68%) aligned exactly 1 time 1190647 (2.39%) aligned >1 times 4.08% overall alignment rate 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 47629950 (95.78%) aligned 0 times 896684 (1.80%) aligned exactly 1 time 1203479 (2.42%) aligned >1 times 4.22% 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: 2247688 Mapping efficiency: 4.5% Sequences with no alignments under any condition: 45094621 Sequences did not map uniquely: 2387804 Sequences which were discarded because genomic sequence could not be extracted: 64 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 467398 ((converted) top strand) CT/GA: 507622 ((converted) bottom strand) GA/CT: 615887 (complementary to (converted) top strand) GA/GA: 656717 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 13889878 Total methylated C's in CpG context: 2000903 Total methylated C's in CHG context: 75085 Total methylated C's in CHH context: 662881 Total methylated C's in Unknown context: 58 Total unmethylated C's in CpG context: 635805 Total unmethylated C's in CHG context: 2459263 Total unmethylated C's in CHH context: 8055941 Total unmethylated C's in Unknown context: 331 C methylated in CpG context: 75.9% C methylated in CHG context: 3.0% C methylated in CHH context: 7.6% C methylated in Unknown context (CN or CHN): 14.9% Bismark completed in 0d 0h 25m 36s ==================== 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1102:4589:10160_1:N:0:GCTTGA Contig20625 1 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1112:7166:72931_1:N:0:ACTTGA Contig19330 108175 Processed 2000000 sequences so far Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1207:5167:66208_1:N:0:ACTTGA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1207:20201:69361_1:N:0:ACTTGA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1207:15290:93700_1:Y:0:ACTTGA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1211:5741:76055_1:N:0:ACTTGA Contig18174 105891 Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1301:3745:72146_1:N:0:ACTTGA Contig20625 2 Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:7991:31925_1:N:0:ACTTGA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:7435:36862_1:N:0:ACTTGA Contig0 1 Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1313:17268:50236_1:N:0:ACTTGA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1314:5734:10097_1:N:0:ACTTGA Contig2 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1314:17987:19647_1:N:0:ACTTGA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2103:11897:82743_1:N:0:ACTTGA Contig20625 1 Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2107:18236:78889_1:Y:0:TCTTGA Contig7 109642 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2108:2275:2574_1:Y:0:ACTTGA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2108:5608:100217_1:N:0:ACTTGA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2109:13115:90506_1:N:0:ACTTGA Contig5 130492 Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2114:12402:37295_1:N:0:ACTTGA Contig19330 108176 Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2205:18844:47485_1:N:0:ACTTGA Contig20625 1 Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2211:10634:68571_1:N:0:ACTTGA Contig9 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2213:10104:87257_1:N:0:ACTTGA Contig3 2 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2305:18687:56671_1:N:0:ACTTGA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2306:21039:34621_1:N:0:ACTTGA Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2308:7668:66733_1:N:0:ACTTGA Contig5 130492 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:1544:78641_1:N:0:ACTTGA Contig18174 105892 Processed 13000000 sequences so far Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1111:15993:58236_1:N:0:ACTTGA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1113:2050:25267_1:N:0:ACTTGA Contig23978 1 Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:15657:77331_1:N:0:ACTTGA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1205:18158:29732_1:N:0:ACTTGA Contig20625 1 Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1209:15252:52392_1:N:0:ACTTGA Contig19330 108175 Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2109:12903:52296_1:N:0:ACTTGA Contig5 130492 Processed 21000000 sequences so far Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:4011:95328_1:Y:0:ACTTGA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2207:15564:44021_1:N:0:ACTTGA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2209:7932:73693_1:N:0:ACTTGA Contig9 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2211:11014:78274_1:Y:0:ACTTGA Contig20140 129023 Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2211:6351:87823_1:N:0:ACTTGA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2214:18701:57498_1:N:0:ACTTGA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:16747:35544_1:N:0:ACTTGA Contig20625 1 Processed 24000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2305:18417:41101_1:N:0:ACTTGA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2307:2241:85682_1:N:0:ACTTGA Contig20625 2 Processed 25000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2316:2399:64562_1:N:0:ACTTTA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1101:11231:41836_1:N:0:ACTTGA Contig18052 116631 Processed 26000000 sequences so far Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1114:7096:52753_1:N:0:ACTTGA Contig16668 101411 Processed 28000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1208:15194:11814_1:N:0:ACTTGA Contig20625 111112 Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:15256:47038_1:N:0:ACTTGA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:13389:58040_1:N:0:ACTTGA Contig0 1 Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1301:10145:61136_1:N:0:ACTTGA Contig0 1 Processed 31000000 sequences so far Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1314:6429:78334_1:N:0:ACTTGA Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2102:9518:64252_1:Y:0:ACTTGC Contig19330 108174 Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2205:3939:65948_1:Y:0:ACTTGA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2208:17502:11676_1:N:0:ACTTGA Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2210:13792:64573_1:Y:0:ACTTGA Contig20625 1 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2303:5580:93015_1:N:0:ACTTGA Contig23978 2 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2307:17671:69014_1:N:0:ACTTGA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2310:9604:66487_1:N:0:ACTTGA Contig18174 105892 Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:14244:3642_1:N:0:ACTTGA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2314:20622:35850_1:N:0:ACTTGA Contig5 130493 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2316:10485:16410_1:N:0:ACTTGA Contig19330 108174 38697189 reads; of these: 38697189 (100.00%) were unpaired; of these: 37499299 (96.90%) aligned 0 times 537122 (1.39%) aligned exactly 1 time 660768 (1.71%) aligned >1 times 3.10% overall alignment rate 38697189 reads; of these: 38697189 (100.00%) were unpaired; of these: 37004951 (95.63%) aligned 0 times 721913 (1.87%) aligned exactly 1 time 970325 (2.51%) aligned >1 times 4.37% overall alignment rate 38697189 reads; of these: 38697189 (100.00%) were unpaired; of these: 37057225 (95.76%) aligned 0 times 679306 (1.76%) aligned exactly 1 time 960658 (2.48%) aligned >1 times 4.24% overall alignment rate 38697189 reads; of these: 38697189 (100.00%) were unpaired; of these: 37526019 (96.97%) aligned 0 times 527788 (1.36%) aligned exactly 1 time 643382 (1.66%) aligned >1 times 3.03% 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: 1779165 Mapping efficiency: 4.6% Sequences with no alignments under any condition: 35045244 Sequences did not map uniquely: 1872780 Sequences which were discarded because genomic sequence could not be extracted: 58 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 357923 ((converted) top strand) CT/GA: 386751 ((converted) bottom strand) GA/CT: 504571 (complementary to (converted) top strand) GA/GA: 529862 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 10983738 Total methylated C's in CpG context: 1642871 Total methylated C's in CHG context: 61069 Total methylated C's in CHH context: 546466 Total methylated C's in Unknown context: 65 Total unmethylated C's in CpG context: 439184 Total unmethylated C's in CHG context: 1942783 Total unmethylated C's in CHH context: 6351365 Total unmethylated C's in Unknown context: 292 C methylated in CpG context: 78.9% C methylated in CHG context: 3.0% C methylated in CHH context: 7.9% C methylated in Unknown context (CN or CHN): 18.2% Bismark completed in 0d 0h 19m 52s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/olurida-bs/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1106:5875:25203_1:N:0:GATCAG Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:1854:37706_1:Y:0:GATCAG Contig20625 1 Processed 2000000 sequences so far Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1113:9323:68153_1:N:0:GATCAG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:16413:14574_1:N:0:GATCAG Contig18174 105893 Processed 4000000 sequences so far Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1204:10020:90736_1:N:0:GATCAG Contig7 109637 Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1207:16813:78642_1:N:0:GATCAG Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1208:2023:28311_1:N:0:GATCAG Contig20140 129024 Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1212:20166:25071_1:N:0:GATCAG Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1212:4117:56688_1:N:0:GATCAG Contig20140 129025 Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1215:11106:83050_1:N:0:GATCAG Contig19826 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1216:9499:81602_1:N:0:GATCAG Contig19826 2 Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:20345:17123_1:N:0:GATCAG Contig84 102773 Processed 10000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1305:18711:43799_1:N:0:GATCAG Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:12718:24069_1:N:0:GATCAG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:5992:49210_1:N:0:GATCAG Contig19330 108174 Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1310:14236:76874_1:N:0:GATCAG Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1312:18657:45193_1:N:0:GATCAG Contig19330 108174 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1315:18054:57795_1:N:0:GATCAG Contig20625 1 Processed 13000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2101:8359:7847_1:N:0:GATCAG Contig23978 1 Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2104:13344:96088_1:N:0:GATCAG Contig20625 1 Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2108:3404:83552_1:N:0:GATCAG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2108:17235:93726_1:N:0:GATCAG Contig9 1 Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2205:9972:10579_1:N:0:GATCAG Contig20625 111110 Processed 19000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2210:19564:50022_1:N:0:GATCAG Contig19826 1 Processed 20000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2212:14807:47838_1:N:0:GATCAG Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2214:1461:53149_1:N:0:GATCAG Contig20625 1 Processed 21000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2301:7704:41825_1:N:0:GATCAG Contig18052 116631 Processed 22000000 sequences so far Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2307:6585:41748_1:N:0:GATCAG Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2309:19732:69166_1:N:0:GATCAG Contig20625 1 Processed 24000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2310:6793:85465_1:N:0:GATCAG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2311:7013:43965_1:N:0:GATCAG Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:7048:79154_1:N:0:GATCAG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:9608:81867_1:N:0:GATCAG Contig20140 129023 Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1108:5396:31210_1:N:0:GATCAG Contig20625 111110 Processed 28000000 sequences so far Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1115:9294:77429_1:N:0:GATCAG Contig18174 105892 Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:17285:70971_1:N:0:GATCAG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:18792:95244_1:N:0:GATCAG Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:17154:82490_1:N:0:GATCAG Contig20140 1 Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1203:5921:89406_1:N:0:AATCAG Contig18174 105892 Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1208:4735:46540_1:N:0:GATCAG Contig23978 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1208:15792:67304_1:N:0:GATCAG Contig18174 105891 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1214:16565:39343_1:N:0:GATCAG Contig5 130492 Processed 34000000 sequences so far Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1303:9641:28803_1:N:0:GATCAG Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1303:14744:74229_1:N:0:GATCAG Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1305:6495:74952_1:N:0:GATCAG Contig0 1 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1309:5988:34052_1:N:0:GATCAG Contig0 1 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1311:1227:2847_1:N:0:GATCAG Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1312:17194:32817_1:N:0:GATCAG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1312:6117:97012_1:N:0:GATCAG Contig19826 2 Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1316:9070:49414_1:N:0:AATCAG Contig3 141627 Processed 39000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2101:10762:61682_1:N:0:GATCAG Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2103:2391:6642_1:N:0:GATCAG Contig16668 2 Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2115:11520:66552_1:N:0:GATCAG Contig16668 101411 Processed 43000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2201:12968:37672_1:N:0:GATCAG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2203:13308:63503_1:N:0:GATCAG Contig20625 1 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2308:6406:68050_1:N:0:GATCAG Contig23978 2 Processed 50000000 sequences so far Processed 51000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1101:10998:18564_1:N:0:GATCAG Contig18174 105892 Processed 52000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1105:3156:91070_1:N:0:GATCAG Contig18174 105892 Processed 53000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1106:18244:38528_1:N:0:GATCAG Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1106:17542:100078_1:N:0:GATCAG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1107:12190:43819_1:N:0:GATCAG Contig20625 1 Processed 54000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:17002:39953_1:N:0:GATCAG Contig18174 105891 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1112:18792:26047_1:N:0:GATCAG Contig20140 129023 Processed 55000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:8990:98664_1:N:0:GATCAG Contig20625 1 Processed 56000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1202:17691:9935_1:N:0:GATCAG Contig19330 108174 Processed 57000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1205:3796:59855_1:N:0:GATCAG Contig20625 111109 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1206:13972:58610_1:N:0:GATCAG Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1206:4952:66868_1:N:0:GATCAG Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1207:3530:39092_1:N:0:GATCAG Contig9 1 Processed 58000000 sequences so far Processed 59000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1214:17441:69193_1:N:0:GATCAG Contig26138 1 Processed 60000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1302:20681:67452_1:N:0:GATCAG Contig18174 105892 Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1311:3503:68899_1:N:0:GATCAG Contig16668 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1311:9512:93419_1:N:0:GATCAG Contig0 1 Processed 64000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1316:6579:12574_1:N:0:GATCAG Contig19330 108174 Processed 65000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2104:6096:10521_1:N:0:GATCAG Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2105:8974:70894_1:N:0:GATCAG Contig26138 2 Processed 66000000 sequences so far Processed 67000000 sequences so far Processed 68000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2114:17621:87055_1:N:0:GATCAG Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2116:19702:92096_1:N:0:GATCAG Contig19646 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2201:2580:14973_1:N:0:GATCAG Contig20625 1 Processed 69000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2203:12880:77295_1:N:0:GATCAG Contig26138 1 Processed 70000000 sequences so far Processed 71000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2211:4978:68695_1:N:0:GATCAG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2212:6906:43974_1:N:0:GATCAG Contig18174 105892 Processed 72000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2212:10607:81728_1:N:0:GATCAG Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2213:11273:72522_1:N:0:GATCAG Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2215:18331:48320_1:N:0:GATCAG Contig0 1 Processed 73000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2302:20507:81793_1:N:0:GATCAG Contig20625 111110 Processed 74000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2304:8047:42484_1:N:0:GATCAG Contig16668 101411 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2306:15187:63528_1:N:0:AATCAG Contig19826 1 Processed 75000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2311:6486:59490_1:N:0:GATCAG Contig20625 111109 Processed 76000000 sequences so far Processed 77000000 sequences so far 77350922 reads; of these: 77350922 (100.00%) were unpaired; of these: 74823669 (96.73%) aligned 0 times 1121530 (1.45%) aligned exactly 1 time 1405723 (1.82%) aligned >1 times 3.27% overall alignment rate 77350922 reads; of these: 77350922 (100.00%) were unpaired; of these: 74037320 (7735092295.72 reads; of these:% ) aligned 0 times 77350922 (1340722 (1.73%) aligned exactly 1 time 1972880 (2.55100.00%%) aligned >1 times) were unpaired; of these: 4.28 %74889241 overall alignment rate ( 96.82%) aligned 0 times 1103684 (1.43%) aligned exactly 1 time 1357997 (1.76%) aligned >1 times 3.18% overall alignment rate 77350922 reads; of these: 77350922 (100.00%) were unpaired; of these: 73906304 (95.55%) aligned 0 times 1459500 (1.89%) aligned exactly 1 time 1985118 (2.57%) aligned >1 times 4.45% 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: 3614877 Mapping efficiency: 4.7% Sequences with no alignments under any condition: 69851458 Sequences did not map uniquely: 3884587 Sequences which were discarded because genomic sequence could not be extracted: 89 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 743807 ((converted) top strand) CT/GA: 809937 ((converted) bottom strand) GA/CT: 999563 (complementary to (converted) top strand) GA/GA: 1061481 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 22085171 Total methylated C's in CpG context: 2591728 Total methylated C's in CHG context: 102822 Total methylated C's in CHH context: 1045017 Total methylated C's in Unknown context: 74 Total unmethylated C's in CpG context: 1010302 Total unmethylated C's in CHG context: 3818600 Total unmethylated C's in CHH context: 13516702 Total unmethylated C's in Unknown context: 741 C methylated in CpG context: 72.0% C methylated in CHG context: 2.6% C methylated in CHH context: 7.2% C methylated in Unknown context (CN or CHN): 9.1% Bismark completed in 0d 0h 40m 7s ==================== 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/v082/ (absolute path is '/gscratch/srlab/sr320/data/olurida-bs/v082/)' 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/sr320/061722-v082'): /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/sr320/061722-v082 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 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/v082/ 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/v082/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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1101:17242:56591_1:N:0:TAGCTT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1104:12397:7545_1:N:0:TAGATT Contig20140 129024 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1106:19204:7206_1:N:0:TAGCTT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1107:14373:56857_1:N:0:TAGCTT Contig20140 129024 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1109:9968:92922_1:N:0:TAGCTT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1110:18595:67306_1:N:0:TAGCTT Contig20625 2 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:3053:43768_1:N:0:TAGCTT Contig18024 1 Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:19105:42611_1:Y:0:TAGCTT Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:17974:17910_1:N:0:TAGCTT Contig18174 105892 Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:12770:71354_1:N:0:TAGCTT Contig19330 108174 Processed 6000000 sequences so far Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1211:13097:89061_1:N:0:TAGCTT Contig20140 129024 Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1309:4071:57849_1:N:0:TAGCTT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1309:19203:58622_1:N:0:TAGCTT Contig19330 108175 Processed 12000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:13455:37227_1:N:0:TAGCTT Contig26138 2 Processed 13000000 sequences so far Processed 14000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2105:6825:9803_1:Y:0:TAGCTT Contig19330 108174 Processed 15000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2110:18692:45780_1:N:0:TAGCTT Contig20625 1 Processed 16000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2112:4943:97595_1:N:0:TAGCTT Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2113:3544:98459_1:N:0:TAGCTT Contig20625 111110 Processed 17000000 sequences so far Processed 18000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:14976:48201_1:N:0:TAGCTT Contig3 2 Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2304:4169:33681_1:N:0:TAGCTT Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2305:3371:35761_1:N:0:TAGCTT Contig20140 129025 Processed 23000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2309:15128:63830_1:N:0:TAGCTT Contig20625 1 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1109:11581:81388_1:N:0:TAGCTT Contig0 1 Processed 29000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1113:4203:75830_1:N:0:TAGCTT Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1113:8033:89949_1:N:0:TAGCTT Contig19826 1 Processed 30000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1202:19380:59452_1:N:0:TAGCTT Contig19330 108174 Processed 31000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1203:19781:44000_1:N:0:TAGCTT Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1204:10410:45994_1:N:0:TAGCTT Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1206:3175:9679_1:N:0:TAGCTT Contig20625 1 Processed 32000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1207:17822:29244_1:N:0:TAGCTT Contig20625 1 Processed 33000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1210:10618:99795_1:N:0:TAGCTT Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1213:8686:6994_1:N:0:TAGCTT Contig5 130492 Processed 34000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1301:6166:26152_1:N:0:TAGCTT Contig19330 108174 Processed 35000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1301:2970:87662_1:N:0:TAGCTT Contig20625 111110 Processed 36000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1305:10062:77325_1:N:0:TAGCTT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1306:4858:36467_1:N:0:TAGCTT Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1307:6189:35283_1:N:0:TAGCTT Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:16339:42261_1:N:0:TAGCTT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:14213:77255_1:N:0:TAGCTT Contig19330 108174 Processed 37000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:12539:89858_1:N:0:TAGCTT Contig18024 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1312:2246:30042_1:N:0:TAGCTT Contig5 1 Processed 38000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1312:13318:72803_1:N:0:TAGCTT Contig20140 129024 Processed 39000000 sequences so far Processed 40000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2103:5549:78583_1:Y:0:TAGCTT Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2104:10610:40292_1:N:0:TTGCTT Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2104:5521:92638_1:N:0:TAGCTT Contig20140 129024 Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2203:21097:45835_1:N:0:TAGCTT Contig18174 105892 Processed 45000000 sequences so far Processed 46000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2210:1827:43539_1:N:0:TAGCTT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2211:7172:43080_1:N:0:TAGCTT Contig18052 116631 Processed 47000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2215:2835:4703_1:N:0:TAGCTT Contig18174 105892 Processed 48000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2303:17032:70977_1:N:0:TAGCTT Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2303:9108:81739_1:N:0:TAGCTT Contig19330 108174 Processed 49000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2306:7355:57531_1:N:0:TAGCTT Contig20625 2 Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1105:2768:64371_1:Y:0:TAGCTT Contig19826 1 Processed 54000000 sequences so far Processed 55000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1112:16883:29009_1:N:0:TAGCTT Contig19646 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1112:13897:86679_1:N:0:TAGCTT Contig19330 108174 Processed 56000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1201:20053:18962_1:N:0:TAGCTT Contig20140 129024 Processed 57000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1205:10408:22059_1:N:0:TAGCTT Contig20140 129023 Processed 58000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1209:2617:76600_1:N:0:TAGCTT Contig26138 1 Processed 59000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1213:6288:2999_1:N:0:TAGCTT Contig19330 108174 Processed 60000000 sequences so far Processed 61000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:4082:30133_1:N:0:TAGCTT Contig19330 108174 Processed 62000000 sequences so far Processed 63000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1309:15936:44487_1:N:0:TAGCTT Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:19767:48413_1:N:0:TAGCTT Contig20140 129024 Processed 64000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:15776:41489_1:N:0:TAGCTT Contig20625 1 Processed 65000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:18053:63576_1:N:0:TAGCTT Contig20625 111110 Processed 66000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2103:17724:95096_1:N:0:TAGCTT Contig18174 105892 Processed 67000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2109:7094:14556_1:N:0:TAGCTT Contig7 109638 Processed 68000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:3424:25262_1:N:0:TAGCTT Contig16668 2 Processed 69000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2115:4586:95395_1:N:0:TAGCTT Contig65 107630 Processed 70000000 sequences so far Processed 71000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2208:17899:93495_1:N:0:TAGCTT Contig19330 108174 Processed 72000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2211:4152:34627_1:N:0:TAGCTT Contig7 109637 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2212:17024:77806_1:N:0:TAGCTT Contig20140 129023 Processed 73000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2214:6000:82149_1:N:0:TAGCTT Contig7 109637 Processed 74000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2303:14089:34346_1:N:0:TAGCTT Contig19330 108174 Processed 75000000 sequences so far Processed 76000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2311:11719:53620_1:N:0:TAGCTT Contig20625 1 Processed 77000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2314:18352:35717_1:N:0:TAGCTT Contig18174 105892 Processed 78000000 sequences so far Processed 79000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1106:3878:83791_1:N:0:AGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:9538:52843_1:N:0:GGCTAC Contig18024 2 Processed 80000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1112:15396:12193_1:N:0:GGCTAC Contig20625 1 Processed 81000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1203:16269:11564_1:N:0:GGCTAC Contig20140 129024 Processed 82000000 sequences so far Processed 83000000 sequences so far Processed 84000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:19759:13604_1:N:0:GGCTAC Contig19330 108174 Processed 85000000 sequences so far Processed 86000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1313:6512:40990_1:N:0:GGCTAC Contig20625 1 Processed 87000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2101:19283:94525_1:N:0:GGCTAC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2102:12415:54563_1:N:0:AGCTAC Contig20625 1 Processed 88000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2105:2687:38041_1:N:0:GGCTAC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2107:5163:48941_1:N:0:GGCTAC Contig20625 1 Processed 89000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2111:8482:44852_1:N:0:GGCTAC Contig18024 2 Processed 90000000 sequences so far Processed 91000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2205:19625:71775_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2206:11027:74326_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2207:2691:64906_1:Y:0:GGCTAC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:17936:81757_1:N:0:GGCTAC Contig18024 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:12960:98287_1:N:0:GGCTAC Contig20625 1 Processed 92000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2213:4024:31991_1:N:0:GGCTAC Contig19330 108174 Processed 93000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2215:17238:26031_1:N:0:GGCTAC Contig16668 2 Processed 94000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2305:14034:28546_1:N:0:GGCTAC Contig19330 108174 Processed 95000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2310:15732:39481_1:N:0:GGCTAC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2311:8943:81889_1:N:0:GGCTAC Contig19330 108174 Processed 96000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1101:7501:83207_1:N:0:GGCTCC Contig20140 1 Processed 97000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1104:10649:97368_1:N:0:GGCTAC Contig20625 2 Processed 98000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1111:6831:50175_1:N:0:GGCTAC Contig84 102773 Processed 99000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:10438:78321_1:N:0:GGCTAC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1201:12577:8515_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:3853:34279_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1203:3863:33956_1:N:0:GGCTAC Contig18174 105891 Processed 100000000 sequences so far Processed 101000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1210:14738:41914_1:N:0:GGCTAC Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1210:9772:98552_1:N:0:GGCTAC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1213:13170:43875_1:N:0:GGCTAC Contig18174 105892 Processed 102000000 sequences so far Processed 103000000 sequences so far Processed 104000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1308:5742:30821_1:N:0:GGCTAC Contig20625 1 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2207:2705:55638_1:N:0:AGCTAC Contig20625 1 Processed 110000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2209:1594:83271_1:N:0:GGCTAC Contig18052 116631 Processed 111000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2215:8216:12487_1:N:0:GGCTAC Contig19330 108176 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2301:4658:81010_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2302:6533:49525_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2302:8699:76715_1:N:0:GGCTAC Contig19330 108174 Processed 112000000 sequences so far Processed 113000000 sequences so far Processed 114000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2314:6931:94543_1:N:0:GGCTAC Contig19330 108175 Processed 115000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1104:16554:12250_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1105:5316:46430_1:N:0:GGCTAC Contig5 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1105:8110:85521_1:Y:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1108:14093:14761_1:N:0:GGCTAC Contig19330 108174 Processed 116000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1108:16893:81184_1:N:0:GGCTAC Contig3 141627 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1109:10694:44846_1:N:0:GGCTAC Contig20625 1 Processed 117000000 sequences so far Processed 118000000 sequences so far Processed 119000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:4733:36697_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:7473:62469_1:N:0:GGCTAC Contig19646 1 Processed 120000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1214:4409:59178_1:N:0:GGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1301:3983:9857_1:N:0:GGCTAC Contig20625 1 Processed 121000000 sequences so far Processed 122000000 sequences so far Processed 123000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1316:2346:20960_1:N:0:GGCTAC Contig20625 1 Processed 124000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2104:13826:24829_1:N:0:GGCTAC Contig19330 108176 Processed 125000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2109:16827:42716_1:N:0:GGCTAC Contig20625 1 Processed 126000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2202:9507:5178_1:N:0:AGCTAC Contig19646 1 Processed 127000000 sequences so far Processed 128000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2210:12700:6815_1:N:0:AGCTAC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2210:16997:97235_1:N:0:GGCTAC Contig19330 108177 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2212:14760:66069_1:N:0:GGCTAC Contig20140 129024 Processed 129000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2213:1656:67963_1:N:0:GGCTAC Contig20140 129024 Processed 130000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2307:6657:60258_1:N:0:GGCTAC Contig16668 1 Processed 131000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2309:11497:19994_1:N:0:GGCTAC Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:15571:47089_1:Y:0:GGCTAC Contig19646 1 Processed 132000000 sequences so far Processed 133000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1102:6692:66182_1:Y:0:CTTGTA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1104:7121:44571_1:N:0:CTTGTA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1104:6225:64692_1:N:0:CTTGTA Contig84 102773 Processed 134000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:19449:52880_1:N:0:CTTGTA Contig19330 108174 Processed 135000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1114:4787:7619_1:N:0:CTTGTA Contig0 1 Processed 136000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1203:16611:97928_1:N:0:CTTGTA Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1205:6074:54985_1:N:0:CTTGTA Contig18174 105892 Processed 137000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1206:18089:39266_1:N:0:CTTGTA Contig18174 105892 Processed 138000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1212:7944:19664_1:N:0:CTTGTA Contig18174 105892 Processed 139000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1303:5456:61868_1:N:0:CTTGTA Contig19826 1 Processed 140000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1306:10392:73347_1:N:0:CTTGTA Contig0 1 Processed 141000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1308:4071:76677_1:N:0:CTTGTA Contig3 141636 Processed 142000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2101:12118:80832_1:N:0:CTTGTA Contig18174 105892 Processed 143000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2102:3224:9291_1:N:0:CTTGTA Contig0 1 Processed 144000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2109:5653:67027_1:N:0:CTTGTA Contig20625 1 Processed 145000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2113:19694:44853_1:N:0:CTTGTA Contig26138 1 Processed 146000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2203:1186:9363_1:N:0:CTTGTA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2204:10250:20221_1:N:0:CTTGTA Contig18052 116630 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2204:19503:86571_1:N:0:CTTGTA Contig20625 111120 Processed 147000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2206:9427:2591_1:N:0:CTTGTA Contig0 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2206:7889:76421_1:N:0:CTTGTA Contig20625 1 Processed 148000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2212:8492:26498_1:N:0:CTTGTA Contig20140 129024 Processed 149000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2216:21287:71613_1:Y:0:CTTGTA Contig0 1 Processed 150000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2307:1246:28336_1:N:0:CTTGTA Contig18174 105892 Processed 151000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2311:3219:9542_1:N:0:CTTGTA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:11017:75216_1:N:0:CTTGTA Contig0 1 Processed 152000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2314:14316:41898_1:N:0:CTTGTA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2314:5546:96460_1:N:0:CTTGTA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2315:8731:41097_1:N:0:CTTGTA Contig19267 115726 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2316:17499:27252_1:N:0:CTTGTA Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:16508:2190_1:N:0:CTTGTA Contig20625 1 Processed 153000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1106:7244:56652_1:N:0:CTTGTA Contig20625 2 Processed 154000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:14342:64013_1:N:0:CTTGTA Contig18024 109269 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:16510:69012_1:N:0:CTTGTA Contig0 1 Processed 155000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:19867:5100_1:N:0:CTTGTA Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:17716:73668_1:N:0:CTTGTA Contig9 2 Processed 156000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1203:9274:47009_1:N:0:CTTGTA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1205:14426:48617_1:N:0:CTTGTA Contig18174 105892 Processed 157000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:19698:65849_1:N:0:CTTGTA Contig19267 115726 Processed 158000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:8119:48266_1:N:0:CTTGTA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:12368:67120_1:N:0:CTTGTA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1213:17406:21250_1:N:0:CTTGTA Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1214:8331:82717_1:N:0:CTTGTA Contig20140 129024 Processed 159000000 sequences so far Processed 160000000 sequences so far Processed 161000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:2247:56592_1:N:0:CTTGTA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:13396:77538_1:N:0:CTTGTA Contig18174 105892 Processed 162000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:2328:58331_1:Y:0:CTTGTA Contig18174 105893 Processed 163000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2103:11567:33992_1:N:0:CTTGTA Contig20625 1 Processed 164000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2111:14070:42147_1:N:0:CTTGTA Contig3 2 Processed 165000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2112:5953:78628_1:Y:0:CTTGTA Contig18024 109269 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2116:6928:33517_1:N:0:CTTGTA Contig18174 105892 Processed 166000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2206:9770:7568_1:Y:0:CTTGTA Contig0 1 Processed 167000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2207:15200:72468_1:N:0:CTTGTA Contig9 1 Processed 168000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2211:13813:40475_1:N:0:CTTGTA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2215:17183:13893_1:N:0:CTTGTA Contig18174 105897 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2215:12961:36914_1:N:0:CTTGTA Contig19330 108174 Processed 169000000 sequences so far Processed 170000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2306:1311:35512_1:N:0:CTTGTA Contig18174 105893 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2307:1227:93260_1:N:0:CTTGTA Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2308:4697:93231_1:N:0:CTTGTA Contig19330 108174 Processed 171000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2311:19982:29243_1:N:0:CTTGTA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:1501:46702_1:N:0:CTTGTA Contig19330 108174 Processed 172000000 sequences so far Processed 173000000 sequences so far Processed 174000000 sequences so far Processed 175000000 sequences so far Processed 176000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:18738:45491_1:Y:0:CTTGTA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:4063:98423_1:N:0:CTTGTA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1204:14478:12198_1:N:0:CTTGTA Contig16668 1 Processed 177000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1208:8839:70664_1:N:0:CTTGTA Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1211:15134:88788_1:N:0:CTTGTA Contig19330 108174 Processed 178000000 sequences so far Processed 179000000 sequences so far Processed 180000000 sequences so far Processed 181000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1311:13773:96267_1:N:0:CTTGTA Contig3 141626 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1313:10685:24880_1:N:0:CTTGTA Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:10456:10960_1:N:0:CTTGTA Contig16668 1 Processed 182000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1315:20005:81089_1:N:0:CTTGTA Contig5 130492 Processed 183000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2105:4748:96719_1:N:0:CTTGTA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2106:14869:93548_1:N:0:CTTGTA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2108:3406:2331_1:N:0:CTTGTA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2108:21133:39441_1:Y:0:CTTGTA Contig18174 105892 Processed 184000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2109:1946:64351_1:Y:0:CTTGTA Contig3 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2113:14061:53994_1:N:0:CTTGTA Contig26138 1 Processed 185000000 sequences so far Processed 186000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2204:9398:60173_1:N:0:CTTGTA Contig20140 129023 Processed 187000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2208:13750:60500_1:N:0:CTTGTA Contig18174 105891 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2210:6619:70592_1:N:0:CTTGAA Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2212:12724:44897_1:N:0:CTTGTA Contig26138 1 Processed 188000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2213:5731:83021_1:N:0:CTTGTA Contig18174 105892 Processed 189000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:1385:3970_1:N:0:CTTGTA Contig19330 108174 Processed 190000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2309:8208:10787_1:N:0:CTTGTA Contig0 1 Processed 191000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2313:14394:88612_1:N:0:CTTGTA Contig19646 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2315:11336:67308_1:N:0:CTTGTA Contig20140 129023 Processed 192000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1102:10249:43758_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1102:5577:90140_1:N:0:AGTCAA Contig18174 105892 Processed 193000000 sequences so far Processed 194000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:8322:65967_1:N:0:AGTCAA Contig0 2 Processed 195000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1114:17031:72979_1:Y:0:AGTCAA Contig26138 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:15214:39115_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:13416:73048_1:N:0:AGTCAA Contig2 1 Processed 196000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1203:3281:98289_1:N:0:AGTCAA Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:10177:16312_1:N:0:AGTCAA Contig18024 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:20648:34837_1:N:0:AGTCAA Contig20625 1 Processed 197000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1208:3986:88842_1:N:0:AGTCAA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1209:4923:58877_1:N:0:AGTCAA Contig23978 1 Processed 198000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1212:18342:17431_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1212:12751:89314_1:N:0:AGTCAA Contig2 1 Processed 199000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1301:3286:26038_1:N:0:AGTCAA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1301:2690:62156_1:Y:0:AGTCAA Contig20140 129025 Processed 200000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1305:12281:42618_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1306:6777:11350_1:N:0:AGTCAA Contig20625 2 Processed 201000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1309:5770:9287_1:N:0:AGTCAA Contig20625 1 Processed 202000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1312:5772:76185_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:19668:31188_1:N:0:AGTCAA Contig20140 129024 Processed 203000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2102:5572:74479_1:N:0:AGTCAA Contig468 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2105:8134:60896_1:N:0:AGTCAA Contig20140 129025 Processed 204000000 sequences so far Processed 205000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2114:13468:4482_1:N:0:AGTCAA Contig20625 2 Processed 206000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2116:6389:22754_1:N:0:AGTCAA Contig19826 1 Processed 207000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2204:12810:72478_1:N:0:AGTCAA Contig5 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2204:16912:76992_1:N:0:AGTCAA Contig19646 2 Processed 208000000 sequences so far Processed 209000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2215:15740:55290_1:N:0:AGTCAA Contig20140 129025 Processed 210000000 sequences so far Processed 211000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2307:7128:3672_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2309:18922:84958_1:N:0:AGTCAA Contig18052 116632 Processed 212000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2311:17664:82896_1:N:0:AGTCAA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2314:2692:51385_1:N:0:AGTCAA Contig20625 1 Processed 213000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1102:17768:56368_1:N:0:AGTCAA Contig20625 111110 Processed 214000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1104:15443:81003_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1104:10046:93362_1:N:0:AATCAA Contig9 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1105:17771:79161_1:N:0:AGTCAA Contig0 1 Processed 215000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1109:13959:87458_1:N:0:AGTCAA Contig16668 1 Processed 216000000 sequences so far Processed 217000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1202:11061:78538_1:N:0:AGTCAA Contig20625 1 Processed 218000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1205:17214:68798_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1206:21039:3930_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1206:14009:73383_1:N:0:AGTCAA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1208:9599:48348_1:N:0:AGTCAA Contig20625 1 Processed 219000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1209:15384:65779_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1211:12510:75311_1:Y:0:AGTCAA Contig17050 2 Processed 220000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1215:16297:47168_1:N:0:AGTCAA Contig19330 108174 Processed 221000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1303:8059:64333_1:N:0:AGTCAA Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1303:17309:81607_1:N:0:AGTCAA Contig19330 108174 Processed 222000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1307:14159:45718_1:N:0:AGTCAA Contig19330 108176 Processed 223000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1311:16039:61182_1:N:0:AGTCAA Contig20625 111110 Processed 224000000 sequences so far Processed 225000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2106:2914:3482_1:Y:0:AGTCAA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2106:9572:19074_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2106:11307:50850_1:N:0:AGTCAA Contig20625 1 Processed 226000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2112:6104:37480_1:N:0:AGTCAA Contig20625 2 Processed 227000000 sequences so far Processed 228000000 sequences so far Processed 229000000 sequences so far Processed 230000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2212:18813:57522_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2212:3080:62298_1:N:0:AGTCAA Contig16668 2 Processed 231000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2301:10481:82028_1:N:0:AGTCAA Contig19330 108174 Processed 232000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2305:17220:57565_1:N:0:AGTCAA Contig19646 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2305:6003:73845_1:N:0:AGTCAA Contig20625 1 Processed 233000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2310:13394:78961_1:N:0:AGTCAA Contig19330 108174 Processed 234000000 sequences so far Processed 235000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:15121:98913_1:N:0:AGTCAA Contig16668 2 Processed 236000000 sequences so far Processed 237000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:10966:25045_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1113:17294:23693_1:Y:0:AGTCAA Contig19646 1 Processed 238000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1201:8503:52581_1:N:0:AGTCAA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1202:18857:28163_1:N:0:AGTCAA Contig18052 116631 Processed 239000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1204:19953:58053_1:N:0:AGTCAA Contig7 109637 Processed 240000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1209:14821:95928_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1211:4109:18041_1:N:0:AGTCAA Contig19267 115726 Processed 241000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:14077:12451_1:N:0:AGTCAA Contig65 107630 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1213:15374:32679_1:N:0:AGTCAA Contig7 109638 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1213:12538:54699_1:N:0:AGTCAA Contig5 130492 Processed 242000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1302:4798:92252_1:N:0:AGTCAA Contig20625 1 Processed 243000000 sequences so far Processed 244000000 sequences so far Processed 245000000 sequences so far Processed 246000000 sequences so far Processed 247000000 sequences so far Processed 248000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2112:4856:83743_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:6833:85134_1:N:0:AGTCAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2114:18699:34645_1:N:0:AGTCAA Contig20140 129023 Processed 249000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2202:16705:23483_1:N:0:AGTCAA Contig20625 1 Processed 250000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2206:10212:19529_1:N:0:AGTCAA Contig0 1 Processed 251000000 sequences so far Processed 252000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2212:2507:100177_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2213:3380:35324_1:N:0:AGTCAA Contig23978 1 Processed 253000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2301:8708:35961_1:N:0:AGTCAA Contig20625 1 Processed 254000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2305:8874:78993_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2306:17424:21251_1:N:0:AGTCAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2308:7047:38239_1:N:0:AGTCAA Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2308:11594:42547_1:N:0:AGTCAA Contig19330 108174 Processed 255000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2311:8074:9649_1:N:0:AGTCAA Contig18174 105892 Processed 256000000 sequences so far Processed 257000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1103:6504:97324_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1105:10246:2385_1:Y:0:AGTTCC Contig19330 108183 Processed 258000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:19998:19709_1:N:0:AGTTCC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:6662:35962_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:1697:76154_1:N:0:AGTTCC Contig19826 1 Processed 259000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1109:8282:91520_1:Y:0:AGTTCC Contig20625 1 Processed 260000000 sequences so far Processed 261000000 sequences so far Processed 262000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1205:16370:77819_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1206:17082:4114_1:N:0:AGTTCC Contig20625 1 Processed 263000000 sequences so far Processed 264000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1211:2887:95205_1:N:0:AGTTCC Contig19330 108175 Processed 265000000 sequences so far Processed 266000000 sequences so far Processed 267000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:1368:83545_1:N:0:AGTTCC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1304:17116:6451_1:N:0:AGTTCC Contig20140 129025 Processed 268000000 sequences so far Processed 269000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1310:4686:92921_1:N:0:AGTTCC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1311:18389:16313_1:N:0:AGTTCC Contig9 1 Processed 270000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1314:15492:48846_1:N:0:GGTTCC Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1314:20332:98396_1:N:0:AGTTCC Contig20625 1 Processed 271000000 sequences so far Processed 272000000 sequences so far Processed 273000000 sequences so far Processed 274000000 sequences so far Processed 275000000 sequences so far Processed 276000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2201:9994:56175_1:N:0:AGTTCC Contig19826 1 Processed 277000000 sequences so far Processed 278000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:12702:90148_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:18690:14767_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:6318:35193_1:N:0:AGTTCC Contig20140 129024 Processed 279000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2212:2758:70243_1:N:0:AGTTCC Contig16668 2 Processed 280000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2216:12846:4440_1:N:0:AGTTCC Contig19330 108175 Processed 281000000 sequences so far Processed 282000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2304:12345:73104_1:N:0:AGTTCC Contig19330 108175 Processed 283000000 sequences so far Processed 284000000 sequences so far Processed 285000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2314:12069:51210_1:N:0:AGTTCC Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2314:2363:74948_1:N:0:AGTTCC Contig20625 1 Processed 286000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1103:6730:92368_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1103:5246:98159_1:N:0:AGTTCC Contig19646 1 Processed 287000000 sequences so far Processed 288000000 sequences so far Processed 289000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:18849:86219_1:Y:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1113:20719:3110_1:Y:0:AGTTCC Contig23978 1 Processed 290000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:17765:10301_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1116:13093:7264_1:Y:0:ACTTCC Contig0 1 Processed 291000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1202:15821:81654_1:N:0:AGTTCC Contig16668 2 Processed 292000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1205:18730:57881_1:N:0:AGTTCC Contig20625 1 Processed 293000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1208:9607:93288_1:N:0:AGTTCC Contig5 2 Processed 294000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1211:18700:86672_1:N:0:AGTTCC Contig3 141626 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:21035:11664_1:N:0:ATTTCC Contig9 1 Processed 295000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1215:18308:58903_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1216:15720:9871_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1301:1708:3882_1:N:0:AGTTCC Contig20625 1 Processed 296000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:14908:88002_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1304:2700:38213_1:N:0:AGTTCC Contig5 2 Processed 297000000 sequences so far Processed 298000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:19636:30817_1:N:0:AGTTCC Contig19826 2 Processed 299000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1312:21177:70426_1:N:0:AGTTCC Contig3 141626 Processed 300000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:10405:53576_1:N:0:AGTTCC Contig19826 2 Processed 301000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2101:16653:83763_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2102:2637:97086_1:N:0:AGTTCC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2104:13247:42084_1:N:0:AGTTCC Contig18174 105891 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2104:20506:81718_1:N:0:AGTTCC Contig20140 129023 Processed 302000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2105:19437:33320_1:N:0:AGTTCC Contig19330 108174 Processed 303000000 sequences so far Processed 304000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:18774:76185_1:N:0:AGTTCC Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2114:5472:79408_1:N:0:AGTTCC Contig20140 129024 Processed 305000000 sequences so far Processed 306000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2204:4274:36303_1:N:0:AGTTCC Contig19330 108175 Processed 307000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2207:4475:7581_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2207:14039:23349_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2208:5588:71672_1:N:0:AGTTCC Contig18052 116631 Processed 308000000 sequences so far Processed 309000000 sequences so far Processed 310000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2215:7124:87829_1:N:0:AGTTCC Contig20625 1 Processed 311000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2306:13257:16317_1:N:0:AGTTCC Contig20625 1 Processed 312000000 sequences so far Processed 313000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2311:16778:14595_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:15908:3593_1:N:0:AGTTCC Contig20625 1 Processed 314000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2315:5723:30368_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2315:15475:88372_1:N:0:AGTTCC Contig18052 116632 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2315:10269:91251_1:N:0:AGTTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2316:6652:38760_1:N:0:AGTTCC Contig20140 129024 Processed 315000000 sequences so far Processed 316000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1104:16690:56996_1:N:0:AGTTCC Contig19646 1 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1208:13578:91107_1:N:0:AGTTCC Contig19330 108174 Processed 323000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1212:10597:6270_1:N:0:AGTTCC Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1213:18677:56728_1:N:0:AGTTCC Contig18052 116631 Processed 324000000 sequences so far Processed 325000000 sequences so far Processed 326000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1304:7604:61747_1:N:0:AGTTCC Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1305:2392:9037_1:N:0:AGTTCC Contig20625 1 Processed 327000000 sequences so far Processed 328000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1310:14393:93118_1:N:0:AGTTCC Contig19330 108174 Processed 329000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:1428:10253_1:N:0:AGTTCC Contig16668 101411 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1316:20398:82445_1:Y:0:AGTTCC Contig18174 105893 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2115:18994:87011_1:N:0:AGTTCC Contig0 1 Processed 335000000 sequences so far Processed 336000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2206:7537:14898_1:N:0:AGTTCC Contig20140 129023 Processed 337000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2208:17549:87424_1:N:0:AGTTCC Contig16668 2 Processed 338000000 sequences so far Processed 339000000 sequences so far Processed 340000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:5771:56680_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:4111:57352_1:N:0:AGTTCC Contig20625 1 Processed 341000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2306:2390:7465_1:N:0:AGTTCC Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2306:12999:42957_1:N:0:AGTTCC Contig20625 1 Processed 342000000 sequences so far Processed 343000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2313:7225:11507_1:N:0:AGTTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2314:18345:8456_1:Y:0:AGTTCC Contig26138 1 Processed 344000000 sequences so far Processed 345000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1105:5744:30400_1:N:0:ATGTCA Contig19330 108183 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:7766:39576_1:N:0:ATGTCA Contig18174 105892 Processed 346000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1111:11504:51345_1:N:0:ATGTCA Contig20625 111109 Processed 347000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1112:13458:83201_1:N:0:ATGTCA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:3212:25625_1:N:0:ATGTCA Contig18024 2 Processed 348000000 sequences so far Processed 349000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1208:19592:65685_1:N:0:ATGTCA Contig5 130493 Processed 350000000 sequences so far Processed 351000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1215:8114:68558_1:N:0:ATGTCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1216:21166:38955_1:N:0:ATGTCA Contig19330 108174 Processed 352000000 sequences so far Processed 353000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1306:19061:38185_1:N:0:ATGTCA Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1307:20770:42150_1:Y:0:ATGTCA Contig0 1 Processed 354000000 sequences so far Processed 355000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1315:6641:23060_1:Y:0:ATGTCA Contig23978 1 Processed 356000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2103:10970:84223_1:N:0:ATGTCA Contig19330 108174 Processed 357000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2107:11673:84243_1:N:0:ATGTCA Contig18174 105892 Processed 358000000 sequences so far Processed 359000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2116:17526:79688_1:N:0:ATGTCA Contig20625 111110 Processed 360000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2203:12845:30505_1:N:0:ATGTCA Contig84 102772 Processed 361000000 sequences so far Processed 362000000 sequences so far Processed 363000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2301:20321:40696_1:N:0:ATGTCA Contig19330 108174 Processed 364000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2304:11835:45186_1:N:0:ATGTCA Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2306:9528:56506_1:N:0:ATGTCA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2307:19124:54700_1:N:0:ATGTCA Contig19330 108174 Processed 365000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2310:13360:30054_1:N:0:ATGTCA Contig84 102773 Processed 366000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:2182:57041_1:N:0:ATGTCA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:7805:75295_1:N:0:ATGTCA Contig19330 108174 Processed 367000000 sequences so far Processed 368000000 sequences so far Processed 369000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1109:3980:10001_1:N:0:ATGTCA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1111:1411:21055_1:N:0:ATGTCA Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:20445:29718_1:N:0:ATGTCA Contig19330 108174 Processed 370000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:5414:48788_1:N:0:ATGTCA Contig20625 1 Processed 371000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:15007:43698_1:N:0:ATGTCA Contig20625 1 Processed 372000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:10433:46793_1:N:0:ATGTCA Contig5 130492 Processed 373000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1211:9765:19824_1:N:0:ATGTCA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1212:6405:43273_1:N:0:ATGTCA Contig19330 108174 Processed 374000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1215:15747:78373_1:N:0:ATGTCA Contig20625 1 Processed 375000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1304:7891:25847_1:N:0:ATGTCA Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1306:16125:33684_1:N:0:ATGTCA Contig20625 1 Processed 376000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1306:13769:100305_1:N:0:ATGTCN Contig18174 105892 Processed 377000000 sequences so far Processed 378000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1315:3140:96489_1:Y:0:ATGTCA Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2101:9636:96610_1:N:0:ATGTCA Contig0 1 Processed 379000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2104:11825:41358_1:Y:0:ATGTCA Contig20625 1 Processed 380000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2108:19037:71605_1:N:0:ATGTCA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2110:1257:44366_1:N:0:ATGTCA Contig18052 116631 Processed 381000000 sequences so far Processed 382000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2116:11796:41809_1:N:0:ATGTCA Contig18174 105892 Processed 383000000 sequences so far Processed 384000000 sequences so far Processed 385000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2214:19213:95810_1:Y:0:ATGTCA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2301:8302:9414_1:N:0:ATGTCA Contig20625 1 Processed 386000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2301:13367:32117_1:N:0:ATGTCA Contig5 130492 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2301:3366:94844_1:N:0:ATGTCA Contig18174 105892 Processed 387000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2307:16640:56194_1:N:0:ATGTCA Contig19330 108175 Processed 388000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2313:20957:33264_1:Y:0:ATGTCA Contig19330 108175 Processed 389000000 sequences so far Processed 390000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1104:16161:81319_1:N:0:ATGTCA Contig19330 108174 Processed 391000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1110:5846:80654_1:N:0:ATGTCA Contig20625 1 Processed 392000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1114:18960:91368_1:N:0:ATGTCA Contig84 102773 Processed 393000000 sequences so far Processed 394000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1204:11354:77441_1:N:0:ATGTCA Contig19826 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1206:7571:93868_1:N:0:ATGTCA Contig19330 108174 Processed 395000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:15100:41433_1:N:0:ATGTCA Contig19330 108174 Processed 396000000 sequences so far Processed 397000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1301:10289:83185_1:N:0:ATGTCA Contig20140 129025 Processed 398000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1306:1931:57709_1:N:0:ATGTCA Contig19330 108174 Processed 399000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1309:9104:59952_1:N:0:ATGTCA Contig20140 129023 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 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2203:19140:32372_1:N:0:ATGTCA Contig7 109638 Processed 406000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2208:20353:18784_1:N:0:ATGTCA Contig20625 1 Processed 407000000 sequences so far Processed 408000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2216:11907:54896_1:N:0:ATGTCA Contig18174 105892 Processed 409000000 sequences so far Processed 410000000 sequences so far Processed 411000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:5563:72679_1:N:0:ATGTCA Contig20140 129024 Processed 412000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2316:13821:47853_1:N:0:ATGTCA Contig20625 111109 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1101:7715:5348_1:Y:0:CCGTCC Contig18052 116631 Processed 413000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1104:3872:85526_1:N:0:CCGTCC Contig19330 108175 Processed 414000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1108:19355:45574_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1109:16930:20856_1:N:0:CCGTCC Contig89 100254 Processed 415000000 sequences so far Processed 416000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:15767:56847_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1116:13985:63994_1:N:0:CCGTCC Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:5608:96035_1:Y:0:CCGTCC Contig19330 108179 Processed 417000000 sequences so far Processed 418000000 sequences so far Processed 419000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1211:6623:28944_1:N:0:CCGTCC Contig19330 108174 Processed 420000000 sequences so far Processed 421000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1304:5796:40412_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1305:17422:47662_1:N:0:CCGTCC Contig19330 108176 Processed 422000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1306:13132:34588_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1309:2716:13523_1:N:0:CCGTCC Contig19330 108174 Processed 423000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1312:17024:24948_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1312:18435:32831_1:N:0:CCGTCC Contig3 141626 Processed 424000000 sequences so far Processed 425000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2101:15293:53013_1:N:0:CCGTCC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2103:14601:62957_1:Y:0:CCGTCC Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2104:16055:19256_1:N:0:CCGTCC Contig20625 1 Processed 426000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2107:13455:14386_1:N:0:CCGTCC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2108:2641:6811_1:N:0:CCGTCC Contig19330 108174 Processed 427000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2110:2922:39420_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2111:2133:73304_1:N:0:CCGTCC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2112:8280:64256_1:N:0:CCGTCC Contig18174 105892 Processed 428000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2116:18610:5571_1:N:0:CCGTCC Contig20625 1 Processed 429000000 sequences so far Processed 430000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2206:18790:3175_1:N:0:CCGTCC Contig23978 1 Processed 431000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2210:3492:86531_1:N:0:CCGTCC Contig20625 1 Processed 432000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2213:14212:61624_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2214:9294:16849_1:N:0:CCGTCC Contig18174 105892 Processed 433000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2303:17656:47675_1:N:0:CCGTCC Contig20625 111110 Processed 434000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2305:14960:60064_1:N:0:CCGTCC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2308:8664:37641_1:N:0:CCGTCC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2308:3212:53444_1:N:0:CCGTCC Contig20625 1 Processed 435000000 sequences so far Processed 436000000 sequences so far Processed 437000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1103:5595:17864_1:N:0:CCATCC Contig20625 2 Processed 438000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:10808:8392_1:N:0:CCGTCC Contig18174 105892 Processed 439000000 sequences so far Processed 440000000 sequences so far Processed 441000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1201:6963:59676_1:N:0:CCGTCC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1203:2734:30354_1:N:0:CCGTCC Contig20625 1 Processed 442000000 sequences so far Processed 443000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1208:16994:88920_1:N:0:CCGTCC Contig3 141626 Processed 444000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1212:8688:51518_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1213:15941:93903_1:N:0:CCGTCC Contig18174 105892 Processed 445000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:16375:18976_1:N:0:CCGTCC Contig5 130492 Processed 446000000 sequences so far Processed 447000000 sequences so far Processed 448000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1313:12044:80518_1:N:0:CCGTCC Contig19330 108174 Processed 449000000 sequences so far Processed 450000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2104:8799:34041_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2104:4692:52056_1:N:0:CCGTCC Contig20625 111109 Processed 451000000 sequences so far Processed 452000000 sequences so far Processed 453000000 sequences so far Processed 454000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2202:3590:76591_1:N:0:CCGTCC Contig19330 108174 Processed 455000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2207:14804:31998_1:N:0:CCGTCC Contig5 130491 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2207:2803:49392_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:20747:25921_1:N:0:CCGTCC Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:20962:43128_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:12402:43901_1:N:0:CCGTCC Contig20625 1 Processed 456000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2212:18877:99135_1:N:0:CCGTCC Contig20625 1 Processed 457000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2216:8220:16429_1:N:0:CCGTCC Contig20625 1 Processed 458000000 sequences so far Processed 459000000 sequences so far Processed 460000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2310:7020:20565_1:N:0:CCGTCC Contig19330 108174 Processed 461000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2313:15163:73550_1:N:0:CCGTCC Contig19330 108174 Processed 462000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1101:4716:69673_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:16221:23183_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:8262:43832_1:N:0:CCGTCC Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1102:3961:95833_1:N:0:CCGTCC Contig18174 105900 Processed 463000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1106:1668:90710_1:N:0:CCGTCC Contig20140 129024 Processed 464000000 sequences so far Processed 465000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1112:9303:52753_1:N:0:CCGTCC Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1113:7240:28744_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:19765:65128_1:N:0:TCGTCC Contig20140 129025 Processed 466000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1203:15093:98825_1:N:0:CCGTCC Contig18174 105892 Processed 467000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1205:9939:41920_1:N:0:CCGTCC Contig20625 1 Processed 468000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:1404:3106_1:N:0:CCGTCC Contig20625 1 Processed 469000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1212:12692:68883_1:N:0:CCGTCC Contig5 130492 Processed 470000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1215:20504:95518_1:N:0:CCGTCC Contig18174 105892 Processed 471000000 sequences so far Processed 472000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1307:19943:59227_1:N:0:CCGTCC Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:13556:28291_1:N:0:CCGTCC Contig20625 1 Processed 473000000 sequences so far Processed 474000000 sequences so far Processed 475000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2103:20638:66370_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2106:3353:13177_1:N:0:CCGTCC Contig20625 1 Processed 476000000 sequences so far Processed 477000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:16681:88643_1:N:0:CCGTCC Contig0 1 Processed 478000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2115:5189:36691_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2116:10033:89717_1:Y:0:CCGTCT Contig19330 108174 Processed 479000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2202:8055:78879_1:N:0:CCGTCC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2204:19048:92601_1:N:0:CCGTCC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2205:6832:44105_1:N:0:CCGTCC Contig18174 105892 Processed 480000000 sequences so far Processed 481000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2211:18244:22219_1:N:0:CCGTCC Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2213:11313:12689_1:N:0:CCGTCC Contig19330 108174 Processed 482000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2301:10010:66694_1:N:0:CCGTCC Contig20625 1 Processed 483000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2302:14466:18680_1:N:0:CCGTCC Contig20140 129025 Processed 484000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2307:5009:99379_1:N:0:CCGTCC Contig84 102774 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2309:21136:39385_1:N:0:CCGTCC Contig18024 2 Processed 485000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:14770:92333_1:N:0:CCGTCC Contig19330 108174 Processed 486000000 sequences so far Processed 487000000 sequences so far Processed 488000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:19565:25996_1:N:0:GTCCGC Contig20625 1 Processed 489000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1116:11642:31135_1:N:0:GTCCGC Contig19330 108174 Processed 490000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1209:2607:7059_1:N:0:GTCCGC Contig17050 1 Processed 491000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:6333:6640_1:N:0:GTCCGC Contig18174 105892 Processed 492000000 sequences so far Processed 493000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1313:4123:95805_1:N:0:GTCCGC Contig20625 1 Processed 494000000 sequences so far Processed 495000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2110:15369:93313_1:N:0:GTCCGC Contig16668 101411 Processed 496000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2115:6776:80777_1:N:0:GTCCGC Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2116:17706:79731_1:N:0:GTCCGC Contig20625 1 Processed 497000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2211:1933:59853_1:N:0:GTCCGC Contig7 109638 Processed 498000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2215:6984:20434_1:N:0:GTCCGC Contig20625 2 Processed 499000000 sequences so far Processed 500000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2311:5426:23726_1:N:0:GTCCGC Contig20140 129025 Processed 501000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1105:10414:73454_1:N:0:GTCCGC Contig20625 1 Processed 502000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:18636:16050_1:Y:0:ATCCGC Contig0 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1114:8299:10821_1:N:0:GTCCGC Contig20625 111110 Processed 503000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1115:18509:26048_1:N:0:GTCCGC Contig23978 1 Processed 504000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1209:14229:7242_1:N:0:GTCCGC Contig23978 2 Processed 505000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1213:16507:34918_1:N:0:GTCCGC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1302:7872:52565_1:N:0:GTCCGC Contig19826 2 Processed 506000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1306:16669:16593_1:N:0:ATCCGC Contig20625 1 Processed 507000000 sequences so far Processed 508000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2103:12419:4991_1:N:0:GTCCGC Contig20625 1 Processed 509000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2111:11809:4892_1:N:0:ATCCGC Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2111:19033:85289_1:Y:0:GTCCGC Contig19330 108174 Processed 510000000 sequences so far Processed 511000000 sequences so far Processed 512000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2215:17683:87194_1:N:0:ATCCGC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2301:8473:84749_1:N:0:GTCCGC Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2302:20333:21938_1:N:0:GTCCGC Contig20625 1 Processed 513000000 sequences so far Processed 514000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2313:7263:55650_1:N:0:GTCCGC Contig84 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2316:8735:83687_1:Y:0:GTCCGC Contig16668 1 Processed 515000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1101:5169:64610_1:N:0:GTCCGC Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1101:14063:73454_1:N:0:GTCCGC Contig26138 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1107:15957:6375_1:N:0:GTCCGC Contig18174 105892 Processed 516000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:11702:34876_1:N:0:GTCCGC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1111:4155:65924_1:N:0:GTCCGC Contig20140 129024 Processed 517000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1202:12382:15203_1:N:0:GTCCGC Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1203:19217:38055_1:N:0:GTCCGC Contig19826 1 Processed 518000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1210:13243:57486_1:N:0:GTCCGC Contig19330 108174 Processed 519000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:11257:9892_1:N:0:GTCCGC Contig18174 105892 Processed 520000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1306:10690:94542_1:N:0:GTCCGC Contig19330 108174 Processed 521000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1315:7467:83052_1:N:0:GTCCGC Contig16668 1 Processed 522000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2104:13190:73051_1:N:0:GTCCGC Contig468 2 Processed 523000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2109:14336:27688_1:N:0:ATCCGC Contig18174 105892 Processed 524000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2114:21015:100130_1:N:0:GTCCGC Contig19330 108175 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2201:11392:40198_1:N:0:GTCCGC Contig18174 105892 Processed 525000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2206:2193:50651_1:Y:0:GTCCGC Contig0 1 Processed 526000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2215:1338:95508_1:N:0:GTCCGC Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2216:6325:84974_1:N:0:GTCCGC Contig65 107630 Processed 527000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2308:6882:78130_1:Y:0:GTCCGT Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2309:19974:3544_1:N:0:GTCCGC Contig5 130492 Processed 528000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2313:5720:54875_1:N:0:GTCCGC Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1101:8422:43552_1:N:0:GTGAAA Contig0 1 Processed 529000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1101:15451:70477_1:N:0:GTGAAA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1105:14982:25107_1:N:0:GTGAAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1106:13308:65324_1:N:0:GTGAAA Contig19330 108173 Processed 530000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1107:3700:4514_1:N:0:GTGAAA Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1108:5105:89213_1:N:0:GTGAAA Contig65 107630 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1109:6326:14304_1:N:0:GTGAAA Contig23978 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1111:10224:15919_1:N:0:GTGAAA Contig20625 2 Processed 531000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1113:21233:14461_1:N:0:GTGAAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:18845:17382_1:N:0:GTGAAA Contig18024 109271 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1115:2697:80361_1:Y:0:GTGAAA Contig26138 2 Processed 532000000 sequences so far Processed 533000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1208:7607:72155_1:N:0:GTGAAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1210:10548:54144_1:N:0:GTGAAA Contig20625 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1210:7519:64795_1:N:0:GTGAAA Contig20625 111110 Processed 534000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1212:4869:27313_1:N:0:GTGAAA Contig19267 115726 Processed 535000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1302:8315:4448_1:N:0:GTGAAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1303:18190:73630_1:N:0:GTGAAA Contig19330 108174 Processed 536000000 sequences so far Processed 537000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1311:6947:76570_1:N:0:GTGAAA Contig18174 105892 Processed 538000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1315:12563:40522_1:N:0:GTGAAA Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1315:15193:76799_1:N:0:GTGAAA Contig16668 101411 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2102:5494:52274_1:N:0:GTGAAA Contig19646 1 Processed 539000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2109:16551:32050_1:N:0:GTGAAA Contig19330 108174 Processed 540000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2112:19621:70789_1:N:0:GTGAAA Contig18174 105892 Processed 541000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2116:5010:52585_1:N:0:GTGAAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2202:10521:30207_1:N:0:GTGAAA Contig16668 1 Processed 542000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2205:16392:98391_1:N:0:GTGAAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2206:14619:24313_1:N:0:GTGAAA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2208:5412:7422_1:N:0:GTGAAA Contig23978 1 Processed 543000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2214:2688:38673_1:N:0:GTGAAA Contig20625 1 Processed 544000000 sequences so far Processed 545000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2309:11916:15368_1:N:0:GTGAAA Contig20625 111110 Processed 546000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2309:18171:95963_1:N:0:GTGAAA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:14065:18109_1:N:0:GTGAAA Contig0 1 Processed 547000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2315:9312:71091_1:N:0:GTGAAA Contig20625 111109 Processed 548000000 sequences so far Processed 549000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:10332:84037_1:N:0:GTGAAT Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1114:9260:27091_1:N:0:ATGAAA Contig5 130492 Processed 550000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1115:3506:62643_1:N:0:GTGAAA Contig5 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1202:6333:66596_1:N:0:ATGAAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1203:11702:79699_1:N:0:GTGAAA Contig18052 116631 Processed 551000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1206:8018:30517_1:N:0:GTGAAA Contig3 141626 Processed 552000000 sequences so far Processed 553000000 sequences so far Processed 554000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1303:5703:39956_1:N:0:GTGAAA Contig19330 108173 Processed 555000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1308:11676:46712_1:N:0:GTGAAA Contig5 130491 Processed 556000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:5018:48312_1:N:0:GTGAAA Contig16668 101411 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1314:10500:78908_1:N:0:GTGAAT Contig5 2 Processed 557000000 sequences so far Processed 558000000 sequences so far Processed 559000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2114:17617:48645_1:N:0:GTGAAA Contig18174 105892 Processed 560000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:13750:2232_1:N:0:GTGAAA Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2205:7479:3040_1:N:0:GTGAAA Contig19267 115726 Processed 561000000 sequences so far Processed 562000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2213:9499:89042_1:N:0:GTGAAA Contig18174 105892 Processed 563000000 sequences so far Processed 564000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2312:5355:34377_1:N:0:GTGAAA Contig16668 101411 Processed 565000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2313:1560:86771_1:N:0:GTGAAT Contig0 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:2314:4609:15320_1:N:0:GTGAAA Contig19330 108174 Processed 566000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1107:5390:27752_1:N:0:GTGAAA Contig18174 105892 Processed 567000000 sequences so far Processed 568000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1115:5281:49984_1:N:0:GTGAAA Contig18174 105892 Processed 569000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1202:10345:99248_1:N:0:GTGAAA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1203:12453:6957_1:N:0:GTGAAA Contig16668 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1204:11759:12246_1:N:0:GTGAAA Contig18052 116631 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1204:11547:28835_1:N:0:GTGAAA Contig19646 1 Processed 570000000 sequences so far Processed 571000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1214:19720:47934_1:N:0:GTGAAA Contig20625 1 Processed 572000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1301:10560:94623_1:N:0:GTGAAA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:10631:82051_1:N:0:GTGAAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1303:4970:84369_1:N:0:GTGAAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1306:8803:21056_1:N:0:GTGAAA Contig20625 111110 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1306:5142:97166_1:N:0:GTGAAA Contig19330 108173 Processed 573000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1308:13938:42620_1:N:0:GTGAAA Contig26138 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1310:11436:36437_1:N:0:GTGAAA Contig20140 129025 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:1311:10819:94782_1:N:0:GTGAAA Contig19330 108174 Processed 574000000 sequences so far Processed 575000000 sequences so far Processed 576000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2111:8016:28345_1:N:0:GTGAAA Contig18174 105892 Processed 577000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2113:15477:40064_1:N:0:GTGAAA Contig20140 129023 Processed 578000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2201:3767:96893_1:N:0:GTGAAA Contig26138 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2202:13033:9177_1:N:0:GTGAAA Contig19330 108174 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2202:4959:12328_1:N:0:GTGAAA Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2206:3540:15711_1:N:0:GTGAAA Contig20625 111110 Processed 579000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2208:10728:73345_1:N:0:GTGAAA Contig20625 111110 Processed 580000000 sequences so far Processed 581000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2305:8838:27193_1:Y:0:GTGAAA Contig20140 129023 Processed 582000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2310:17277:99490_1:N:0:GTGAAA Contig18174 105892 Processed 583000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:3:2312:12604:60551_1:N:0:GTGAAA Contig20625 1 Processed 584000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1103:16534:5633_1:N:0:ATCACG Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1103:12131:65981_1:N:0:ATCACG Contig18174 105892 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1105:6630:96074_1:N:0:ATCACG Contig26138 2 Processed 585000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1112:13880:76614_1:N:0:ATCACG Contig20140 129024 Processed 586000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1114:2189:53720_1:N:0:ATCACG Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1201:13018:86049_1:N:0:ATCACG Contig20140 129025 Processed 587000000 sequences so far Processed 588000000 sequences so far Processed 589000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1215:2426:62329_1:N:0:ATCACG Contig19330 108175 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1304:4911:66919_1:N:0:ATCACG Contig20625 1 Processed 590000000 sequences so far Processed 591000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:1312:13910:17074_1:Y:0:ATCACG Contig17050 2 Processed 592000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2101:19631:79270_1:N:0:ATCACG Contig20140 129024 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2101:15013:99907_1:N:0:ATCACG Contig20140 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2107:16470:23357_1:N:0:ATCACG Contig19330 108174 Processed 593000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2112:9753:66320_1:N:0:ATCACG Contig0 2 Processed 594000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2203:17395:32246_1:N:0:ATCACG Contig20625 1 Processed 595000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2204:10353:45978_1:N:0:ATCACG Contig20625 1 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:17170:20650_1:N:0:ATCACG Contig20140 129023 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2209:14197:23035_1:Y:0:ATCACG Contig18174 105892 Processed 596000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2214:6307:42608_1:N:0:ATCACG Contig23978 2 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2216:6223:14433_1:N:0:ATCACG Contig18174 105892 Processed 597000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2304:14427:33417_1:N:0:ATCACG Contig16668 2 Processed 598000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:1:2312:8420:10635_1:N:0:ATCACG Contig19330 108175 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:2:1110:3922:42139_1:N:0:ATCACG Contig84 102773 Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1112:15193:7498_1:N:0:ATCACG Contig0 1 Processed 602000000 sequences so far Chromosomal sequence could not be extracted for HWI-C00124:164:C7URDANXX:2:1115:6006:51596_1:N:0:ACCACG Contig20625 1 Processed 603000000 sequences so far Processed 604000000 sequences so far Processed 605000000 sequences so far 605809374605809374 reads; of these: reads; of these: 605809374 (605809374 (100.00%) were unpaired; of these: 587454850 (96.97%) aligned 0 times100.00 % ) were unpaired; of these:8440822 ( 1.39582113496% () aligned exactly 1 time96.09 % ) aligned 0 times9913702 ( 1.6410038469% () aligned >1 times1.66 %3.03) aligned exactly 1 time% overall alignment rate 13657409 (2.25%) aligned >1 times 3.91% overall alignment rate 605809374 reads; of these: 605809374 (100.00%) were unpaired; of these: 581205437 (95.94%) aligned 0 times 10809417 (1.78%) aligned exactly 1 time 13794520 (2.28%) aligned >1 times 4.06% overall alignment rate 605809374 reads; of these: 605809374 (100.00%) were unpaired; of these: 587003712 (96.90%) aligned 0 times 8682816 (1.43%) aligned exactly 1 time 10122846 (1.67%) aligned >1 times 3.10% 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: 27806680 Mapping efficiency: 4.6% Sequences with no alignments under any condition: 550394238 Sequences did not map uniquely: 27608456 Sequences which were discarded because genomic sequence could not be extracted: 671 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 5864343 ((converted) top strand) CT/GA: 6330145 ((converted) bottom strand) GA/CT: 7523167 (complementary to (converted) top strand) GA/GA: 8088354 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 172354157 Total methylated C's in CpG context: 27953676 Total methylated C's in CHG context: 967507 Total methylated C's in CHH context: 8116739 Total methylated C's in Unknown context: 972 Total unmethylated C's in CpG context: 7703035 Total unmethylated C's in CHG context: 30588122 Total unmethylated C's in CHH context: 97025078 Total unmethylated C's in Unknown context: 3699 C methylated in CpG context: 78.4% C methylated in CHG context: 3.1% C methylated in CHH context: 7.7% C methylated in Unknown context (CN or CHN): 20.8% Bismark completed in 0d 5h 9m 54s ==================== 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: 3147151 Total number duplicated alignments removed: 2837021 (90.15%) Duplicated alignments were found at: 175832 different position(s) Total count of deduplicated leftover sequences: 310130 (9.85% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 2533256 Total number duplicated alignments removed: 2228585 (87.97%) Duplicated alignments were found at: 144132 different position(s) Total count of deduplicated leftover sequences: 304671 (12.03% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 2728244 Total number duplicated alignments removed: 2310879 (84.70%) Duplicated alignments were found at: 193445 different position(s) Total count of deduplicated leftover sequences: 417365 (15.30% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 3006730 Total number duplicated alignments removed: 2635369 (87.65%) Duplicated alignments were found at: 183029 different position(s) Total count of deduplicated leftover sequences: 371361 (12.35% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 4288102 Total number duplicated alignments removed: 3840822 (89.57%) Duplicated alignments were found at: 226432 different position(s) Total count of deduplicated leftover sequences: 447280 (10.43% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 3168935 Total number duplicated alignments removed: 2803236 (88.46%) Duplicated alignments were found at: 179085 different position(s) Total count of deduplicated leftover sequences: 365699 (11.54% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 3531987 Total number duplicated alignments removed: 3136869 (88.81%) Duplicated alignments were found at: 194707 different position(s) Total count of deduplicated leftover sequences: 395118 (11.19% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 1869165 Total number duplicated alignments removed: 1578377 (84.44%) Duplicated alignments were found at: 133346 different position(s) Total count of deduplicated leftover sequences: 290788 (15.56% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 2536630 Total number duplicated alignments removed: 2151933 (84.83%) Duplicated alignments were found at: 182700 different position(s) Total count of deduplicated leftover sequences: 384697 (15.17% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 2117393 Total number duplicated alignments removed: 1758255 (83.04%) Duplicated alignments were found at: 165505 different position(s) Total count of deduplicated leftover sequences: 359138 (16.96% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 2050901 Total number duplicated alignments removed: 1699079 (82.85%) Duplicated alignments were found at: 162203 different position(s) Total count of deduplicated leftover sequences: 351822 (17.15% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 2160178 Total number duplicated alignments removed: 1795758 (83.13%) Duplicated alignments were found at: 168982 different position(s) Total count of deduplicated leftover sequences: 364420 (16.87% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 2010065 Total number duplicated alignments removed: 1670445 (83.10%) Duplicated alignments were found at: 156416 different position(s) Total count of deduplicated leftover sequences: 339620 (16.90% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 2079460 Total number duplicated alignments removed: 1690809 (81.31%) Duplicated alignments were found at: 171673 different position(s) Total count of deduplicated leftover sequences: 388651 (18.69% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 2013209 Total number duplicated alignments removed: 1629030 (80.92%) Duplicated alignments were found at: 170292 different position(s) Total count of deduplicated leftover sequences: 384179 (19.08% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 2247624 Total number duplicated alignments removed: 1878851 (83.59%) Duplicated alignments were found at: 171559 different position(s) Total count of deduplicated leftover sequences: 368773 (16.41% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 1779107 Total number duplicated alignments removed: 1464613 (82.32%) Duplicated alignments were found at: 142349 different position(s) Total count of deduplicated leftover sequences: 314494 (17.68% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 3614788 Total number duplicated alignments removed: 3133239 (86.68%) Duplicated alignments were found at: 235196 different position(s) Total count of deduplicated leftover sequences: 481549 (13.32% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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: 27806009 Total number duplicated alignments removed: 26676032 (95.94%) Duplicated alignments were found at: 637756 different position(s) Total count of deduplicated leftover sequences: 1129977 (4.06% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Contig0 LN:116746 skipping header line: @SQ SN:Contig2 LN:139250 skipping header line: @SQ SN:Contig3 LN:141657 skipping header line: @SQ SN:Contig5 LN:130522 skipping header line: @SQ SN:Contig7 LN:109667 skipping header line: @SQ SN:Contig9 LN:112192 skipping header line: @SQ SN:Contig65 LN:107659 skipping header line: @SQ SN:Contig84 LN:102803 skipping header line: @SQ SN:Contig89 LN:100284 skipping header line: @SQ SN:Contig468 LN:111883 skipping header line: @SQ SN:Contig15326 LN:102312 skipping header line: @SQ SN:Contig16524 LN:122429 skipping header line: @SQ SN:Contig16668 LN:101442 skipping header line: @SQ SN:Contig16915 LN:114892 skipping header line: @SQ SN:Contig17050 LN:125421 skipping header line: @SQ SN:Contig17624 LN:122541 skipping header line: @SQ SN:Contig17876 LN:129629 skipping header line: @SQ SN:Contig18024 LN:109300 skipping header line: @SQ SN:Contig18052 LN:116661 skipping header line: @SQ SN:Contig18174 LN:105922 skipping header line: @SQ SN:Contig18571 LN:110864 skipping header line: @SQ SN:Contig19267 LN:115756 skipping header line: @SQ SN:Contig19330 LN:108204 skipping header line: @SQ SN:Contig19646 LN:194507 skipping header line: @SQ SN:Contig19826 LN:107763 skipping header line: @SQ SN:Contig20140 LN:129054 skipping header line: @SQ SN:Contig20625 LN:111140 skipping header line: @SQ SN:Contig22814 LN:138260 skipping header line: @SQ SN:Contig23978 LN:107801 skipping header line: @SQ SN:Contig23979 LN:128837 skipping header line: @SQ SN:Contig26138 LN:101662 skipping header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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/sr320/061722-v082') 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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_10_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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 310130 lines in total Total number of methylation call strings processed: 310130 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1940126 Total methylated C's in CpG context: 184224 Total methylated C's in CHG context: 13483 Total methylated C's in CHH context: 221285 Total C to T conversions in CpG context: 81087 Total C to T conversions in CHG context: 249490 Total C to T conversions in CHH context: 1190557 C methylated in CpG context: 69.4% C methylated in CHG context: 5.1% C methylated in CHH context: 15.7% 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/sr320/061722-v082/CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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 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. 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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_11_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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_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 304671 lines in total Total number of methylation call strings processed: 304671 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1903561 Total methylated C's in CpG context: 205058 Total methylated C's in CHG context: 12613 Total methylated C's in CHH context: 183446 Total C to T conversions in CpG context: 85540 Total C to T conversions in CHG context: 251339 Total C to T conversions in CHH context: 1165565 C methylated in CpG context: 70.6% C methylated in CHG context: 4.8% C methylated in CHH context: 13.6% 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/sr320/061722-v082/CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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 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 Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_12_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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_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 417365 lines in total Total number of methylation call strings processed: 417365 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2575743 Total methylated C's in CpG context: 226998 Total methylated C's in CHG context: 14505 Total methylated C's in CHH context: 249861 Total C to T conversions in CpG context: 117529 Total C to T conversions in CHG context: 349443 Total C to T conversions in CHH context: 1617407 C methylated in CpG context: 65.9% C methylated in CHG context: 4.0% C methylated in CHH context: 13.4% 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/sr320/061722-v082/CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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 Now reading in Bismark result file zr1394_13_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_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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_13_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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_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 371361 lines in total Total number of methylation call strings processed: 371361 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2317028 Total methylated C's in CpG context: 246179 Total methylated C's in CHG context: 15000 Total methylated C's in CHH context: 227786 Total C to T conversions in CpG context: 93775 Total C to T conversions in CHG context: 307464 Total C to T conversions in CHH context: 1426824 C methylated in CpG context: 72.4% C methylated in CHG context: 4.7% C methylated in CHH context: 13.8% 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/sr320/061722-v082/CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_s456_trimmed.fq" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '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 447280 lines in total Total number of methylation call strings processed: 447280 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2753570 Total methylated C's in CpG context: 286266 Total methylated C's in CHG context: 17092 Total methylated C's in CHH context: 251098 Total C to T conversions in CpG context: 112046 Total C to T conversions in CHG context: 356809 Total C to T conversions in CHH context: 1730259 C methylated in CpG context: 71.9% C methylated in CHG context: 4.6% C methylated in CHH context: 12.7% 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/sr320/061722-v082/CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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 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 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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_15_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '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 365699 lines in total Total number of methylation call strings processed: 365699 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2275320 Total methylated C's in CpG context: 252344 Total methylated C's in CHG context: 15544 Total methylated C's in CHH context: 227198 Total C to T conversions in CpG context: 87619 Total C to T conversions in CHG context: 300108 Total C to T conversions in CHH context: 1392507 C methylated in CpG context: 74.2% C methylated in CHG context: 4.9% C methylated in CHH context: 14.0% 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/sr320/061722-v082/CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_16_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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_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 395118 lines in total Total number of methylation call strings processed: 395118 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2439608 Total methylated C's in CpG context: 263400 Total methylated C's in CHG context: 16049 Total methylated C's in CHH context: 234544 Total C to T conversions in CpG context: 101061 Total C to T conversions in CHG context: 317768 Total C to T conversions in CHH context: 1506786 C methylated in CpG context: 72.3% C methylated in CHG context: 4.8% C methylated in CHH context: 13.5% 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/sr320/061722-v082/CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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 Now reading in Bismark result file zr1394_17_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_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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_17_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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_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 290788 lines in total Total number of methylation call strings processed: 290788 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1825743 Total methylated C's in CpG context: 202011 Total methylated C's in CHG context: 12480 Total methylated C's in CHH context: 193496 Total C to T conversions in CpG context: 70791 Total C to T conversions in CHG context: 249245 Total C to T conversions in CHH context: 1097720 C methylated in CpG context: 74.1% C methylated in CHG context: 4.8% C methylated in CHH context: 15.0% 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/sr320/061722-v082/CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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 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 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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '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 384697 lines in total Total number of methylation call strings processed: 384697 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2391747 Total methylated C's in CpG context: 228558 Total methylated C's in CHG context: 13938 Total methylated C's in CHH context: 225068 Total C to T conversions in CpG context: 102063 Total C to T conversions in CHG context: 328800 Total C to T conversions in CHH context: 1493320 C methylated in CpG context: 69.1% C methylated in CHG context: 4.1% C methylated in CHH context: 13.1% 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/sr320/061722-v082/CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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 359138 lines in total Total number of methylation call strings processed: 359138 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2224066 Total methylated C's in CpG context: 219081 Total methylated C's in CHG context: 13541 Total methylated C's in CHH context: 210878 Total C to T conversions in CpG context: 100089 Total C to T conversions in CHG context: 301405 Total C to T conversions in CHH context: 1379072 C methylated in CpG context: 68.6% C methylated in CHG context: 4.3% C methylated in CHH context: 13.3% 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/sr320/061722-v082/CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '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 351822 lines in total Total number of methylation call strings processed: 351822 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2184474 Total methylated C's in CpG context: 213059 Total methylated C's in CHG context: 13257 Total methylated C's in CHH context: 216278 Total C to T conversions in CpG context: 94747 Total C to T conversions in CHG context: 300551 Total C to T conversions in CHH context: 1346582 C methylated in CpG context: 69.2% C methylated in CHG context: 4.2% C methylated in CHH context: 13.8% 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/sr320/061722-v082/CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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 Now reading in Bismark result file zr1394_3_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_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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_3_s456_trimmed.fq" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '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 364420 lines in total Total number of methylation call strings processed: 364420 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2247377 Total methylated C's in CpG context: 220270 Total methylated C's in CHG context: 13219 Total methylated C's in CHH context: 205636 Total C to T conversions in CpG context: 97022 Total C to T conversions in CHG context: 300651 Total C to T conversions in CHH context: 1410579 C methylated in CpG context: 69.4% C methylated in CHG context: 4.2% C methylated in CHH context: 12.7% 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/sr320/061722-v082/CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_4_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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_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 339620 lines in total Total number of methylation call strings processed: 339620 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2113978 Total methylated C's in CpG context: 222919 Total methylated C's in CHG context: 13165 Total methylated C's in CHH context: 199090 Total C to T conversions in CpG context: 81651 Total C to T conversions in CHG context: 288530 Total C to T conversions in CHH context: 1308623 C methylated in CpG context: 73.2% C methylated in CHG context: 4.4% C methylated in CHH context: 13.2% 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/sr320/061722-v082/CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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 388651 lines in total Total number of methylation call strings processed: 388651 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2397810 Total methylated C's in CpG context: 196351 Total methylated C's in CHG context: 13520 Total methylated C's in CHH context: 238368 Total C to T conversions in CpG context: 123953 Total C to T conversions in CHG context: 328465 Total C to T conversions in CHH context: 1497153 C methylated in CpG context: 61.3% C methylated in CHG context: 4.0% C methylated in CHH context: 13.7% 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/sr320/061722-v082/CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_6_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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 384179 lines in total Total number of methylation call strings processed: 384179 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2354787 Total methylated C's in CpG context: 198359 Total methylated C's in CHG context: 12844 Total methylated C's in CHH context: 216864 Total C to T conversions in CpG context: 101931 Total C to T conversions in CHG context: 320460 Total C to T conversions in CHH context: 1504329 C methylated in CpG context: 66.1% C methylated in CHG context: 3.9% C methylated in CHH context: 12.6% 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/sr320/061722-v082/CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_7_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '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 368773 lines in total Total number of methylation call strings processed: 368773 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2285525 Total methylated C's in CpG context: 231457 Total methylated C's in CHG context: 14129 Total methylated C's in CHH context: 213306 Total C to T conversions in CpG context: 97876 Total C to T conversions in CHG context: 310464 Total C to T conversions in CHH context: 1418293 C methylated in CpG context: 70.3% C methylated in CHG context: 4.4% C methylated in CHH context: 13.1% 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/sr320/061722-v082/CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_8_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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_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 314494 lines in total Total number of methylation call strings processed: 314494 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1963151 Total methylated C's in CpG context: 213026 Total methylated C's in CHG context: 11872 Total methylated C's in CHH context: 183281 Total C to T conversions in CpG context: 74232 Total C to T conversions in CHG context: 269542 Total C to T conversions in CHH context: 1211198 C methylated in CpG context: 74.2% C methylated in CHG context: 4.2% C methylated in CHH context: 13.1% 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/sr320/061722-v082/CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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_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 481549 lines in total Total number of methylation call strings processed: 481549 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2945477 Total methylated C's in CpG context: 251709 Total methylated C's in CHG context: 16074 Total methylated C's in CHH context: 272980 Total C to T conversions in CpG context: 128793 Total C to T conversions in CHG context: 389241 Total C to T conversions in CHH context: 1886680 C methylated in CpG context: 66.2% C methylated in CHG context: 4.0% C methylated in CHH context: 12.6% 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/sr320/061722-v082/CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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:Contig0 LN:116746 skipping SAM header line: @SQ SN:Contig2 LN:139250 skipping SAM header line: @SQ SN:Contig3 LN:141657 skipping SAM header line: @SQ SN:Contig5 LN:130522 skipping SAM header line: @SQ SN:Contig7 LN:109667 skipping SAM header line: @SQ SN:Contig9 LN:112192 skipping SAM header line: @SQ SN:Contig65 LN:107659 skipping SAM header line: @SQ SN:Contig84 LN:102803 skipping SAM header line: @SQ SN:Contig89 LN:100284 skipping SAM header line: @SQ SN:Contig468 LN:111883 skipping SAM header line: @SQ SN:Contig15326 LN:102312 skipping SAM header line: @SQ SN:Contig16524 LN:122429 skipping SAM header line: @SQ SN:Contig16668 LN:101442 skipping SAM header line: @SQ SN:Contig16915 LN:114892 skipping SAM header line: @SQ SN:Contig17050 LN:125421 skipping SAM header line: @SQ SN:Contig17624 LN:122541 skipping SAM header line: @SQ SN:Contig17876 LN:129629 skipping SAM header line: @SQ SN:Contig18024 LN:109300 skipping SAM header line: @SQ SN:Contig18052 LN:116661 skipping SAM header line: @SQ SN:Contig18174 LN:105922 skipping SAM header line: @SQ SN:Contig18571 LN:110864 skipping SAM header line: @SQ SN:Contig19267 LN:115756 skipping SAM header line: @SQ SN:Contig19330 LN:108204 skipping SAM header line: @SQ SN:Contig19646 LN:194507 skipping SAM header line: @SQ SN:Contig19826 LN:107763 skipping SAM header line: @SQ SN:Contig20140 LN:129054 skipping SAM header line: @SQ SN:Contig20625 LN:111140 skipping SAM header line: @SQ SN:Contig22814 LN:138260 skipping SAM header line: @SQ SN:Contig23978 LN:107801 skipping SAM header line: @SQ SN:Contig23979 LN:128837 skipping SAM header line: @SQ SN:Contig26138 LN:101662 skipping SAM header line: @SQ SN:Contig34578 LN:138978 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/v082/ -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 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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 1129977 lines in total Total number of methylation call strings processed: 1129977 Final Cytosine Methylation Report ================================= Total number of C's analysed: 6688214 Total methylated C's in CpG context: 537926 Total methylated C's in CHG context: 50095 Total methylated C's in CHH context: 784788 Total C to T conversions in CpG context: 276545 Total C to T conversions in CHG context: 833957 Total C to T conversions in CHH context: 4204903 C methylated in CpG context: 66.0% C methylated in CHG context: 5.7% C methylated in CHH context: 15.7% 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/sr320/061722-v082/CpG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/CpG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/061722-v082/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... Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_10_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1651 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1720 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1178 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1571 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1630 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1470 different covered positions) Writing cytosine report for chromosome Contig65 (stored 946 different covered positions) Writing cytosine report for chromosome Contig84 (stored 762 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1037 different covered positions) Writing cytosine report for chromosome Contig468 (stored 691 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1130 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1034 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 983 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 875 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1181 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1128 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1618 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 840 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 946 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 858 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1587 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1291 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1156 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 1642 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1387 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1189 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1224 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1285 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 883 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1143 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 895 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 306 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_10_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_10_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_11_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1683 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1778 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1212 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1599 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1576 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1534 different covered positions) Writing cytosine report for chromosome Contig65 (stored 986 different covered positions) Writing cytosine report for chromosome Contig84 (stored 760 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1063 different covered positions) Writing cytosine report for chromosome Contig468 (stored 682 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1065 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1083 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 966 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 765 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1112 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1133 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1569 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 833 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 987 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 872 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1703 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1305 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1235 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 1668 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1430 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1275 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1181 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1344 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 872 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1151 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 1005 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 275 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_11_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_11_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_12_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 2082 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1939 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1499 different covered positions) Writing cytosine report for chromosome Contig5 (stored 2003 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1853 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1725 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1221 different covered positions) Writing cytosine report for chromosome Contig84 (stored 890 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1268 different covered positions) Writing cytosine report for chromosome Contig468 (stored 1016 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1327 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1147 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1225 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 1208 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1798 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1481 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1876 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1211 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1137 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 1137 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1727 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1540 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1315 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 3013 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1537 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1440 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1564 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1587 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 1104 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1426 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 1042 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 433 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_12_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_12_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_13_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1887 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1773 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1311 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1778 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1719 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1583 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1055 different covered positions) Writing cytosine report for chromosome Contig84 (stored 751 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1127 different covered positions) Writing cytosine report for chromosome Contig468 (stored 756 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1223 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1101 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1073 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 963 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1311 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1210 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1728 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 973 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 988 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 979 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1715 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1433 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1273 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 1848 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1452 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1275 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1347 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1465 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 931 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1286 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 1031 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 371 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_13_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_13_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_14_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 2012 different covered positions) Writing cytosine report for chromosome Contig2 (stored 2022 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1501 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1931 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1870 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1748 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1223 different covered positions) Writing cytosine report for chromosome Contig84 (stored 969 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1259 different covered positions) Writing cytosine report for chromosome Contig468 (stored 829 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1318 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1247 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1219 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 1094 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1399 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1385 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1941 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1065 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1190 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 1037 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1879 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1599 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1502 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 2141 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1619 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1505 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1467 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1595 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 1028 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1483 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 1440 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 391 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_14_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_14_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_15_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1795 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1869 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1303 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1769 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1700 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1579 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1115 different covered positions) Writing cytosine report for chromosome Contig84 (stored 800 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1096 different covered positions) Writing cytosine report for chromosome Contig468 (stored 744 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1176 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1151 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1015 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 888 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1288 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1203 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1731 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 987 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1089 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 979 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1722 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1358 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1278 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 1891 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1474 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1276 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1323 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1447 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 952 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1322 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 986 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 337 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_15_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_15_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_16_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1888 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1979 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1394 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1833 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1774 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1661 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1179 different covered positions) Writing cytosine report for chromosome Contig84 (stored 808 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1204 different covered positions) Writing cytosine report for chromosome Contig468 (stored 777 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1238 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1153 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1127 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 1004 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1374 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1304 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1819 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1015 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1167 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 1024 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1807 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1508 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1336 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 2039 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1553 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1372 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1339 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1506 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 984 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1356 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 1044 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 352 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_16_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_16_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_17_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1635 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1552 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1122 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1603 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1592 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1430 different covered positions) Writing cytosine report for chromosome Contig65 (stored 933 different covered positions) Writing cytosine report for chromosome Contig84 (stored 670 different covered positions) Writing cytosine report for chromosome Contig89 (stored 969 different covered positions) Writing cytosine report for chromosome Contig468 (stored 663 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1136 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 976 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 917 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 869 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1220 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1103 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1509 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 878 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 866 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 897 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1509 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1228 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1118 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 1814 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1291 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1093 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1178 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1242 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 862 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1061 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 858 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 316 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_17_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_17_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_18_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1944 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1784 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1388 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1837 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1763 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1631 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1148 different covered positions) Writing cytosine report for chromosome Contig84 (stored 800 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1160 different covered positions) Writing cytosine report for chromosome Contig468 (stored 926 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1289 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1084 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1070 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 1148 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1594 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1246 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1717 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1169 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1053 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 1043 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1681 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1496 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1242 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 2192 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1457 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1253 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1396 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1510 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 1085 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1364 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 962 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 399 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_18_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_18_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_1_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1944 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1914 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1370 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1856 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1797 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1668 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1182 different covered positions) Writing cytosine report for chromosome Contig84 (stored 877 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1147 different covered positions) Writing cytosine report for chromosome Contig468 (stored 886 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1296 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1155 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1120 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 962 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1457 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1294 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1747 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1125 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1097 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 995 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1728 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1480 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1226 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 1897 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1532 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1348 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1445 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1539 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 972 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1361 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 1030 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 363 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_1_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_1_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_2_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1972 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1791 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1424 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1815 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1774 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1590 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1169 different covered positions) Writing cytosine report for chromosome Contig84 (stored 848 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1142 different covered positions) Writing cytosine report for chromosome Contig468 (stored 929 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1256 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1048 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1150 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 1180 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1649 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1237 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1818 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1224 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1076 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 1042 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1664 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1461 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1195 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 2067 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1442 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1269 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1450 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1403 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 1073 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1319 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 959 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 398 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_2_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_2_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_3_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1938 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1823 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1340 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1852 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1787 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1620 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1172 different covered positions) Writing cytosine report for chromosome Contig84 (stored 812 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1149 different covered positions) Writing cytosine report for chromosome Contig468 (stored 849 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1274 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1084 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1060 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 908 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1429 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1274 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1841 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1112 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1057 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 1050 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1652 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1514 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1282 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 1909 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1507 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1318 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1444 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1462 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 970 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1312 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 1049 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 363 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_3_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_3_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_4_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1854 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1685 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1283 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1707 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1710 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1591 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1072 different covered positions) Writing cytosine report for chromosome Contig84 (stored 765 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1077 different covered positions) Writing cytosine report for chromosome Contig468 (stored 861 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1230 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 997 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1078 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 1131 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1474 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1125 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1692 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1103 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 880 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 962 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1633 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1379 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1189 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 1762 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1396 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1161 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1346 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1360 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 976 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1253 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 1253 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 355 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_4_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_4_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_5_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 2044 different covered positions) Writing cytosine report for chromosome Contig2 (stored 2014 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1513 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1963 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1852 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1765 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1266 different covered positions) Writing cytosine report for chromosome Contig84 (stored 990 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1260 different covered positions) Writing cytosine report for chromosome Contig468 (stored 1013 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1307 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1206 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1219 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 1135 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1710 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1437 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1869 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1246 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1332 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 1118 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1779 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1579 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1316 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 2597 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1586 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1461 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1540 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1564 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 1087 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1393 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 1105 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 432 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_5_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_5_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_6_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 2038 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1719 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1389 different covered positions) Writing cytosine report for chromosome Contig5 (stored 2011 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1811 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1643 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1291 different covered positions) Writing cytosine report for chromosome Contig84 (stored 922 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1214 different covered positions) Writing cytosine report for chromosome Contig468 (stored 1049 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1410 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1056 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1158 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 1408 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1811 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1227 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1776 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1343 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1016 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 1059 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1674 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1537 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1237 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 2095 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1489 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1259 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1536 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1509 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 1148 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1383 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 974 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 454 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_6_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_6_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_7_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1944 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1873 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1376 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1851 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1819 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1632 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1070 different covered positions) Writing cytosine report for chromosome Contig84 (stored 811 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1154 different covered positions) Writing cytosine report for chromosome Contig468 (stored 868 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1277 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1141 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1100 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 891 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1416 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1196 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1821 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1062 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1024 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 1036 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1725 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1496 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1249 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 1846 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1498 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1306 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1431 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1462 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 1008 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1315 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 1008 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 385 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_7_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_7_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_8_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 1777 different covered positions) Writing cytosine report for chromosome Contig2 (stored 1577 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1227 different covered positions) Writing cytosine report for chromosome Contig5 (stored 1687 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1660 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1460 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1075 different covered positions) Writing cytosine report for chromosome Contig84 (stored 729 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1019 different covered positions) Writing cytosine report for chromosome Contig468 (stored 797 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1220 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 994 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1028 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 1072 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1469 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1070 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1610 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1086 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 827 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 916 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1536 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1338 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1144 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 1633 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1370 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1052 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1307 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1345 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 1011 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1111 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 911 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 346 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_8_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_8_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_9_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 2106 different covered positions) Writing cytosine report for chromosome Contig2 (stored 2067 different covered positions) Writing cytosine report for chromosome Contig3 (stored 1553 different covered positions) Writing cytosine report for chromosome Contig5 (stored 2098 different covered positions) Writing cytosine report for chromosome Contig7 (stored 1942 different covered positions) Writing cytosine report for chromosome Contig9 (stored 1845 different covered positions) Writing cytosine report for chromosome Contig65 (stored 1306 different covered positions) Writing cytosine report for chromosome Contig84 (stored 910 different covered positions) Writing cytosine report for chromosome Contig89 (stored 1295 different covered positions) Writing cytosine report for chromosome Contig468 (stored 953 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 1393 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 1212 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 1243 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 1287 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 1754 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 1447 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 1951 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1227 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 1263 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 1193 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 1874 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 1648 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 1412 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 2276 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 1628 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 1533 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 1584 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 1683 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 1119 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 1533 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 1136 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 472 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_9_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_9_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/061722-v082/< Genome directory: >/gscratch/srlab/sr320/data/olurida-bs/v082/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/olurida-bs/v082/ chr Contig0 (116746 bp) chr Contig2 (139250 bp) chr Contig3 (141657 bp) chr Contig5 (130522 bp) chr Contig7 (109667 bp) chr Contig9 (112192 bp) chr Contig65 (107659 bp) chr Contig84 (102803 bp) chr Contig89 (100284 bp) chr Contig468 (111883 bp) chr Contig15326 (102312 bp) chr Contig16524 (122429 bp) chr Contig16668 (101442 bp) chr Contig16915 (114892 bp) chr Contig17050 (125421 bp) chr Contig17624 (122541 bp) chr Contig17876 (129629 bp) chr Contig18024 (109300 bp) chr Contig18052 (116661 bp) chr Contig18174 (105922 bp) chr Contig18571 (110864 bp) chr Contig19267 (115756 bp) chr Contig19330 (108204 bp) chr Contig19646 (194507 bp) chr Contig19826 (107763 bp) chr Contig20140 (129054 bp) chr Contig20625 (111140 bp) chr Contig22814 (138260 bp) chr Contig23978 (107801 bp) chr Contig23979 (128837 bp) chr Contig26138 (101662 bp) chr Contig34578 (138978 bp) Stored sequence information of 32 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr1394_all_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Contig0 Writing cytosine report for chromosome Contig0 (stored 2744 different covered positions) Writing cytosine report for chromosome Contig2 (stored 3625 different covered positions) Writing cytosine report for chromosome Contig3 (stored 2782 different covered positions) Writing cytosine report for chromosome Contig5 (stored 3062 different covered positions) Writing cytosine report for chromosome Contig7 (stored 2675 different covered positions) Writing cytosine report for chromosome Contig9 (stored 2927 different covered positions) Writing cytosine report for chromosome Contig65 (stored 2336 different covered positions) Writing cytosine report for chromosome Contig84 (stored 2132 different covered positions) Writing cytosine report for chromosome Contig89 (stored 2301 different covered positions) Writing cytosine report for chromosome Contig468 (stored 1515 different covered positions) Writing cytosine report for chromosome Contig15326 (stored 2085 different covered positions) Writing cytosine report for chromosome Contig16524 (stored 2374 different covered positions) Writing cytosine report for chromosome Contig16668 (stored 2082 different covered positions) Writing cytosine report for chromosome Contig16915 (stored 2231 different covered positions) Writing cytosine report for chromosome Contig17050 (stored 2591 different covered positions) Writing cytosine report for chromosome Contig17624 (stored 2810 different covered positions) Writing cytosine report for chromosome Contig17876 (stored 3086 different covered positions) Writing cytosine report for chromosome Contig18024 (stored 1872 different covered positions) Writing cytosine report for chromosome Contig18052 (stored 3039 different covered positions) Writing cytosine report for chromosome Contig18174 (stored 1757 different covered positions) Writing cytosine report for chromosome Contig18571 (stored 2869 different covered positions) Writing cytosine report for chromosome Contig19267 (stored 2815 different covered positions) Writing cytosine report for chromosome Contig19330 (stored 2343 different covered positions) Writing cytosine report for chromosome Contig19646 (stored 5041 different covered positions) Writing cytosine report for chromosome Contig19826 (stored 2703 different covered positions) Writing cytosine report for chromosome Contig20140 (stored 3333 different covered positions) Writing cytosine report for chromosome Contig20625 (stored 2147 different covered positions) Writing cytosine report for chromosome Contig22814 (stored 2779 different covered positions) Writing cytosine report for chromosome Contig23978 (stored 1965 different covered positions) Writing cytosine report for chromosome Contig23979 (stored 2591 different covered positions) Writing cytosine report for chromosome Contig26138 (stored 2086 different covered positions) Writing cytosine report for last chromosome Contig34578 (stored 883 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 32 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr1394_all_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_all_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq!