Path to genome folder specified as: /gscratch/srlab/sr320/data/ecoli-MG1655/ Using 28 threads for the top and bottom strand indexing processes each, so using 56 cores in total Aligner to be used: >> Bowtie 2 << (default) Writing bisulfite genomes out into a single MFA (multi FastA) file Bismark Genome Preparation - Step I: Preparing folders Path to Bowtie 2 specified as: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ Bisulfite Genome Indexer version v0.21.0 (last modified: 05 Feb 2019) Created Bisulfite Genome folder /gscratch/srlab/sr320/data/ecoli-MG1655/Bisulfite_Genome/ Created Bisulfite Genome folder /gscratch/srlab/sr320/data/ecoli-MG1655/Bisulfite_Genome/CT_conversion/ Created Bisulfite Genome folder /gscratch/srlab/sr320/data/ecoli-MG1655/Bisulfite_Genome/GA_conversion/ Step I - Prepare genome folders - completed Bismark Genome Preparation - Step II: Bisulfite converting reference genome conversions performed: chromosome C->T G->A NC_000913.3 1180091 1177437 Total number of conversions performed: C->T: 1180091 G->A: 1177437 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/ecoli-MG1655/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: 41443 Using parameters --bmax 31083 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 31083 --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 42, merged 129; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 24, merged 27; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 10, merged 14; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 2; iterating... Avg bucket size: 22864.3 (target: 31082) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 2 of 203 Getting block 4 of 203 Getting block 5 of 203 Getting block 6 of 203 Getting block 8 of 203 Getting block 7 of 203 Getting block 10 of 203 Getting block 1 of 203 Getting block 9 of 203 Getting block 3 of 203 Reserving size (31083) for bucket 2 Getting block 11 of 203 Getting block 12 of 203 Reserving size (31083) for bucket 4 Reserving size (31083) for bucket 5 Getting block 13 of 203 Reserving size (31083) for bucket 6 Reserving size (31083) for bucket 8 Reserving size (31083) for bucket 7 Getting block 14 of 203 Getting block 15 of 203 Getting block 16 of 203 Getting block 17 of 203 Reserving size (31083) for bucket 10 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 Getting block 24 of 203 Reserving size (31083) for bucket 1 Reserving size (31083) for bucket 9 Getting block 25 of 203 Getting block 26 of 203 Getting block 27 of 203 Reserving size (31083) for bucket 3 Calculating Z arrays for bucket 2 Reserving size (31083) for bucket 11 Reserving size (31083) for bucket 12 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Reserving size (31083) for bucket 13 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 7 Reserving size (31083) for bucket 14 Reserving size (31083) for bucket 15 Reserving size (31083) for bucket 16 Reserving size (31083) for bucket 17 Calculating Z arrays for bucket 10 Reserving size (31083) for bucket 18 Reserving size (31083) for bucket 19 Reserving size (31083) for bucket 20 Reserving size (31083) for bucket 21 Reserving size (31083) for bucket 22 Reserving size (31083) for bucket 23 Reserving size (31083) for bucket 24 Calculating Z arrays for bucket 1 Calculating Z arrays for bucket 9 Reserving size (31083) for bucket 25 Reserving size (31083) for bucket 26 Reserving size (31083) for bucket 27 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 11 Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 12 Calculating Z arrays for bucket 13 Entering block accumulator loop for bucket 4: Calculating Z arrays for bucket 15 Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 5: Calculating Z arrays for bucket 14 Entering block accumulator loop for bucket 8: Calculating Z arrays for bucket 17 Entering block accumulator loop for bucket 7: Calculating Z arrays for bucket 16 Calculating Z arrays for bucket 18 Calculating Z arrays for bucket 19 Entering block accumulator loop for bucket 10: Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 23 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 9: Calculating Z arrays for bucket 27 Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 3: 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 15: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 27: Entering block accumulator loop for bucket 26: bucket 1: 10% bucket 4: 10% bucket 8: 10% bucket 3: 10% bucket 6: 10% bucket 10: 10% bucket 9: 10% bucket 11: 10% bucket 2: 10% bucket 13: 10% bucket 7: 10% bucket 5: 10% bucket 14: 10% bucket 12: 10% bucket 15: 10% bucket 17: 10% bucket 18: 10% bucket 20: 10% bucket 19: 10% bucket 22: 10% bucket 27: 10% bucket 25: 10% bucket 21: 10% bucket 23: 10% bucket 26: 10% bucket 16: 10% bucket 24: 10% bucket 1: 20% bucket 4: 20% bucket 8: 20% bucket 3: 20% bucket 2: 20% bucket 5: 20% bucket 6: 20% bucket 11: 20% bucket 9: 20% bucket 10: 20% bucket 13: 20% bucket 14: 20% bucket 7: 20% bucket 12: 20% bucket 15: 20% bucket 17: 20% bucket 18: 20% bucket 20: 20% bucket 19: 20% bucket 22: 20% bucket 27: 20% bucket 25: 20% bucket 21: 20% bucket 23: 20% bucket 26: 20% bucket 16: 20% bucket 1: 30% bucket 24: 20% bucket 4: 30% bucket 2: 30% bucket 3: 30% bucket 8: 30% bucket 5: 30% bucket 6: 30% bucket 11: 30% bucket 9: 30% bucket 10: 30% bucket 13: 30% bucket 14: 30% bucket 7: 30% bucket 12: 30% bucket 15: 30% bucket 17: 30% bucket 18: 30% bucket 20: 30% bucket 19: 30% bucket 22: 30% bucket 27: 30% bucket 25: 30% bucket 1: 40% bucket 21: 30% bucket 23: 30% bucket 16: 30% bucket 26: 30% bucket 2: 40% bucket 4: 40% bucket 24: 30% bucket 3: 40% bucket 8: 40% bucket 5: 40% bucket 6: 40% bucket 11: 40% bucket 9: 40% bucket 10: 40% bucket 13: 40% bucket 14: 40% bucket 7: 40% bucket 12: 40% bucket 15: 40% bucket 17: 40% bucket 1: 50% bucket 18: 40% bucket 20: 40% bucket 19: 40% bucket 22: 40% bucket 2: 50% bucket 27: 40% bucket 25: 40% bucket 16: 40% bucket 4: 50% bucket 21: 40% bucket 23: 40% bucket 26: 40% bucket 3: 50% bucket 8: 50% bucket 5: 50% bucket 24: 40% bucket 6: 50% bucket 11: 50% bucket 9: 50% bucket 10: 50% bucket 13: 50% bucket 14: 50% bucket 7: 50% bucket 12: 50% bucket 1: 60% bucket 15: 50% bucket 17: 50% bucket 2: 60% bucket 18: 50% bucket 20: 50% bucket 19: 50% bucket 4: 60% bucket 22: 50% bucket 3: 60% bucket 8: 60% bucket 27: 50% bucket 25: 50% bucket 5: 60% bucket 16: 50% bucket 23: 50% bucket 21: 50% bucket 26: 50% bucket 6: 60% bucket 11: 60% bucket 9: 60% bucket 1: 70% bucket 24: 50% bucket 10: 60% bucket 13: 60% bucket 14: 60% bucket 7: 60% bucket 12: 60% bucket 2: 70% bucket 15: 60% bucket 17: 60% bucket 4: 70% bucket 18: 60% bucket 20: 60% bucket 3: 70% bucket 19: 60% bucket 8: 70% bucket 5: 70% bucket 22: 60% bucket 27: 60% bucket 16: 60% bucket 25: 60% bucket 1: 80% bucket 6: 70% bucket 23: 60% bucket 21: 60% bucket 11: 70% bucket 26: 60% bucket 9: 70% bucket 2: 80% bucket 10: 70% bucket 13: 70% bucket 14: 70% bucket 24: 60% bucket 7: 70% bucket 12: 70% bucket 15: 70% bucket 4: 80% bucket 17: 70% bucket 3: 80% bucket 5: 80% bucket 8: 80% bucket 18: 70% bucket 20: 70% bucket 19: 70% bucket 1: 90% bucket 22: 70% bucket 6: 80% bucket 11: 80% bucket 16: 70% bucket 27: 70% bucket 25: 70% bucket 2: 90% bucket 9: 80% bucket 23: 70% bucket 21: 70% bucket 10: 80% bucket 13: 80% bucket 14: 80% bucket 26: 70% bucket 7: 80% bucket 12: 80% bucket 4: 90% bucket 24: 70% bucket 3: 90% bucket 15: 80% bucket 17: 80% bucket 5: 90% bucket 8: 90% bucket 1: 100% Sorting block of length 10777 for bucket 1 (Using difference cover) bucket 18: 80% bucket 20: 80% bucket 19: 80% bucket 2: 100% Sorting block of length 29803 for bucket 2 (Using difference cover) bucket 6: 90% bucket 11: 90% bucket 22: 80% bucket 9: 90% bucket 16: 80% Sorting block time: 00:00:00 Returning block of 10778 for bucket 1 bucket 27: 80% bucket 25: 80% bucket 10: 90% bucket 13: 90% bucket 14: 90% bucket 23: 80% bucket 21: 80% bucket 4: 100% Sorting block of length 18523 for bucket 4 (Using difference cover) bucket 12: 90% bucket 7: 90% bucket 3: 100% Sorting block of length 25901 for bucket 3 (Using difference cover) bucket 26: 80% bucket 5: 100% Sorting block of length 16840 for bucket 5 (Using difference cover) bucket 15: 90% bucket 8: 100% Sorting block of length 7375 for bucket 8 (Using difference cover) bucket 24: 80% bucket 17: 90% Getting block 28 of 203 Reserving size (31083) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 18: 90% bucket 20: 90% bucket 19: 90% bucket 6: 100% Sorting block of length 29710 for bucket 6 (Using difference cover) bucket 11: 100% Sorting block of length 14795 for bucket 11 (Using difference cover) Sorting block time: 00:00:00 Returning block of 7376 for bucket 8 bucket 9: 100% Sorting block of length 24461 for bucket 9 (Using difference cover) bucket 22: 90% bucket 16: 90% bucket 10: 100% bucket 13: 100% Sorting block of length 30665 for bucket 10 (Using difference cover) Sorting block of length 17382 for bucket 13 bucket 14: 100% Sorting block of length 17396 for bucket 14 (Using difference cover) (Using difference cover) bucket 27: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 16841 for bucket 5 Sorting block time: 00:00:00 Returning block of 29804 for bucket 2 Returning block of 18524 for bucket 4 bucket 25: 90% bucket 12: 100% Sorting block of length 27202 for bucket 12 (Using difference cover) bucket 7: 100% Sorting block of length 29537 for bucket 7 (Using difference cover) bucket 23: 90% Sorting block time: 00:00:00 Returning block of 25902 for bucket 3 Getting block 29 of 203 Reserving size (31083) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 21: 90% bucket 15: 100% Sorting block of length 27052 for bucket 15 (Using difference cover) bucket 17: 100% Sorting block of length 26585 for bucket 17 (Using difference cover) bucket 26: 90% Getting block 30 of 203 bucket 24: 90% Reserving size (31083) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 28: 10% Getting block 31 of 203 Reserving size (31083) for bucket 31 Getting block 32 of 203 Calculating Z arrays for bucket 31 Reserving size (31083) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 31: Entering block accumulator loop for bucket 32: bucket 20: 100% Sorting block of length 13131 for bucket 20 (Using difference cover) bucket 18: 100% Sorting block of length 26043 for bucket 18 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14796 for bucket 11 bucket 19: 100% Sorting block of length 29838 for bucket 19 (Using difference cover) Getting block 33 of 203 Reserving size (31083) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: bucket 22: 100% Sorting block of length 19372 for bucket 22 (Using difference cover) bucket 16: 100% Sorting block of length 20981 for bucket 16 (Using difference cover) bucket 27: 100% Sorting block of length 17045 for bucket 27 (Using difference cover) Sorting block time: 00:00:00 Returning block of 17397 for bucket 14 Getting block 34 of 203 Reserving size (31083) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: bucket 23: 100% Sorting block of length 22006 for bucket 23 (Using difference cover) bucket 29: 10% bucket 25: 100% Sorting block of length 22355 for bucket 25 (Using difference cover) Sorting block time: 00:00:00 Returning block of 29711 for bucket 6 bucket 21: 100% Sorting block of length 27771 for bucket 21 (Using difference cover) Sorting block time: 00:00:00 Returning block of 17383 for bucket 13 Getting block 35 of 203 Reserving size (31083) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: Sorting block time: 00:00:00 Returning block of 27203 for bucket 12 bucket 24: 100% Sorting block of length 25290 for bucket 24 (Using difference cover) bucket 28: 20% bucket 30: 10% bucket 26: 100% Sorting block of length 22952 for bucket 26 (Using difference cover) Sorting block time: 00:00:00 Returning block of 13132 for bucket 20 Sorting block time: 00:00:00 Returning block of 24462 for bucket 9 Sorting block time: 00:00:00 Returning block of 27053 for bucket 15 bucket 32: 10% bucket 31: 10% Sorting block time: 00:00:00 Returning block of 26586 for bucket 17 Sorting block time: 00:00:00 Returning block of 30666 for bucket 10 Getting block 36 of 203 Reserving size (31083) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: bucket 33: 10% Sorting block time: 00:00:00 Returning block of 26044 for bucket 18 Sorting block time: 00:00:00 Returning block of 17046 for bucket 27 Sorting block time: 00:00:00 Returning block of 19373 for bucket 22 Getting block 37 of 203 Reserving size (31083) for bucket 37 Getting block 38 of 203 Calculating Z arrays for bucket 37 Reserving size (31083) 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 20982 for bucket 16 Getting block 39 of 203 Reserving size (31083) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Getting block 40 of 203 Reserving size (31083) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: bucket 34: 10% bucket 29: 20% Sorting block time: 00:00:00 Returning block of 22007 for bucket 23 Getting block 41 of 203 Reserving size (31083) for bucket 41 Calculating Z arrays for bucket 41 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 22356 for bucket 25 Returning block of 29538 for bucket 7 Entering block accumulator loop for bucket 41: Getting block 42 of 203 Sorting block time: 00:00:00 Reserving size (31083) for bucket 42 Returning block of 29839 for bucket 19 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: Sorting block time: 00:00:00 Returning block of 27772 for bucket 21 bucket 30: 20% Getting block 43 of 203 Reserving size (31083) for bucket 43 Getting block 44 of 203 Sorting block time: 00:00:00 bucket 28: 30% Calculating Z arrays for bucket 43 Reserving size (31083) for bucket 44 Returning block of 22953 for bucket 26 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 43: Entering block accumulator loop for bucket 44: bucket 35: 10% Sorting block time: 00:00:00 Getting block 45 of 203 Returning block of 25291 for bucket 24 Reserving size (31083) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Getting block 46 of 203 Reserving size (31083) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: Getting block 47 of 203 Reserving size (31083) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 31: 20% bucket 32: 20% Getting block 48 of 203 Reserving size (31083) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Getting block 49 of 203 Reserving size (31083) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: Getting block 50 of 203 Reserving size (31083) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 33: 20% bucket 36: 10% Getting block 51 of 203 Reserving size (31083) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 38: 10% bucket 39: 10% bucket 37: 10% bucket 29: 30% bucket 40: 10% bucket 34: 20% bucket 41: 10% bucket 28: 40% bucket 30: 30% bucket 42: 10% bucket 35: 20% bucket 43: 10% bucket 44: 10% bucket 45: 10% bucket 31: 30% bucket 46: 10% bucket 32: 30% bucket 47: 10% bucket 48: 10% bucket 33: 30% bucket 50: 10% bucket 36: 20% bucket 49: 10% bucket 29: 40% bucket 39: 20% bucket 38: 20% bucket 37: 20% bucket 40: 20% bucket 28: 50% bucket 34: 30% bucket 30: 40% Getting block 52 of 203 Reserving size (31083) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: Getting block 53 of 203 Reserving size (31083) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 41: 20% Getting block 54 of 203 Reserving size (31083) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 42: 20% bucket 35: 30% bucket 31: 40% bucket 44: 20% bucket 43: 20% bucket 32: 40% bucket 45: 20% bucket 46: 20% bucket 47: 20% bucket 33: 40% bucket 29: 50% bucket 50: 20% bucket 51: 10% bucket 36: 30% bucket 39: 30% bucket 48: 20% bucket 38: 30% bucket 37: 30% bucket 49: 20% bucket 28: 60% bucket 40: 30% bucket 30: 50% bucket 34: 40% bucket 52: 10% bucket 41: 30% bucket 53: 10% bucket 31: 50% bucket 35: 40% bucket 54: 10% bucket 42: 30% bucket 32: 50% bucket 44: 30% bucket 43: 30% bucket 45: 30% bucket 29: 60% bucket 46: 30% bucket 33: 50% bucket 47: 30% bucket 50: 30% bucket 39: 40% bucket 36: 40% bucket 28: 70% bucket 38: 40% bucket 37: 40% bucket 30: 60% bucket 48: 30% bucket 40: 40% bucket 49: 30% bucket 34: 50% bucket 31: 60% bucket 41: 40% bucket 52: 20% bucket 53: 20% bucket 35: 50% bucket 32: 60% bucket 42: 40% bucket 54: 20% bucket 29: 70% bucket 44: 40% bucket 43: 40% bucket 51: 20% bucket 33: 60% bucket 45: 40% bucket 46: 40% bucket 28: 80% bucket 39: 50% bucket 50: 40% bucket 47: 40% bucket 36: 50% bucket 30: 70% bucket 38: 50% bucket 37: 50% bucket 40: 50% bucket 48: 40% bucket 31: 70% bucket 34: 60% bucket 32: 70% bucket 49: 40% bucket 29: 80% bucket 41: 50% bucket 35: 60% bucket 53: 30% bucket 42: 50% bucket 54: 30% bucket 33: 70% bucket 44: 50% bucket 28: 90% bucket 43: 50% bucket 45: 50% bucket 46: 50% bucket 39: 60% bucket 30: 80% bucket 50: 50% bucket 36: 60% bucket 47: 50% bucket 38: 60% bucket 37: 60% bucket 40: 60% bucket 31: 80% bucket 29: 90% bucket 34: 70% bucket 32: 80% bucket 48: 50% bucket 35: 70% bucket 51: 30% bucket 41: 60% bucket 53: 40% bucket 49: 50% bucket 28: 100% Sorting block of length 21336 for bucket 28 (Using difference cover) bucket 42: 60% bucket 33: 80% bucket 54: 40% bucket 44: 60% bucket 30: 90% bucket 39: 70% bucket 45: 60% bucket 46: 60% bucket 43: 60% bucket 50: 60% bucket 36: 70% bucket 38: 70% bucket 37: 70% bucket 31: 90% bucket 47: 60% bucket 29: 100% Sorting block of length 29512 for bucket 29 (Using difference cover) bucket 40: 70% Sorting block time: 00:00:00 Returning block of 21337 for bucket 28 bucket 32: 90% bucket 34: 80% Getting block 55 of 203 Reserving size (31083) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 35: 80% bucket 41: 70% bucket 52: 30% bucket 48: 60% bucket 33: 90% bucket 53: 50% bucket 42: 70% bucket 30: 100% Sorting block of length 27728 for bucket 30 (Using difference cover) bucket 54: 50% bucket 49: 60% bucket 39: 80% bucket 44: 70% bucket 50: 70% bucket 45: 70% bucket 36: 80% bucket 46: 70% Sorting block time: 00:00:00 Returning block of 29513 for bucket 29 bucket 31: 100% Sorting block of length 26300 for bucket 31 (Using difference cover) bucket 51: 40% bucket 43: 70% bucket 38: 80% bucket 37: 80% bucket 40: 80% bucket 47: 70% bucket 32: 100% Sorting block of length 18336 for bucket 32 (Using difference cover) bucket 34: 90% bucket 35: 90% Sorting block time: 00:00:00 Returning block of 27729 for bucket 30 bucket 33: 100% bucket 55: 10% Sorting block of length 26103 for bucket 33 (Using difference cover) bucket 41: 80% bucket 52: 40% bucket 53: 60% bucket 48: 70% bucket 42: 80% bucket 39: 90% bucket 54: 60% Sorting block time: 00:00:00 Returning block of 18337 for bucket 32 Sorting block time: 00:00:00 Returning block of 26301 for bucket 31 bucket 49: 70% bucket 44: 80% bucket 50: 80% bucket 36: 90% Getting block 56 of 203 Reserving size (31083) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 46: 80% bucket 45: 80% Getting block 57 of 203 Reserving size (31083) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 38: 90% bucket 37: 90% bucket 40: 90% bucket 43: 80% bucket 47: 80% Sorting block time: 00:00:00 Returning block of 26104 for bucket 33 bucket 34: 100% Sorting block of length 10458 for bucket 34 (Using difference cover) bucket 35: 100% Sorting block of length 29645 for bucket 35 (Using difference cover) Getting block 58 of 203 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (31083) for bucket 58 bucket 41: 90% bucket 52: 50% bucket 55: 20% bucket 51: 50% bucket 53: 70% bucket 39: 100% Returning block of 10459 for bucket 34 bucket 42: 90% bucket 48: 80% bucket 54: 70% bucket 44: 90% bucket 36: 100% bucket 50: 90% bucket 49: 80% bucket 38: 100% bucket 46: 90% bucket 56: 10% bucket 37: 100% bucket 40: 100% bucket 45: 90% bucket 57: 10% Returning block of 29646 for bucket 35 Getting block 59 of 203 Calculating Z arrays for bucket 58 Sorting block of length 22895 for bucket 39 (Using difference cover) bucket 47: 90% bucket 43: 90% Sorting block of length 27647 for bucket 36 (Using difference cover) Sorting block of length 30075 for bucket 38 (Using difference cover) Sorting block of length 28833 for bucket 37 (Using difference cover) Sorting block of length 28037 for bucket 40 (Using difference cover) Getting block 60 of 203 Reserving size (31083) for bucket 59 Entering block accumulator loop for bucket 58: Getting block 61 of 203 Reserving size (31083) for bucket 60 Calculating Z arrays for bucket 59 Reserving size (31083) for bucket 61 Calculating Z arrays for bucket 60 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 59: Entering block accumulator loop for bucket 60: Entering block accumulator loop for bucket 61: Getting block 62 of 203 Reserving size (31083) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 41: 100% Sorting block of length 21295 for bucket 41 (Using difference cover) bucket 53: 80% bucket 42: 100% Sorting block of length 24421 for bucket 42 (Using difference cover) bucket 52: 60% bucket 50: 100% Sorting block of length 29059 for bucket 50 (Using difference cover) bucket 44: 100% Sorting block of length 28518 for bucket 44 (Using difference cover) bucket 46: 100% Sorting block of length 24346 for bucket 46 (Using difference cover) bucket 54: 80% bucket 56: 20% bucket 55: 30% bucket 45: 100% Sorting block of length 28164 for bucket 45 (Using difference cover) bucket 48: 90% bucket 57: 20% bucket 49: 90% bucket 51: 60% Sorting block time: 00:00:00 Returning block of 22896 for bucket 39 Sorting block time: 00:00:00 Returning block of 27648 for bucket 36 Sorting block time: 00:00:00 Returning block of 30076 for bucket 38 Sorting block time: 00:00:00 Returning block of 28834 for bucket 37 Getting block 63 of 203 Reserving size (31083) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 47: 100% Sorting block of length 20442 for bucket 47 (Using difference cover) Sorting block time: 00:00:00 Returning block of 28038 for bucket 40 Getting block 64 of 203 Reserving size (31083) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 61: 10% Getting block 65 of 203 Reserving size (31083) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: bucket 59: 10% bucket 43: 100% Sorting block of length 23181 for bucket 43 (Using difference cover) bucket 58: 10% bucket 60: 10% bucket 62: 10% Getting block 66 of 203 Reserving size (31083) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: Sorting block time: 00:00:00 Returning block of 21296 for bucket 41 Sorting block time: 00:00:00 Returning block of 24422 for bucket 42 bucket 53: 90% Getting block 67 of 203 Reserving size (31083) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: Sorting block time: 00:00:00 Returning block of 24347 for bucket 46 bucket 52: 70% Getting block 68 of 203 Reserving size (31083) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: Getting block 69 of 203 Reserving size (31083) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: bucket 54: 90% Sorting block time: 00:00:00 Returning block of 29060 for bucket 50 Sorting block time: 00:00:00 bucket 56: 30% Returning block of 28165 for bucket 45 bucket 55: 40% bucket 48: 100% Sorting block of length 30729 for bucket 48 (Using difference cover) bucket 57: 30% Sorting block time: 00:00:00 Returning block of 20443 for bucket 47 bucket 49: 100% Sorting block of length 17891 for bucket 49 (Using difference cover) Getting block 70 of 203 Reserving size (31083) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: Getting block 71 of 203 Reserving size (31083) for bucket 71 Calculating Z arrays for bucket 71 Sorting block time: 00:00:00 Returning block of 23182 for bucket 43 Entering block accumulator loop for bucket 71: Getting block 72 of 203 Reserving size (31083) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: Sorting block time: 00:00:00 Returning block of 28519 for bucket 44 bucket 64: 10% bucket 63: 10% bucket 65: 10% bucket 61: 20% bucket 59: 20% bucket 51: 70% bucket 58: 20% bucket 62: 20% bucket 60: 20% bucket 66: 10% Sorting block time: 00:00:00 Returning block of 17892 for bucket 49 bucket 53: 100% Sorting block of length 14548 for bucket 53 (Using difference cover) bucket 67: 10% bucket 52: 80% Sorting block time: 00:00:00 Returning block of 30730 for bucket 48 bucket 68: 10% bucket 56: 40% bucket 54: 100% bucket 69: 10% Sorting block of length 26888 for bucket 54 (Using difference cover) bucket 55: 50% bucket 57: 40% bucket 70: 10% bucket 71: 10% Sorting block time: 00:00:00 Returning block of 14549 for bucket 53 bucket 72: 10% Getting block 73 of 203 Reserving size (31083) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: Getting block 74 of 203 Reserving size (31083) for bucket 74 bucket 64: 20% Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: Getting block 75 of 203 Reserving size (31083) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 63: 20% Getting block 76 of 203 Reserving size (31083) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 65: 20% Getting block 77 of 203 Reserving size (31083) for bucket 77 bucket 61: 30% Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 59: 30% bucket 62: 30% bucket 58: 30% bucket 66: 20% Sorting block time: 00:00:00 Returning block of 26889 for bucket 54 bucket 60: 30% Getting block 78 of 203 Reserving size (31083) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 67: 20% bucket 51: 80% bucket 56: 50% bucket 68: 20% bucket 69: 20% bucket 52: 90% bucket 55: 60% bucket 57: 50% bucket 70: 20% bucket 71: 20% bucket 72: 20% bucket 64: 30% bucket 63: 30% bucket 65: 30% bucket 73: 10% bucket 61: 40% bucket 74: 10% bucket 62: 40% bucket 75: 10% bucket 59: 40% bucket 76: 10% bucket 66: 30% bucket 77: 10% bucket 58: 40% bucket 60: 40% bucket 67: 30% bucket 56: 60% bucket 78: 10% bucket 52: 100% bucket 55: 70% Sorting block of length 28030 for bucket 52 (Using difference cover) bucket 68: 30% bucket 69: 30% bucket 57: 60% Getting block 79 of 203 Reserving size (31083) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 51: 90% bucket 70: 30% bucket 71: 30% bucket 64: 40% bucket 63: 40% bucket 72: 30% bucket 65: 40% bucket 61: 50% bucket 62: 50% bucket 59: 50% bucket 74: 20% bucket 66: 40% bucket 73: 20% bucket 58: 50% Sorting block time: 00:00:00 Returning block of 28031 for bucket 52 bucket 76: 20% bucket 67: 40% bucket 60: 50% bucket 75: 20% bucket 77: 20% bucket 56: 70% bucket 69: 40% bucket 55: 80% Getting block 80 of 203 Reserving size (31083) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 68: 40% bucket 78: 20% bucket 57: 70% bucket 64: 50% bucket 70: 40% bucket 71: 40% bucket 63: 50% bucket 79: 10% bucket 65: 50% bucket 51: 100% Sorting block of length 27336 for bucket 51 (Using difference cover) bucket 72: 40% bucket 61: 60% bucket 62: 60% bucket 59: 60% bucket 66: 50% bucket 58: 60% bucket 74: 30% bucket 67: 50% bucket 56: 80% bucket 60: 60% bucket 73: 30% bucket 76: 30% bucket 69: 50% bucket 55: 90% bucket 68: 50% bucket 77: 30% bucket 75: 30% bucket 80: 10% bucket 57: 80% bucket 64: 60% bucket 78: 30% bucket 70: 50% bucket 63: 60% bucket 71: 50% bucket 65: 60% Sorting block time: 00:00:00 Returning block of 27337 for bucket 51 bucket 72: 50% bucket 62: 70% bucket 61: 70% bucket 79: 20% bucket 59: 70% bucket 66: 60% bucket 67: 60% bucket 58: 70% bucket 56: 90% bucket 74: 40% bucket 69: 60% bucket 60: 70% bucket 68: 60% bucket 55: 100% Sorting block of length 28855 for bucket 55 (Using difference cover) bucket 76: 40% bucket 73: 40% bucket 64: 70% bucket 77: 40% bucket 57: 90% bucket 75: 40% bucket 80: 20% bucket 63: 70% bucket 70: 60% bucket 71: 60% bucket 65: 70% bucket 78: 40% bucket 62: 80% bucket 72: 60% bucket 61: 80% bucket 66: 70% bucket 59: 80% bucket 79: 30% bucket 67: 70% Sorting block time: 00:00:00 Returning block of 28856 for bucket 55 bucket 56: 100% Sorting block of length 4119 for bucket 56 (Using difference cover) bucket 58: 80% bucket 69: 70% Getting block 81 of 203 Reserving size (31083) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: Getting block 82 of 203 Reserving size (31083) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 74: 50% bucket 60: 80% Sorting block time: 00:00:00 Returning block of 4120 for bucket 56 bucket 68: 70% bucket 64: 80% Getting block 83 of 203 Reserving size (31083) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 76: 50% bucket 57: 100% Sorting block of length 28561 for bucket 57 (Using difference cover) bucket 63: 80% bucket 77: 50% bucket 73: 50% bucket 65: 80% bucket 75: 50% bucket 70: 70% bucket 71: 70% bucket 80: 30% bucket 62: 90% bucket 78: 50% bucket 61: 90% bucket 72: 70% bucket 66: 80% bucket 59: 90% bucket 67: 80% bucket 79: 40% bucket 69: 80% bucket 58: 90% bucket 64: 90% bucket 68: 80% Sorting block time: 00:00:00 Returning block of 28562 for bucket 57 bucket 60: 90% bucket 74: 60% bucket 82: 10% bucket 63: 90% bucket 83: 10% bucket 81: 10% Getting block 84 of 203 Reserving size (31083) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 65: 90% bucket 71: 80% bucket 70: 80% bucket 76: 60% bucket 77: 60% bucket 73: 60% bucket 75: 60% bucket 80: 40% bucket 62: 100% Sorting block of length 25053 for bucket 62 (Using difference cover) bucket 61: 100% Sorting block of length 29719 for bucket 61 (Using difference cover) bucket 72: 80% bucket 66: 90% bucket 78: 60% bucket 59: 100% Sorting block of length 14535 for bucket 59 (Using difference cover) bucket 67: 90% bucket 69: 90% bucket 64: 100% Sorting block of length 10521 for bucket 64 (Using difference cover) bucket 79: 50% bucket 58: 100% Sorting block of length 23510 for bucket 58 (Using difference cover) bucket 68: 90% bucket 60: 100% Sorting block of length 23224 for bucket 60 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14536 for bucket 59 bucket 63: 100% Sorting block of length 21728 for bucket 63 (Using difference cover) bucket 74: 70% bucket 65: 100% Sorting block of length 24549 for bucket 65 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25054 for bucket 62 bucket 82: 20% bucket 71: 90% bucket 83: 20% bucket 70: 90% Getting block 85 of 203 Reserving size (31083) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 81: 20% bucket 84: 10% Sorting block time: 00:00:00 Returning block of 10522 for bucket 64 Getting block 86 of 203 Reserving size (31083) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 76: 70% Sorting block time: 00:00:00 Returning block of 29720 for bucket 61 bucket 77: 70% bucket 80: 50% Getting block 87 of 203 Reserving size (31083) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 75: 70% bucket 73: 70% bucket 66: 100% Sorting block of length 18880 for bucket 66 (Using difference cover) bucket 72: 90% Getting block 88 of 203 Reserving size (31083) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: Sorting block time: 00:00:00 Returning block of 23511 for bucket 58 bucket 67: 100% Sorting block of length 26227 for bucket 67 (Using difference cover) bucket 78: 70% Sorting block time: 00:00:00 Returning block of 23225 for bucket 60 Getting block 89 of 203 Reserving size (31083) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: Sorting block time: 00:00:00 Returning block of 21729 for bucket 63 bucket 69: 100% Sorting block of length 15232 for bucket 69 (Using difference cover) Sorting block time: 00:00:00 Returning block of 24550 for bucket 65 Getting block 90 of 203 Reserving size (31083) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 79: 60% bucket 68: 100% Sorting block of length 29659 for bucket 68 (Using difference cover) Sorting block time: 00:00:00 Returning block of 18881 for bucket 66 Getting block 91 of 203 Reserving size (31083) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 74: 80% Getting block 92 of 203 Reserving size (31083) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: bucket 71: 100% Sorting block of length 25039 for bucket 71 (Using difference cover) bucket 70: 100% Sorting block of length 26947 for bucket 70 (Using difference cover) bucket 82: 30% bucket 83: 30% Sorting block time: 00:00:00 Returning block of 15233 for bucket 69 bucket 85: 10% bucket 81: 30% bucket 84: 20% bucket 86: 10% Sorting block time: 00:00:00 Returning block of 26228 for bucket 67 bucket 76: 80% Getting block 93 of 203 Reserving size (31083) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 80: 60% Getting block 94 of 203 Reserving size (31083) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: bucket 77: 80% bucket 72: 100% Sorting block of length 24886 for bucket 72 (Using difference cover) bucket 75: 80% Getting block 95 of 203 Reserving size (31083) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 87: 10% bucket 73: 80% bucket 88: 10% bucket 78: 80% Sorting block time: 00:00:00 Returning block of 29660 for bucket 68 bucket 89: 10% Getting block 96 of 203 Reserving size (31083) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: Sorting block time: 00:00:00 Returning block of 25040 for bucket 71 Sorting block time: 00:00:00 Returning block of 26948 for bucket 70 bucket 79: 70% bucket 90: 10% Getting block 97 of 203 Reserving size (31083) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: Getting block 98 of 203 Reserving size (31083) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 74: 90% Sorting block time: 00:00:00 Returning block of 24887 for bucket 72 bucket 82: 40% bucket 83: 40% bucket 92: 10% Getting block 99 of 203 bucket 81: 40% Reserving size (31083) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: bucket 85: 20% bucket 84: 30% bucket 76: 90% bucket 80: 70% bucket 86: 20% bucket 93: 10% bucket 77: 90% bucket 94: 10% bucket 87: 20% bucket 73: 90% bucket 95: 10% bucket 75: 90% bucket 88: 20% bucket 78: 90% bucket 89: 20% bucket 79: 80% bucket 96: 10% bucket 74: 100% Sorting block of length 25491 for bucket 74 (Using difference cover) bucket 82: 50% bucket 90: 20% bucket 83: 50% bucket 97: 10% bucket 98: 10% bucket 81: 50% bucket 92: 20% bucket 84: 40% bucket 85: 30% bucket 80: 80% bucket 76: 100% bucket 99: 10% Sorting block of length 28232 for bucket 76 (Using difference cover) bucket 86: 30% bucket 77: 100% Sorting block of length 13680 for bucket 77 (Using difference cover) bucket 93: 20% bucket 87: 30% bucket 73: 100% Sorting block of length 28099 for bucket 73 (Using difference cover) bucket 95: 20% bucket 75: 100% Sorting block of length 5750 for bucket 75 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25492 for bucket 74 bucket 78: 100% Sorting block of length 30513 for bucket 78 (Using difference cover) bucket 88: 30% Sorting block time: 00:00:00 Returning block of 13681 for bucket 77 Sorting block time: 00:00:00 Returning block of 5751 for bucket 75 bucket 79: 90% bucket 89: 30% Getting block 100 of 203 Reserving size (31083) for bucket 100 Calculating Z arrays for bucket 100 Getting block 101 of 203 Reserving size (31083) for bucket 101 Entering block accumulator loop for bucket 100: Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: Getting block 102 of 203 Reserving size (31083) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 96: 20% bucket 82: 60% bucket 83: 60% Sorting block time: 00:00:00 Returning block of 28233 for bucket 76 bucket 81: 60% bucket 90: 30% bucket 97: 20% bucket 84: 50% bucket 98: 20% bucket 85: 40% Getting block 103 of 203 Reserving size (31083) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: bucket 92: 30% bucket 80: 90% bucket 91: 10% Sorting block time: 00:00:00 Returning block of 28100 for bucket 73 bucket 86: 40% bucket 99: 20% Sorting block time: 00:00:00 Returning block of 30514 for bucket 78 Getting block 104 of 203 Reserving size (31083) for bucket 104 Calculating Z arrays for bucket 104 bucket 93: 30% Entering block accumulator loop for bucket 104: bucket 87: 40% Getting block 105 of 203 Reserving size (31083) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 95: 30% bucket 88: 40% bucket 79: 100% Sorting block of length 29952 for bucket 79 (Using difference cover) bucket 89: 40% bucket 83: 70% bucket 82: 70% bucket 101: 10% bucket 100: 10% bucket 81: 70% bucket 96: 30% bucket 84: 60% bucket 85: 50% bucket 90: 40% bucket 103: 10% bucket 97: 30% bucket 80: 100% Sorting block of length 10810 for bucket 80 (Using difference cover) bucket 98: 30% bucket 92: 40% bucket 102: 10% bucket 86: 50% bucket 91: 20% bucket 99: 30% bucket 104: 10% bucket 93: 40% bucket 87: 50% Sorting block time: 00:00:00 Returning block of 10811 for bucket 80 bucket 105: 10% Sorting block time: 00:00:00 Returning block of 29953 for bucket 79 bucket 94: 20% bucket 95: 40% Getting block 106 of 203 Reserving size (31083) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 88: 50% Getting block 107 of 203 Reserving size (31083) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 83: 80% bucket 82: 80% bucket 89: 50% bucket 81: 80% bucket 84: 70% bucket 85: 60% bucket 96: 40% bucket 101: 20% bucket 100: 20% bucket 86: 60% bucket 92: 50% bucket 90: 50% bucket 97: 40% bucket 98: 40% bucket 103: 20% bucket 91: 30% bucket 87: 60% bucket 104: 20% bucket 93: 50% bucket 99: 40% bucket 102: 20% bucket 105: 20% bucket 94: 30% bucket 106: 10% bucket 95: 50% bucket 88: 60% bucket 107: 10% bucket 83: 90% bucket 82: 90% bucket 89: 60% bucket 81: 90% bucket 84: 80% bucket 85: 70% bucket 96: 50% bucket 86: 70% bucket 92: 60% bucket 101: 30% bucket 90: 60% bucket 98: 50% bucket 100: 30% bucket 97: 50% bucket 91: 40% bucket 103: 30% bucket 87: 70% bucket 104: 30% bucket 93: 60% bucket 99: 50% bucket 105: 30% bucket 94: 40% bucket 106: 20% bucket 102: 30% bucket 95: 60% bucket 83: 100% Sorting block of length 21668 for bucket 83 (Using difference cover) bucket 88: 70% bucket 82: 100% Sorting block of length 10473 for bucket 82 (Using difference cover) bucket 107: 20% bucket 81: 100% Sorting block of length 24647 for bucket 81 (Using difference cover) bucket 89: 70% bucket 84: 90% bucket 85: 80% Sorting block time: 00:00:00 Returning block of 10474 for bucket 82 bucket 86: 80% bucket 96: 60% bucket 92: 70% Getting block 108 of 203 Reserving size (31083) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: Sorting block time: 00:00:00 Returning block of 21669 for bucket 83 bucket 98: 60% bucket 97: 60% bucket 90: 70% bucket 101: 40% bucket 100: 40% bucket 91: 50% bucket 87: 80% Getting block 109 of 203 Reserving size (31083) for bucket 109 Calculating Z arrays for bucket 109 bucket 103: 40% Entering block accumulator loop for bucket 109: bucket 104: 40% bucket 93: 70% Sorting block time: 00:00:00 Returning block of 24648 for bucket 81 bucket 99: 60% bucket 105: 40% bucket 94: 50% Getting block 110 of 203 Reserving size (31083) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 95: 70% bucket 88: 80% bucket 106: 30% bucket 107: 30% bucket 84: 100% Sorting block of length 14403 for bucket 84 (Using difference cover) bucket 89: 80% bucket 102: 40% bucket 85: 90% bucket 86: 90% bucket 92: 80% bucket 96: 70% Sorting block time: 00:00:00 Returning block of 14404 for bucket 84 bucket 108: 10% bucket 98: 70% bucket 97: 70% Getting block 111 of 203 Reserving size (31083) for bucket 111 Calculating Z arrays for bucket 111 bucket 90: 80% Entering block accumulator loop for bucket 111: bucket 87: 90% bucket 91: 60% bucket 109: 10% bucket 104: 50% bucket 101: 50% bucket 93: 80% bucket 100: 50% bucket 103: 50% bucket 94: 60% bucket 105: 50% bucket 99: 70% bucket 110: 10% bucket 95: 80% bucket 106: 40% bucket 88: 90% bucket 107: 40% bucket 85: 100% Sorting block of length 26140 for bucket 85 (Using difference cover) bucket 89: 90% bucket 86: 100% Sorting block of length 17103 for bucket 86 (Using difference cover) bucket 102: 50% bucket 92: 90% bucket 96: 80% bucket 108: 20% bucket 98: 80% bucket 111: 10% bucket 97: 80% bucket 87: 100% Sorting block of length 27388 for bucket 87 (Using difference cover) bucket 91: 70% bucket 90: 90% bucket 104: 60% bucket 109: 20% Sorting block time: 00:00:00 Returning block of 17104 for bucket 86 bucket 93: 90% bucket 94: 70% bucket 101: 60% Sorting block time: 00:00:00 Returning block of 26141 for bucket 85 bucket 105: 60% bucket 100: 60% bucket 99: 80% bucket 103: 60% bucket 110: 20% bucket 95: 90% Getting block 112 of 203 Reserving size (31083) for bucket 112 Calculating Z arrays for bucket 112 bucket 106: 50% Entering block accumulator loop for bucket 112: bucket 107: 50% bucket 88: 100% Sorting block of length 29882 for bucket 88 (Using difference cover) Getting block 113 of 203 Reserving size (31083) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 89: 100% Sorting block of length 25385 for bucket 89 (Using difference cover) Sorting block time: 00:00:00 Returning block of 27389 for bucket 87 bucket 92: 100% Sorting block of length 30716 for bucket 92 (Using difference cover) Getting block 114 of 203 Reserving size (31083) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 96: 90% bucket 108: 30% bucket 102: 60% bucket 111: 20% bucket 98: 90% bucket 104: 70% bucket 91: 80% bucket 97: 90% bucket 109: 30% bucket 90: 100% Sorting block of length 30646 for bucket 90 (Using difference cover) bucket 93: 100% Sorting block of length 26754 for bucket 93 (Using difference cover) bucket 94: 80% bucket 105: 70% Sorting block time: 00:00:00 Returning block of 29883 for bucket 88 Sorting block time: 00:00:00 Returning block of 25386 for bucket 89 bucket 101: 70% bucket 99: 90% bucket 100: 70% bucket 103: 70% bucket 110: 30% Getting block 115 of 203 Reserving size (31083) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 106: 60% bucket 107: 60% bucket 95: 100% Sorting block of length 28054 for bucket 95 (Using difference cover) bucket 112: 10% bucket 113: 10% Sorting block time: 00:00:00 Returning block of 30717 for bucket 92 Sorting block time: 00:00:00 Returning block of 26755 for bucket 93 bucket 114: 10% bucket 108: 40% Sorting block time: 00:00:00 Returning block of 30647 for bucket 90 bucket 96: 100% Sorting block of length 12802 for bucket 96 (Using difference cover) bucket 111: 30% bucket 104: 80% bucket 98: 100% Sorting block of length 9108 for bucket 98 (Using difference cover) bucket 109: 40% bucket 97: 100% Sorting block of length 30130 for bucket 97 (Using difference cover) bucket 102: 70% bucket 91: 90% bucket 94: 90% Getting block 116 of 203 Reserving size (31083) for bucket 116 Calculating Z arrays for bucket 116 bucket 105: 80% Entering block accumulator loop for bucket 116: Sorting block time: 00:00:00 Returning block of 28055 for bucket 95 Getting block 117 of 203 Reserving size (31083) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: Getting block 118 of 203 Reserving size (31083) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: Getting block 119 of 203 Reserving size (31083) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: Sorting block time: 00:00:00 Returning block of 9109 for bucket 98 Sorting block time: 00:00:00 Returning block of 12803 for bucket 96 bucket 110: 40% bucket 103: 80% bucket 99: 100% Sorting block of length 16198 for bucket 99 (Using difference cover) bucket 101: 80% bucket 115: 10% bucket 100: 80% Getting block 120 of 203 Reserving size (31083) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 106: 70% bucket 107: 70% bucket 112: 20% bucket 113: 20% Sorting block time: 00:00:00 Returning block of 16199 for bucket 99 Sorting block time: 00:00:00 Returning block of 30131 for bucket 97 Getting block 121 of 203 Reserving size (31083) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 114: 20% bucket 108: 50% bucket 111: 40% bucket 104: 90% bucket 109: 50% bucket 116: 10% bucket 105: 90% bucket 94: 100% Sorting block of length 4370 for bucket 94 (Using difference cover) bucket 91: 100% Sorting block of length 26511 for bucket 91 (Using difference cover) bucket 117: 10% bucket 118: 10% bucket 102: 80% Sorting block time: 00:00:00 Returning block of 4371 for bucket 94 bucket 110: 50% bucket 115: 20% bucket 119: 10% bucket 103: 90% bucket 120: 10% bucket 101: 90% bucket 106: 80% bucket 107: 80% bucket 100: 90% bucket 112: 30% bucket 113: 30% Getting block 122 of 203 Reserving size (31083) 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 26512 for bucket 91 bucket 121: 10% bucket 108: 60% bucket 114: 30% bucket 104: 100% Sorting block of length 14239 for bucket 104 (Using difference cover) bucket 111: 50% Getting block 123 of 203 Reserving size (31083) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 109: 60% Getting block 124 of 203 Reserving size (31083) for bucket 124 Getting block 125 of 203 Calculating Z arrays for bucket 124 Reserving size (31083) for bucket 125 Calculating Z arrays for bucket 125 Getting block 126 of 203 Entering block accumulator loop for bucket 124: Reserving size (31083) for bucket 126 Entering block accumulator loop for bucket 125: Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: bucket 116: 20% bucket 105: 100% Sorting block of length 28550 for bucket 105 (Using difference cover) bucket 117: 20% bucket 118: 20% bucket 110: 60% bucket 115: 30% bucket 103: 100% Sorting block of length 28847 for bucket 103 (Using difference cover) bucket 119: 20% bucket 120: 20% bucket 106: 90% bucket 107: 90% bucket 101: 100% Sorting block of length 20843 for bucket 101 (Using difference cover) bucket 100: 100% Sorting block of length 29345 for bucket 100 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14240 for bucket 104 bucket 112: 40% bucket 113: 40% bucket 122: 10% Getting block 127 of 203 Reserving size (31083) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 102: 90% bucket 108: 70% bucket 121: 20% bucket 114: 40% bucket 111: 60% Sorting block time: 00:00:00 Returning block of 28551 for bucket 105 bucket 109: 70% bucket 123: 10% bucket 116: 30% bucket 124: 10% Sorting block time: 00:00:00 Returning block of 20844 for bucket 101 bucket 118: 30% bucket 117: 30% bucket 125: 10% bucket 126: 10% bucket 110: 70% bucket 115: 40% bucket 119: 30% bucket 120: 30% bucket 106: 100% Sorting block of length 18563 for bucket 106 (Using difference cover) bucket 107: 100% Sorting block of length 28937 for bucket 107 (Using difference cover) Sorting block time: 00:00:00 Returning block of 28848 for bucket 103 Sorting block time: 00:00:00 Returning block of 29346 for bucket 100 bucket 113: 50% bucket 112: 50% bucket 122: 20% bucket 127: 10% Sorting block time: 00:00:00 Returning block of 18564 for bucket 106 bucket 108: 80% bucket 121: 30% bucket 114: 50% bucket 111: 70% bucket 109: 80% bucket 102: 100% Sorting block of length 28366 for bucket 102 (Using difference cover) bucket 116: 40% Getting block 128 of 203 Reserving size (31083) for bucket 128 Calculating Z arrays for bucket 128 bucket 123: 20% Entering block accumulator loop for bucket 128: bucket 118: 40% bucket 117: 40% Sorting block time: 00:00:00 bucket 124: 20% Sorting block time: 00:00:00 Returning block of 28938 for bucket 107 bucket 125: 20% bucket 126: 20% bucket 115: 50% bucket 110: 80% bucket 120: 40% bucket 119: 40% bucket 113: 60% bucket 112: 60% bucket 122: 30% Returning block of 28367 for bucket 102 bucket 127: 20% bucket 108: 90% Getting block 129 of 203 Getting block 130 of 203 Getting block 131 of 203 Getting block 132 of 203 bucket 121: 40% Reserving size (31083) for bucket 129 Reserving size (31083) for bucket 130 Reserving size (31083) for bucket 131 Reserving size (31083) for bucket 132 Calculating Z arrays for bucket 129 Calculating Z arrays for bucket 130 Calculating Z arrays for bucket 131 Calculating Z arrays for bucket 132 bucket 111: 80% bucket 114: 60% Entering block accumulator loop for bucket 129: Entering block accumulator loop for bucket 130: Entering block accumulator loop for bucket 131: Entering block accumulator loop for bucket 132: bucket 109: 90% bucket 116: 50% bucket 123: 30% bucket 118: 50% bucket 117: 50% bucket 124: 30% bucket 128: 10% bucket 115: 60% bucket 110: 90% bucket 108: 100% Sorting block of length 10256 for bucket 108 (Using difference cover) bucket 120: 50% bucket 119: 50% bucket 113: 70% bucket 112: 70% bucket 109: 100% bucket 122: 40% Sorting block of length 30571 for bucket 109 (Using difference cover) bucket 111: 90% bucket 126: 30% bucket 121: 50% bucket 114: 70% bucket 127: 30% bucket 125: 30% bucket 116: 60% bucket 129: 10% bucket 132: 10% bucket 130: 10% bucket 131: 10% bucket 118: 60% bucket 117: 60% bucket 123: 40% Sorting block time: 00:00:00 Returning block of 10257 for bucket 108 bucket 124: 40% bucket 128: 20% Sorting block time: 00:00:00 Returning block of 30572 for bucket 109 bucket 115: 70% bucket 110: 100% Sorting block of length 16099 for bucket 110 (Using difference cover) bucket 113: 80% bucket 119: 60% bucket 120: 60% bucket 111: 100% bucket 112: 80% Sorting block of length 29103 for bucket 111 (Using difference cover) bucket 121: 60% bucket 116: 70% bucket 122: 50% bucket 114: 80% bucket 126: 40% bucket 127: 40% bucket 129: 20% Getting block 133 of 203 bucket 125: 40% Reserving size (31083) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 132: 20% bucket 118: 70% bucket 130: 20% bucket 117: 70% bucket 131: 20% Getting block 134 of 203 Reserving size (31083) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 123: 50% Getting block 135 of 203 Reserving size (31083) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 124: 50% Sorting block time: 00:00:00 Returning block of 16100 for bucket 110 Getting block 136 of 203 Reserving size (31083) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 128: 30% Getting block 137 of 203 Reserving size (31083) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: Sorting block time: 00:00:00 Returning block of 29104 for bucket 111 Getting block 138 of 203 Reserving size (31083) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 115: 80% bucket 113: 90% bucket 119: 70% bucket 116: 80% bucket 112: 90% bucket 121: 70% bucket 114: 90% bucket 122: 60% bucket 120: 70% bucket 126: 50% bucket 129: 30% bucket 127: 50% bucket 118: 80% bucket 117: 80% bucket 132: 30% bucket 133: 10% bucket 125: 50% bucket 130: 30% bucket 123: 60% bucket 131: 30% bucket 124: 60% bucket 135: 10% bucket 136: 10% bucket 128: 40% bucket 134: 10% bucket 137: 10% bucket 115: 90% bucket 138: 10% bucket 116: 90% bucket 113: 100% Sorting block of length 23235 for bucket 113 (Using difference cover) bucket 119: 80% bucket 112: 100% bucket 121: 80% Sorting block of length 22671 for bucket 112 (Using difference cover) bucket 114: 100% Sorting block of length 13755 for bucket 114 (Using difference cover) bucket 122: 70% bucket 118: 90% bucket 126: 60% bucket 120: 80% bucket 129: 40% bucket 117: 90% bucket 127: 60% bucket 132: 40% bucket 125: 60% bucket 123: 70% bucket 130: 40% bucket 133: 20% bucket 131: 40% bucket 124: 70% Sorting block time: 00:00:00 Returning block of 13756 for bucket 114 bucket 136: 20% bucket 128: 50% Getting block 139 of 203 Reserving size (31083) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 135: 20% bucket 134: 20% Sorting block time: 00:00:00 Returning block of 22672 for bucket 112 Sorting block time: 00:00:00 Returning block of 23236 for bucket 113 bucket 137: 20% Getting block 140 of 203 Reserving size (31083) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: bucket 115: 100% Sorting block of length 22509 for bucket 115 (Using difference cover) Getting block 141 of 203 Reserving size (31083) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 116: 100% Sorting block of length 30195 for bucket 116 (Using difference cover) bucket 138: 20% bucket 119: 90% bucket 121: 90% bucket 118: 100% Sorting block of length 10758 for bucket 118 (Using difference cover) bucket 122: 80% bucket 120: 90% bucket 126: 70% bucket 129: 50% bucket 117: 100% Sorting block of length 28511 for bucket 117 (Using difference cover) bucket 127: 70% bucket 132: 50% bucket 123: 80% Sorting block time: 00:00:00 Returning block of 22510 for bucket 115 bucket 125: 70% bucket 130: 50% Sorting block time: 00:00:00 Returning block of 10759 for bucket 118 bucket 133: 30% bucket 124: 80% bucket 131: 50% bucket 136: 30% bucket 128: 60% Getting block 142 of 203 Reserving size (31083) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: Getting block 143 of 203 Reserving size (31083) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 139: 10% bucket 134: 30% Sorting block time: 00:00:00 Returning block of 30196 for bucket 116 bucket 135: 30% bucket 137: 30% Getting block 144 of 203 Reserving size (31083) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: Sorting block time: 00:00:00 Returning block of 28512 for bucket 117 bucket 140: 10% bucket 141: 10% Getting block 145 of 203 Reserving size (31083) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 121: 100% Sorting block of length 19734 for bucket 121 (Using difference cover) bucket 138: 30% bucket 120: 100% Sorting block of length 26671 for bucket 120 (Using difference cover) bucket 122: 90% bucket 129: 60% bucket 119: 100% Sorting block of length 29897 for bucket 119 (Using difference cover) bucket 126: 80% bucket 127: 80% bucket 132: 60% bucket 123: 90% bucket 130: 60% bucket 125: 80% bucket 133: 40% bucket 124: 90% Sorting block time: 00:00:00 Returning block of 19735 for bucket 121 bucket 131: 60% bucket 136: 40% bucket 128: 70% bucket 143: 10% bucket 142: 10% bucket 139: 20% Sorting block time: 00:00:00 Returning block of 26672 for bucket 120 bucket 134: 40% bucket 135: 40% Sorting block time: 00:00:00 Returning block of 29898 for bucket 119 bucket 137: 40% bucket 144: 10% Getting block 146 of 203 Reserving size (31083) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: Getting block 147 of 203 Reserving size (31083) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: Getting block 148 of 203 bucket 140: 20% Reserving size (31083) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 141: 20% bucket 138: 40% bucket 145: 10% bucket 122: 100% Sorting block of length 21414 for bucket 122 (Using difference cover) bucket 129: 70% bucket 126: 90% bucket 127: 90% bucket 123: 100% Sorting block of length 30726 for bucket 123 (Using difference cover) bucket 132: 70% bucket 130: 70% bucket 133: 50% bucket 125: 90% bucket 124: 100% Sorting block of length 24081 for bucket 124 (Using difference cover) bucket 136: 50% bucket 128: 80% Sorting block time: 00:00:00 Returning block of 21415 for bucket 122 bucket 131: 70% bucket 143: 20% bucket 142: 20% Getting block 149 of 203 Reserving size (31083) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: bucket 134: 50% bucket 139: 30% bucket 135: 50% bucket 144: 20% bucket 137: 50% bucket 146: 10% bucket 141: 30% bucket 148: 10% bucket 140: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 24082 for bucket 124 Returning block of 30727 for bucket 123 bucket 138: 50% bucket 145: 20% bucket 129: 80% Getting block 150 of 203 Reserving size (31083) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 126: 100% Sorting block of length 28946 for bucket 126 (Using difference cover) Getting block 151 of 203 Reserving size (31083) for bucket 151 Calculating Z arrays for bucket 151 bucket 127: 100% Sorting block of length 23754 for bucket 127 (Using difference cover) Entering block accumulator loop for bucket 151: bucket 132: 80% bucket 147: 10% bucket 133: 60% bucket 130: 80% bucket 125: 100% Sorting block of length 29874 for bucket 125 (Using difference cover) bucket 136: 60% bucket 128: 90% bucket 131: 80% bucket 143: 30% bucket 142: 30% bucket 134: 60% bucket 149: 10% bucket 139: 40% Sorting block time: 00:00:00 Returning block of 23755 for bucket 127 bucket 144: 30% bucket 135: 60% Sorting block time: 00:00:00 Returning block of 28947 for bucket 126 bucket 137: 60% Getting block 152 of 203 Reserving size (31083) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: bucket 146: 20% bucket 141: 40% Getting block 153 of 203 Reserving size (31083) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 148: 20% bucket 140: 40% bucket 138: 60% bucket 129: 90% bucket 145: 30% Sorting block time: 00:00:00 Returning block of 29875 for bucket 125 bucket 150: 10% bucket 151: 10% bucket 132: 90% bucket 133: 70% bucket 130: 90% bucket 136: 70% bucket 128: 100% Sorting block of length 30403 for bucket 128 (Using difference cover) bucket 143: 40% bucket 131: 90% bucket 142: 40% bucket 149: 20% bucket 139: 50% Getting block 154 of 203 Reserving size (31083) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 144: 40% bucket 134: 70% bucket 147: 20% bucket 135: 70% bucket 137: 70% bucket 141: 50% bucket 146: 30% bucket 152: 10% bucket 138: 70% bucket 153: 10% bucket 148: 30% bucket 140: 50% bucket 129: 100% Sorting block of length 3521 for bucket 129 (Using difference cover) bucket 145: 40% Sorting block time: 00:00:00 Returning block of 30404 for bucket 128 bucket 150: 20% Sorting block time: 00:00:00 Returning block of 3522 for bucket 129 bucket 151: 20% bucket 132: 100% Sorting block of length 12476 for bucket 132 (Using difference cover) Getting block 155 of 203 Reserving size (31083) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: Getting block 156 of 203 Reserving size (31083) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 133: 80% bucket 130: 100% Sorting block of length 30319 for bucket 130 (Using difference cover) bucket 136: 80% bucket 143: 50% Sorting block time: 00:00:00 Returning block of 12477 for bucket 132 bucket 142: 50% bucket 131: 100% Sorting block of length 25170 for bucket 131 (Using difference cover) Getting block 157 of 203 Reserving size (31083) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 139: 60% bucket 144: 50% bucket 149: 30% bucket 154: 10% bucket 147: 30% bucket 135: 80% bucket 141: 60% bucket 137: 80% bucket 146: 40% bucket 152: 20% bucket 138: 80% bucket 153: 20% bucket 148: 40% bucket 140: 60% Sorting block time: 00:00:00 Returning block of 30320 for bucket 130 bucket 145: 50% bucket 134: 80% bucket 150: 30% Sorting block time: 00:00:00 Returning block of 25171 for bucket 131 bucket 156: 10% bucket 151: 30% bucket 133: 90% bucket 155: 10% bucket 136: 90% Getting block 158 of 203 Reserving size (31083) for bucket 158 Calculating Z arrays for bucket 158 Getting block 159 of 203 Reserving size (31083) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 158: Entering block accumulator loop for bucket 159: bucket 143: 60% bucket 142: 60% bucket 157: 10% bucket 144: 60% bucket 139: 70% bucket 149: 40% bucket 147: 40% bucket 141: 70% bucket 154: 20% bucket 135: 90% bucket 146: 50% bucket 137: 90% bucket 138: 90% bucket 152: 30% bucket 153: 30% bucket 148: 50% bucket 140: 70% bucket 145: 60% bucket 156: 20% bucket 134: 90% bucket 150: 40% bucket 151: 40% bucket 133: 100% Sorting block of length 22490 for bucket 133 (Using difference cover) bucket 136: 100% Sorting block of length 29196 for bucket 136 (Using difference cover) bucket 155: 20% bucket 159: 10% bucket 158: 10% bucket 143: 70% bucket 142: 70% bucket 157: 20% bucket 144: 70% bucket 139: 80% bucket 141: 80% bucket 147: 50% bucket 149: 50% Sorting block time: 00:00:00 Returning block of 22491 for bucket 133 bucket 135: 100% bucket 154: 30% Sorting block of length 25215 for bucket 135 (Using difference cover) bucket 146: 60% bucket 137: 100% Sorting block of length 28462 for bucket 137 (Using difference cover) bucket 138: 100% Sorting block of length 12520 for bucket 138 (Using difference cover) Sorting block time: 00:00:00 Returning block of 29197 for bucket 136 bucket 152: 40% bucket 153: 40% bucket 156: 30% bucket 148: 60% bucket 140: 80% Getting block 160 of 203 Reserving size (31083) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 134: 100% Sorting block of length 12976 for bucket 134 (Using difference cover) bucket 145: 70% bucket 150: 50% Getting block 161 of 203 Reserving size (31083) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 151: 50% Sorting block time: 00:00:00 Returning block of 12521 for bucket 138 bucket 159: 20% bucket 155: 30% bucket 158: 20% Getting block 162 of 203 Reserving size (31083) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 143: 80% Sorting block time: 00:00:00 Returning block of 12977 for bucket 134 Sorting block time: 00:00:00 Returning block of 25216 for bucket 135 bucket 157: 30% bucket 142: 80% Getting block 163 of 203 Reserving size (31083) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: Sorting block time: 00:00:00 Returning block of 28463 for bucket 137 bucket 144: 80% Getting block 164 of 203 Reserving size (31083) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 139: 90% Getting block 165 of 203 Reserving size (31083) for bucket 165 Calculating Z arrays for bucket 165 bucket 141: 90% Entering block accumulator loop for bucket 165: bucket 147: 60% bucket 149: 60% bucket 146: 70% bucket 154: 40% bucket 156: 40% bucket 153: 50% bucket 148: 70% bucket 152: 50% bucket 140: 90% bucket 160: 10% bucket 145: 80% bucket 161: 10% bucket 150: 60% bucket 151: 60% bucket 159: 30% bucket 158: 30% bucket 155: 40% bucket 143: 90% bucket 157: 40% bucket 162: 10% bucket 142: 90% bucket 163: 10% bucket 164: 10% bucket 144: 90% bucket 141: 100% Sorting block of length 14760 for bucket 141 (Using difference cover) bucket 165: 10% bucket 139: 100% Sorting block of length 20559 for bucket 139 (Using difference cover) bucket 147: 70% bucket 149: 70% bucket 146: 80% bucket 156: 50% bucket 154: 50% bucket 161: 20% Sorting block time: 00:00:00 Returning block of 14761 for bucket 141 bucket 153: 60% bucket 148: 80% bucket 160: 20% bucket 152: 60% bucket 140: 100% Sorting block of length 16495 for bucket 140 (Using difference cover) bucket 150: 70% bucket 145: 90% Getting block 166 of 203 Reserving size (31083) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 151: 70% Sorting block time: 00:00:00 Returning block of 20560 for bucket 139 bucket 158: 40% bucket 159: 40% bucket 157: 50% bucket 162: 20% Getting block 167 of 203 Reserving size (31083) for bucket 167 bucket 143: 100% Calculating Z arrays for bucket 167 Sorting block of length 25253 for bucket 143 (Using difference cover) Entering block accumulator loop for bucket 167: bucket 163: 20% bucket 142: 100% bucket 155: 50% Sorting block of length 22919 for bucket 142 (Using difference cover) Sorting block time: 00:00:00 Returning block of 16496 for bucket 140 bucket 164: 20% bucket 144: 100% Sorting block of length 26563 for bucket 144 (Using difference cover) Getting block 168 of 203 Reserving size (31083) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 165: 20% bucket 147: 80% bucket 149: 80% bucket 156: 60% bucket 146: 90% bucket 161: 30% Sorting block time: 00:00:00 Returning block of 22920 for bucket 142 bucket 154: 60% Sorting block time: 00:00:00 Returning block of 25254 for bucket 143 bucket 160: 30% bucket 153: 70% bucket 148: 90% bucket 150: 80% Getting block 169 of 203 Reserving size (31083) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 145: 100% Sorting block of length 30537 for bucket 145 (Using difference cover) bucket 152: 70% bucket 166: 10% Sorting block time: 00:00:00 Returning block of 26564 for bucket 144 Getting block 170 of 203 bucket 151: 80% Reserving size (31083) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 158: 50% bucket 159: 50% Getting block 171 of 203 Reserving size (31083) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 157: 60% bucket 163: 30% bucket 167: 10% bucket 162: 30% bucket 155: 60% bucket 164: 30% bucket 168: 10% bucket 165: 30% bucket 147: 90% bucket 156: 70% Sorting block time: 00:00:00 Returning block of 30538 for bucket 145 bucket 146: 100% Sorting block of length 14268 for bucket 146 (Using difference cover) bucket 161: 40% Getting block 172 of 203 Reserving size (31083) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: bucket 149: 90% bucket 160: 40% bucket 154: 70% bucket 153: 80% bucket 148: 100% Sorting block of length 28913 for bucket 148 (Using difference cover) bucket 150: 90% bucket 169: 10% bucket 166: 20% bucket 152: 80% Sorting block time: 00:00:00 Returning block of 14269 for bucket 146 bucket 151: 90% bucket 158: 60% bucket 170: 10% bucket 159: 60% bucket 157: 70% Getting block 173 of 203 Reserving size (31083) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: bucket 171: 10% bucket 163: 40% bucket 167: 20% bucket 162: 40% bucket 164: 40% bucket 155: 70% bucket 168: 20% bucket 165: 40% bucket 156: 80% Sorting block time: 00:00:00 Returning block of 28914 for bucket 148 bucket 147: 100% Sorting block of length 18765 for bucket 147 (Using difference cover) bucket 161: 50% bucket 172: 10% bucket 160: 50% bucket 149: 100% Sorting block of length 13334 for bucket 149 (Using difference cover) bucket 169: 20% bucket 150: 100% bucket 153: 90% Sorting block of length 31044 for bucket 150 (Using difference cover) bucket 154: 80% bucket 166: 30% bucket 158: 70% Sorting block time: 00:00:00 Returning block of 18766 for bucket 147 bucket 151: 100% Sorting block of length 13662 for bucket 151 (Using difference cover) bucket 152: 90% bucket 170: 20% bucket 157: 80% bucket 159: 70% bucket 163: 50% bucket 171: 20% bucket 173: 10% Getting block 174 of 203 Reserving size (31083) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: Sorting block time: 00:00:00 Returning block of 13335 for bucket 149 bucket 162: 50% bucket 167: 30% Getting block 175 of 203 Reserving size (31083) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 164: 50% Getting block 176 of 203 Reserving size (31083) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: Sorting block time: 00:00:00 Returning block of 13663 for bucket 151 bucket 168: 30% bucket 155: 80% bucket 156: 90% bucket 165: 50% bucket 161: 60% Sorting block time: 00:00:00 Returning block of 31045 for bucket 150 Getting block 177 of 203 Reserving size (31083) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 172: 20% bucket 160: 60% bucket 169: 30% bucket 153: 100% Sorting block of length 20645 for bucket 153 (Using difference cover) bucket 166: 40% bucket 158: 80% bucket 154: 90% bucket 157: 90% bucket 159: 80% bucket 170: 30% bucket 152: 100% Sorting block of length 28094 for bucket 152 (Using difference cover) bucket 163: 60% bucket 171: 30% bucket 173: 20% bucket 174: 10% bucket 162: 60% bucket 167: 40% bucket 164: 60% bucket 176: 10% bucket 168: 40% bucket 156: 100% Sorting block of length 24778 for bucket 156 (Using difference cover) bucket 175: 10% Sorting block time: 00:00:00 Returning block of 20646 for bucket 153 bucket 155: 90% bucket 165: 60% bucket 161: 70% Sorting block time: 00:00:00 Returning block of 28095 for bucket 152 bucket 177: 10% bucket 160: 70% bucket 172: 30% bucket 169: 40% bucket 158: 90% Sorting block time: 00:00:00 Returning block of 24779 for bucket 156 bucket 157: 100% Sorting block of length 21975 for bucket 157 (Using difference cover) bucket 166: 50% bucket 154: 100% Sorting block of length 22365 for bucket 154 (Using difference cover) bucket 159: 90% bucket 163: 70% bucket 170: 40% bucket 162: 70% bucket 171: 40% bucket 174: 20% bucket 173: 30% bucket 167: 50% Getting block 178 of 203 Reserving size (31083) for bucket 178 Calculating Z arrays for bucket 178 bucket 164: 70% Getting block 179 of 203 Entering block accumulator loop for bucket 178: Reserving size (31083) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 176: 20% bucket 168: 50% bucket 175: 20% Sorting block time: 00:00:00 bucket 161: 80% Returning block of 21976 for bucket 157 bucket 165: 70% bucket 155: 100% Sorting block of length 17015 for bucket 155 (Using difference cover) Getting block 180 of 203 Reserving size (31083) for bucket 180 Calculating Z arrays for bucket 180 Sorting block time: 00:00:00 Returning block of 22366 for bucket 154 Getting block 181 of 203 Reserving size (31083) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: Entering block accumulator loop for bucket 180: Getting block 182 of 203 Reserving size (31083) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 177: 20% Getting block 183 of 203 Reserving size (31083) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: bucket 160: 80% bucket 169: 50% bucket 172: 40% bucket 158: 100% Sorting block of length 25059 for bucket 158 (Using difference cover) Sorting block time: 00:00:00 Returning block of 17016 for bucket 155 bucket 166: 60% bucket 163: 80% bucket 159: 100% Sorting block of length 29227 for bucket 159 (Using difference cover) bucket 170: 50% bucket 162: 80% bucket 171: 50% bucket 174: 30% bucket 164: 80% bucket 173: 40% bucket 167: 60% bucket 178: 10% Getting block 184 of 203 Reserving size (31083) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 176: 30% bucket 179: 10% bucket 168: 60% bucket 161: 90% bucket 175: 30% bucket 165: 80% Sorting block time: 00:00:00 Returning block of 25060 for bucket 158 Getting block 185 of 203 Reserving size (31083) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 182: 10% bucket 181: 10% Sorting block time: 00:00:00 Returning block of 29228 for bucket 159 bucket 177: 30% bucket 180: 10% bucket 160: 90% bucket 183: 10% Getting block 186 of 203 Reserving size (31083) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: bucket 169: 60% bucket 172: 50% bucket 163: 90% bucket 166: 70% bucket 162: 90% bucket 174: 40% bucket 171: 60% bucket 170: 60% bucket 164: 90% bucket 167: 70% bucket 178: 20% bucket 173: 50% bucket 184: 10% bucket 176: 40% bucket 179: 20% bucket 161: 100% Sorting block of length 30788 for bucket 161 (Using difference cover) bucket 168: 70% bucket 165: 90% bucket 175: 40% bucket 185: 10% bucket 182: 20% bucket 181: 20% bucket 177: 40% bucket 160: 100% Sorting block of length 29091 for bucket 160 (Using difference cover) bucket 180: 20% bucket 186: 10% bucket 183: 20% bucket 169: 70% bucket 172: 60% bucket 163: 100% Sorting block of length 22892 for bucket 163 (Using difference cover) Sorting block time: 00:00:00 Returning block of 30789 for bucket 161 bucket 166: 80% bucket 162: 100% Sorting block of length 26965 for bucket 162 (Using difference cover) bucket 174: 50% bucket 164: 100% Sorting block of length 24325 for bucket 164 (Using difference cover) Getting block 187 of 203 Reserving size (31083) for bucket 187 Calculating Z arrays for bucket 187 bucket 171: 70% Entering block accumulator loop for bucket 187: bucket 170: 70% bucket 167: 80% bucket 178: 30% bucket 184: 20% bucket 173: 60% bucket 176: 50% bucket 179: 30% bucket 168: 80% bucket 165: 100% Sorting block of length 27446 for bucket 165 (Using difference cover) bucket 175: 50% Sorting block time: 00:00:00 Returning block of 22893 for bucket 163 Sorting block time: 00:00:00 Returning block of 29092 for bucket 160 bucket 185: 20% bucket 182: 30% Getting block 188 of 203 Reserving size (31083) for bucket 188 Calculating Z arrays for bucket 188 Sorting block time: 00:00:00 Returning block of 26966 for bucket 162 Entering block accumulator loop for bucket 188: bucket 177: 50% Getting block 189 of 203 Reserving size (31083) for bucket 189 Calculating Z arrays for bucket 189 Sorting block time: 00:00:00 Returning block of 24326 for bucket 164 Entering block accumulator loop for bucket 189: bucket 181: 30% Getting block 190 of 203 Reserving size (31083) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 180: 30% bucket 186: 20% bucket 183: 30% Getting block 191 of 203 Reserving size (31083) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: bucket 169: 80% bucket 172: 70% Sorting block time: 00:00:00 Returning block of 27447 for bucket 165 bucket 187: 10% bucket 166: 90% bucket 174: 60% bucket 171: 80% bucket 170: 80% bucket 167: 90% bucket 184: 30% bucket 178: 40% bucket 173: 70% bucket 168: 90% bucket 179: 40% bucket 176: 60% bucket 185: 30% bucket 175: 60% bucket 182: 40% bucket 188: 10% bucket 189: 10% bucket 177: 60% bucket 190: 10% bucket 186: 30% bucket 181: 40% bucket 183: 40% bucket 180: 40% bucket 191: 10% bucket 169: 90% bucket 172: 80% bucket 187: 20% bucket 174: 70% bucket 171: 90% bucket 184: 40% bucket 170: 90% bucket 167: 100% bucket 166: 100% bucket 178: 50% bucket 173: 80% bucket 168: 100% bucket 179: 50% bucket 176: 70% bucket 185: 40% bucket 175: 70% Getting block 192 of 203 bucket 182: 50% Sorting block of length 17285 for bucket 167 (Using difference cover) Sorting block of length 23114 for bucket 166 (Using difference cover) Sorting block of length 29757 for bucket 168 (Using difference cover) Reserving size (31083) for bucket 192 bucket 188: 20% bucket 189: 20% Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 177: 70% bucket 186: 40% bucket 190: 20% bucket 181: 50% Sorting block time: 00:00:00 Returning block of 17286 for bucket 167 Getting block 193 of 203 Reserving size (31083) 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 23115 for bucket 166 Getting block 194 of 203 Reserving size (31083) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: Sorting block time: 00:00:00 Returning block of 29758 for bucket 168 Getting block 195 of 203 Reserving size (31083) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 187: 30% bucket 183: 50% bucket 184: 50% bucket 191: 20% bucket 185: 50% bucket 169: 100% bucket 174: 80% Sorting block of length 24853 for bucket 169 (Using difference cover) bucket 192: 10% bucket 171: 100% Sorting block of length 17596 for bucket 171 (Using difference cover) bucket 178: 60% bucket 189: 30% bucket 182: 60% bucket 170: 100% Sorting block of length 16448 for bucket 170 (Using difference cover) bucket 188: 30% bucket 180: 50% bucket 172: 90% bucket 173: 90% bucket 176: 80% bucket 179: 60% bucket 175: 80% bucket 177: 80% bucket 186: 50% bucket 190: 30% bucket 181: 60% Sorting block time: 00:00:00 Returning block of 17597 for bucket 171 Sorting block time: 00:00:00 Returning block of 16449 for bucket 170 bucket 193: 10% Getting block 196 of 203 Reserving size (31083) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: Sorting block time: 00:00:00 Returning block of 24854 for bucket 169 Getting block 197 of 203 Reserving size (31083) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: bucket 194: 10% Getting block 198 of 203 Reserving size (31083) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 187: 40% bucket 195: 10% bucket 185: 60% bucket 192: 20% bucket 184: 60% bucket 191: 30% bucket 174: 90% bucket 189: 40% bucket 183: 60% bucket 182: 70% bucket 178: 70% bucket 188: 40% bucket 176: 90% bucket 173: 100% bucket 175: 90% bucket 179: 70% Sorting block of length 27450 for bucket 173 (Using difference cover) bucket 180: 60% bucket 172: 100% Sorting block of length 26725 for bucket 172 (Using difference cover) bucket 186: 60% bucket 190: 40% bucket 177: 90% bucket 181: 70% Preparing indexing of GA converted genome in /gscratch/srlab/sr320/data/ecoli-MG1655/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 bucket 193: 20% bucket 196: 10% bucket 197: 10% bucket 194: 20% Sorting block time: 00:00:00 Returning block of 27451 for bucket 173 bucket 198: 10% Sorting block time: 00:00:00 Returning block of 26726 for bucket 172 bucket 187: 50% bucket 195: 20% bucket 192: 30% bucket 185: 70% bucket 184: 70% bucket 189: 50% bucket 191: 40% bucket 174: 100% Sorting block of length 16101 for bucket 174 (Using difference cover) bucket 183: 70% bucket 182: 80% bucket 188: 50% bucket 178: 80% Getting block 199 of 203 Reserving size (31083) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: bucket 176: 100% Sorting block of length 25446 for bucket 176 (Using difference cover) bucket 175: 100% bucket 179: 80% Sorting block of length 27571 for bucket 175 (Using difference cover) bucket 180: 70% bucket 186: 70% bucket 190: 50% bucket 177: 100% Sorting block of length 9627 for bucket 177 (Using difference cover) bucket 181: 80% Sorting block time: 00:00:00 Returning block of 16102 for bucket 174 Getting block 200 of 203 Reserving size (31083) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 193: 30% bucket 196: 20% Sorting block time: 00:00:00 Returning block of 9628 for bucket 177 bucket 197: 20% Getting block 201 of 203 Reserving size (31083) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: bucket 194: 30% bucket 198: 20% Sorting block time: 00:00:00 Returning block of 25447 for bucket 176 Sorting block time: 00:00:00 Returning block of 27572 for bucket 175 bucket 187: 60% bucket 192: 40% bucket 195: 30% Getting block 202 of 203 Reserving size (31083) for bucket 202 bucket 185: 80% Calculating Z arrays for bucket 202 bucket 184: 80% bucket 189: 60% bucket 191: 50% bucket 182: 90% bucket 188: 60% bucket 178: 90% bucket 199: 10% bucket 183: 80% Getting block 203 of 203 Entering block accumulator loop for bucket 202: Reserving size (31083) for bucket 203 bucket 179: 90% bucket 186: 80% bucket 180: 80% bucket 190: 60% bucket 181: 90% bucket 193: 40% bucket 196: 30% bucket 200: 10% Calculating Z arrays for bucket 203 bucket 197: 30% bucket 194: 40% bucket 201: 10% bucket 198: 30% bucket 187: 70% bucket 192: 50% bucket 185: 90% bucket 195: 40% bucket 182: 100% bucket 184: 90% bucket 189: 70% bucket 191: 60% bucket 199: 20% bucket 188: 70% bucket 178: 100% bucket 183: 90% Entering block accumulator loop for bucket 203: Sorting block of length 30982 for bucket 182 (Using difference cover) Sorting block of length 27740 for bucket 178 (Using difference cover) bucket 200: 20% bucket 193: 50% bucket 196: 40% bucket 186: 90% bucket 190: 70% bucket 179: 100% Sorting block of length 16206 for bucket 179 (Using difference cover) bucket 181: 100% Sorting block of length 15272 for bucket 181 (Using difference cover) bucket 180: 90% Sorting block time: 00:00:00 Returning block of 16207 for bucket 179 Sorting block time: 00:00:00 Returning block of 27741 for bucket 178 bucket 203: 10% Sorting block time: 00:00:00 Returning block of 15273 for bucket 181 Sorting block time: 00:00:00 Returning block of 30983 for bucket 182 bucket 201: 20% bucket 194: 50% bucket 192: 60% bucket 187: 80% bucket 185: 100% bucket 202: 10% Sorting block of length 13357 for bucket 185 (Using difference cover) bucket 184: 100% bucket 198: 40% Sorting block of length 27526 for bucket 184 (Using difference cover) bucket 197: 40% bucket 199: 30% bucket 189: 80% bucket 188: 80% bucket 191: 70% bucket 195: 50% bucket 183: 100% Sorting block of length 23301 for bucket 183 (Using difference cover) Sorting block time: 00:00:00 Returning block of 13358 for bucket 185 bucket 200: 30% bucket 193: 60% bucket 196: 50% bucket 186: 100% Sorting block of length 27228 for bucket 186 (Using difference cover) bucket 190: 80% bucket 180: 100% Sorting block of length 30044 for bucket 180 (Using difference cover) bucket 203: 20% Sorting block time: 00:00:00 Returning block of 27527 for bucket 184 Sorting block time: 00:00:00 Returning block of 23302 for bucket 183 bucket 201: 30% bucket 194: 60% bucket 192: 70% bucket 187: 90% bucket 202: 20% bucket 197: 50% bucket 198: 50% bucket 199: 40% bucket 189: 90% bucket 191: 80% bucket 188: 90% Sorting block time: 00:00:00 Returning block of 27229 for bucket 186 bucket 195: 60% Sorting block time: 00:00:00 Returning block of 30045 for bucket 180 bucket 200: 40% bucket 203: 30% bucket 196: 60% bucket 193: 70% bucket 190: 90% 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 bucket 201: 40% bucket 187: 100% bucket 194: 70% Sorting block of length 22813 for bucket 187 (Using difference cover) bucket 192: 80% bucket 202: 30% bucket 197: 60% bucket 198: 60% bucket 199: 50% bucket 189: 100% Sorting block of length 30985 for bucket 189 (Using difference cover) bucket 191: 90% bucket 203: 40% bucket 188: 100% Sorting block of length 22827 for bucket 188 (Using difference cover) bucket 200: 50% bucket 195: 70% bucket 196: 70% bucket 193: 80% bucket 190: 100% Sorting block of length 23015 for bucket 190 (Using difference cover) Sorting block time: 00:00:00 Returning block of 22814 for bucket 187 Sorting block time: 00:00:00 Returning block of 22828 for bucket 188 bucket 203: 50% Sorting block time: 00:00:00 Returning block of 30986 for bucket 189 bucket 201: 50% bucket 192: 90% bucket 194: 80% bucket 202: 40% bucket 197: 70% bucket 199: 60% bucket 198: 70% Sorting block time: 00:00:00 Returning block of 23016 for bucket 190 bucket 191: 100% Sorting block of length 26192 for bucket 191 (Using difference cover) bucket 200: 60% bucket 196: 80% bucket 193: 90% bucket 195: 80% bucket 203: 60% Sorting block time: 00:00:00 Returning block of 26193 for bucket 191 bucket 192: 100% Sorting block of length 15632 for bucket 192 (Using difference cover) bucket 194: 90% bucket 201: 60% bucket 202: 50% bucket 199: 70% bucket 197: 80% bucket 198: 80% bucket 200: 70% bucket 203: 70% Sorting block time: 00:00:00 Returning block of 15633 for bucket 192 bucket 196: 90% bucket 193: 100% Sorting block of length 23242 for bucket 193 (Using difference cover) bucket 195: 90% bucket 194: 100% Sorting block of length 9138 for bucket 194 (Using difference cover) bucket 201: 70% bucket 202: 60% Sorting block time: 00:00:00 Returning block of 23243 for bucket 193 bucket 199: 80% bucket 197: 90% bucket 203: 80% bucket 198: 90% Sorting block time: 00:00:00 Returning block of 9139 for bucket 194 bucket 200: 80% bucket 196: 100% Sorting block of length 30778 for bucket 196 (Using difference cover) bucket 195: 100% Sorting block of length 15633 for bucket 195 (Using difference cover) bucket 203: 90% Sorting block time: 00:00:00 Returning block of 15634 for bucket 195 bucket 201: 80% bucket 202: 70% bucket 199: 90% bucket 197: 100% Sorting block of length 20122 for bucket 197 (Using difference cover) bucket 198: 100% Sorting block of length 27380 for bucket 198 (Using difference cover) Sorting block time: 00:00:00 Returning block of 30779 for bucket 196 bucket 200: 90% bucket 203: 100% Sorting block of length 12089 for bucket 203 (Using difference cover) Sorting block time: 00:00:00 Returning block of 20123 for bucket 197 Sorting block time: 00:00:00 Returning block of 27381 for bucket 198 Sorting block time: 00:00:00 Returning block of 12090 for bucket 203 bucket 201: 90% bucket 202: 80% Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences bucket 199: 100% Sorting block of length 23154 for bucket 199 (Using difference cover) bucket 200: 100% Sorting block of length 28469 for bucket 200 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23155 for bucket 199 bucket 201: 100% Sorting block of length 18014 for bucket 201 (Using difference cover) bucket 202: 90% Sorting block time: 00:00:00 Returning block of 28470 for bucket 200 Sorting block time: 00:00:00 Returning block of 18015 for bucket 201 bucket 202: 100% Sorting block of length 28713 for bucket 202 (Using difference cover) Sorting block time: 00:00:00 Returning block of 28714 for bucket 202 Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 41443 Using parameters --bmax 31083 --dcv 1024 Doing ahead-of-time memory usage test Exited Ebwt loop fchr[A]: 0 fchr[C]: 1142742 fchr[G]: 1142742 fchr[T]: 2320179 fchr[$]: 4641652 Passed! Constructing with these parameters: --bmax 31083 --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 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 5741754 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 1160420 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 4641652 bwtLen: 4641653 sz: 1160413 bwtSz: 1160414 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 290104 offsSz: 1160416 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 24176 numLines: 24176 ebwtTotLen: 1547264 ebwtTotSz: 1547264 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:01 Reading reference sizes Splitting and merging Splitting and merging time: 00:00:00 Split 37, merged 125; iterating... Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Splitting and merging Splitting and merging time: 00:00:00 Split 16, merged 15; iterating... Time to join reference sequences: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 41443 Using parameters --bmax 31083 --dcv 1024 Doing ahead-of-time memory usage test Splitting and merging Splitting and merging time: 00:00:00 Split 8, merged 12; iterating... Passed! Constructing with these parameters: --bmax 31083 --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 Splitting and merging Splitting and merging time: 00:00:00 Split 5, merged 6; iterating... 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 1, merged 4; iterating... Avg bucket size: 22531.3 (target: 31082) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 206 Reserving size (31083) for bucket 1 Getting block 2 of 206 Getting block 3 of 206 Getting block 4 of 206 Getting block 5 of 206 Getting block 6 of 206 Getting block 7 of 206 Getting block 8 of 206 Getting block 9 of 206 Getting block 10 of 206 Getting block 11 of 206 Getting block 12 of 206 Getting block 13 of 206 Getting block 14 of 206 Getting block 15 of 206 Getting block 16 of 206 Getting block 17 of 206 Getting block 18 of 206 Getting block 19 of 206 Getting block 20 of 206 Getting block 21 of 206 Getting block 22 of 206 Getting block 23 of 206 Getting block 24 of 206 Calculating Z arrays for bucket 1 Reserving size (31083) for bucket 2 Getting block 25 of 206 Getting block 26 of 206 Getting block 27 of 206 Reserving size (31083) for bucket 3 Reserving size (31083) for bucket 4 Reserving size (31083) for bucket 5 Reserving size (31083) for bucket 6 Reserving size (31083) for bucket 7 Reserving size (31083) for bucket 8 Reserving size (31083) for bucket 9 Reserving size (31083) for bucket 10 Reserving size (31083) for bucket 11 Reserving size (31083) for bucket 12 Reserving size (31083) for bucket 13 Reserving size (31083) for bucket 14 Reserving size (31083) for bucket 15 Reserving size (31083) for bucket 16 Reserving size (31083) for bucket 17 Reserving size (31083) for bucket 18 Reserving size (31083) for bucket 19 Reserving size (31083) for bucket 20 Reserving size (31083) for bucket 21 Reserving size (31083) for bucket 22 Reserving size (31083) for bucket 23 Reserving size (31083) for bucket 24 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 2 Reserving size (31083) for bucket 25 Reserving size (31083) for bucket 26 Reserving size (31083) for bucket 27 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 9 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 16 Calculating Z arrays for bucket 15 Calculating Z arrays for bucket 17 Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 18 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 26 Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 10: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 27: bucket 1: 10% bucket 4: 10% bucket 2: 10% bucket 3: 10% bucket 6: 10% bucket 5: 10% bucket 7: 10% bucket 10: 10% bucket 11: 10% bucket 8: 10% bucket 9: 10% bucket 12: 10% bucket 15: 10% bucket 18: 10% bucket 13: 10% Splitting and merging bucket 17: 10% bucket 14: 10% bucket 19: 10% bucket 23: 10% bucket 20: 10% Splitting and merging time: 00:00:00 Split 45, merged 131; iterating... bucket 21: 10% bucket 24: 10% bucket 24: 20% bucket 24: 30% bucket 16: 10% bucket 22: 10% bucket 26: 10% bucket 27: 10% bucket 25: 10% bucket 13: 20% bucket 1: 20% bucket 4: 20% bucket 2: 20% bucket 3: 20% bucket 6: 20% bucket 5: 20% bucket 24: 40% bucket 7: 20% bucket 10: 20% bucket 11: 20% bucket 8: 20% bucket 9: 20% bucket 12: 20% bucket 15: 20% bucket 18: 20% bucket 14: 20% bucket 19: 20% bucket 23: 20% bucket 20: 20% bucket 21: 20% bucket 16: 20% bucket 22: 20% bucket 17: 20% bucket 26: 20% bucket 27: 20% bucket 25: 20% bucket 1: 30% bucket 4: 30% bucket 2: 30% bucket 3: 30% bucket 6: 30% bucket 5: 30% bucket 7: 30% bucket 24: 50% bucket 13: 30% bucket 11: 30% bucket 10: 30% bucket 8: 30% bucket 12: 30% bucket 9: 30% bucket 15: 30% bucket 18: 30% bucket 14: 30% bucket 17: 30% bucket 19: 30% bucket 23: 30% bucket 20: 30% bucket 21: 30% bucket 16: 30% bucket 22: 30% bucket 26: 30% bucket 27: 30% bucket 25: 30% bucket 1: 40% bucket 4: 40% bucket 2: 40% bucket 3: 40% bucket 6: 40% bucket 5: 40% bucket 7: 40% bucket 11: 40% bucket 10: 40% bucket 13: 40% bucket 8: 40% Splitting and merging Splitting and merging time: 00:00:00 Split 20, merged 22; iterating... bucket 12: 40% bucket 9: 40% bucket 24: 60% bucket 15: 40% bucket 18: 40% bucket 14: 40% bucket 17: 40% bucket 20: 40% bucket 19: 40% bucket 23: 40% bucket 21: 40% bucket 16: 40% bucket 22: 40% bucket 26: 40% bucket 27: 40% bucket 25: 40% bucket 1: 50% bucket 4: 50% bucket 2: 50% bucket 3: 50% bucket 6: 50% bucket 5: 50% bucket 7: 50% bucket 10: 50% bucket 11: 50% bucket 13: 50% bucket 8: 50% bucket 9: 50% bucket 12: 50% bucket 15: 50% bucket 18: 50% bucket 17: 50% bucket 14: 50% bucket 24: 70% bucket 20: 50% bucket 19: 50% bucket 23: 50% bucket 21: 50% bucket 16: 50% bucket 22: 50% bucket 26: 50% bucket 1: 60% bucket 27: 50% bucket 4: 60% bucket 2: 60% bucket 25: 50% bucket 3: 60% bucket 6: 60% bucket 5: 60% bucket 7: 60% bucket 10: 60% bucket 11: 60% bucket 13: 60% bucket 8: 60% bucket 9: 60% bucket 12: 60% bucket 15: 60% bucket 18: 60% bucket 17: 60% bucket 14: 60% bucket 19: 60% bucket 20: 60% bucket 23: 60% bucket 1: 70% bucket 24: 80% bucket 21: 60% bucket 16: 60% bucket 22: 60% bucket 4: 70% bucket 2: 70% bucket 26: 60% bucket 27: 60% bucket 3: 70% bucket 6: 70% bucket 24: 90% bucket 24: 100% Sorting block of length 9199 for bucket 24 (Using difference cover) Sorting block time: 00:00:00 Returning block of 9200 for bucket 24 bucket 25: 60% bucket 5: 70% bucket 7: 70% bucket 11: 70% bucket 13: 70% bucket 8: 70% bucket 9: 70% bucket 12: 70% bucket 15: 70% bucket 14: 70% bucket 1: 80% bucket 6: 80% bucket 19: 70% bucket 20: 70% bucket 23: 70% bucket 4: 80% bucket 2: 80% bucket 21: 70% Splitting and merging Splitting and merging time: 00:00:00 Split 14, merged 14; iterating... bucket 16: 70% bucket 22: 70% bucket 3: 80% bucket 17: 70% bucket 26: 70% bucket 10: 70% bucket 18: 70% bucket 25: 70% bucket 27: 70% bucket 5: 80% bucket 7: 80% bucket 11: 80% bucket 8: 80% bucket 13: 80% bucket 12: 80% bucket 9: 80% bucket 15: 80% bucket 14: 80% bucket 1: 90% bucket 6: 90% Getting block 28 of 206 bucket 2: 90% bucket 4: 90% bucket 19: 80% bucket 20: 80% bucket 23: 80% bucket 21: 80% bucket 3: 90% bucket 5: 90% bucket 7: 90% bucket 22: 80% bucket 16: 80% bucket 17: 80% bucket 18: 80% bucket 25: 80% bucket 26: 80% bucket 27: 80% bucket 11: 90% bucket 8: 90% bucket 12: 90% bucket 13: 90% bucket 10: 80% bucket 1: 100% bucket 6: 100% Reserving size (31083) for bucket 28 bucket 9: 90% bucket 15: 90% bucket 14: 90% Sorting block of length 24394 for bucket 1 (Using difference cover) bucket 2: 100% bucket 4: 100% Sorting block of length 30370 for bucket 6 (Using difference cover) Splitting and merging Splitting and merging time: 00:00:00 Split 8, merged 11; iterating... Sorting block time: 00:00:00 Calculating Z arrays for bucket 28 bucket 3: 100% bucket 5: 100% Sorting block time: 00:00:00 bucket 7: 100% bucket 8: 100% bucket 11: 100% bucket 10: 90% bucket 18: 90% bucket 19: 90% bucket 12: 100% bucket 17: 90% bucket 20: 90% bucket 23: 90% bucket 13: 100% bucket 21: 90% bucket 22: 90% bucket 26: 90% bucket 25: 90% bucket 27: 90% bucket 16: 90% Sorting block of length 15857 for bucket 2 (Using difference cover) Sorting block of length 15489 for bucket 4 (Using difference cover) bucket 9: 100% Returning block of 30371 for bucket 6 Entering block accumulator loop for bucket 28: Sorting block of length 17397 for bucket 3 (Using difference cover) Sorting block of length 26561 for bucket 5 (Using difference cover) Returning block of 24395 for bucket 1 bucket 15: 100% bucket 14: 100% Sorting block of length 18600 for bucket 7 (Using difference cover) Sorting block of length 23638 for bucket 8 (Using difference cover) Sorting block of length 14857 for bucket 11 (Using difference cover) Sorting block of length 24156 for bucket 12 (Using difference cover) Sorting block of length 23565 for bucket 13 (Using difference cover) Sorting block of length 29540 for bucket 9 (Using difference cover) Sorting block of length 5879 for bucket 15 (Using difference cover) Sorting block of length 29774 for bucket 14 (Using difference cover) Getting block 29 of 206 Reserving size (31083) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: Getting block 30 of 206 Reserving size (31083) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 10: 100% Sorting block of length 17928 for bucket 10 (Using difference cover) bucket 18: 100% Sorting block of length 10801 for bucket 18 (Using difference cover) bucket 20: 100% Sorting block of length 22823 for bucket 20 (Using difference cover) bucket 23: 100% Sorting block of length 24120 for bucket 23 (Using difference cover) bucket 21: 100% Sorting block of length 26652 for bucket 21 (Using difference cover) bucket 22: 100% Sorting block of length 23190 for bucket 22 (Using difference cover) bucket 26: 100% Sorting block of length 7496 for bucket 26 (Using difference cover) bucket 27: 100% Sorting block of length 25780 for bucket 27 (Using difference cover) bucket 19: 100% Sorting block of length 22967 for bucket 19 (Using difference cover) bucket 16: 100% Sorting block of length 30074 for bucket 16 (Using difference cover) bucket 17: 100% Sorting block of length 23256 for bucket 17 (Using difference cover) bucket 28: 10% bucket 25: 100% Sorting block of length 30808 for bucket 25 (Using difference cover) bucket 29: 10% Sorting block time: 00:00:00 Returning block of 5880 for bucket 15 bucket 30: 10% Getting block 31 of 206 Reserving size (31083) for bucket 31 Calculating Z arrays for bucket 31 Sorting block time: 00:00:00 Returning block of 14858 for bucket 11 Entering block accumulator loop for bucket 31: Getting block 32 of 206 Reserving size (31083) 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 18601 for bucket 7 Getting block 33 of 206 Reserving size (31083) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: Splitting and merging Splitting and merging time: 00:00:00 Split 4, merged 6; iterating... Avg bucket size: 22314.6 (target: 31082) Converting suffix-array elements to index image Allocating ftab, absorbFtab Sorting block time: 00:00:00 Returning block of 15490 for bucket 4 Sorting block time: 00:00:00 Returning block of 7497 for bucket 26 Sorting block time: 00:00:00 Returning block of 15858 for bucket 2 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 17398 for bucket 3 Returning block of 23639 for bucket 8 bucket 28: 20% Sorting block time: 00:00:00 Returning block of 10802 for bucket 18 Getting block 34 of 206 Reserving size (31083) for bucket 34 Getting block 35 of 206 Calculating Z arrays for bucket 34 Reserving size (31083) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 34: Entering block accumulator loop for bucket 35: bucket 29: 20% Getting block 36 of 206 Entering Ebwt loop Reserving size (31083) for bucket 36 Getting block 37 of 206 Calculating Z arrays for bucket 36 Reserving size (31083) for bucket 37 Calculating Z arrays for bucket 37 Getting block 1 of 208 Entering block accumulator loop for bucket 36: Entering block accumulator loop for bucket 37: Reserving size (31083) for bucket 1 Getting block 2 of 208 Getting block 3 of 208 bucket 30: 20% Getting block 4 of 208 Getting block 38 of 206 Reserving size (31083) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: Getting block 5 of 208 Calculating Z arrays for bucket 1 Reserving size (31083) for bucket 2 bucket 31: 10% bucket 32: 10% bucket 33: 10% Getting block 39 of 206 Reserving size (31083) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: bucket 28: 30% bucket 35: 10% bucket 30: 30% bucket 37: 10% bucket 36: 10% bucket 38: 10% bucket 29: 30% bucket 31: 20% bucket 32: 20% bucket 33: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 29541 for bucket 9 Sorting block time: 00:00:00 Returning block of 23191 for bucket 22 Returning block of 24157 for bucket 12 Sorting block time: 00:00:00 Returning block of 26562 for bucket 5 Getting block 40 of 206 Reserving size (31083) for bucket 40 Getting block 41 of 206 Calculating Z arrays for bucket 40 Reserving size (31083) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 40: Entering block accumulator loop for bucket 41: Sorting block time: 00:00:00 Returning block of 29775 for bucket 14 Getting block 42 of 206 Reserving size (31083) for bucket 42 Calculating Z arrays for bucket 42 bucket 28: 40% Entering block accumulator loop for bucket 42: Getting block 43 of 206 Reserving size (31083) for bucket 43 Calculating Z arrays for bucket 43 Sorting block time: 00:00:00 Returning block of 22824 for bucket 20 Entering block accumulator loop for bucket 43: Sorting block time: 00:00:00 Returning block of 23566 for bucket 13 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 22968 for bucket 19 Sorting block time: 00:00:00 Returning block of 24121 for bucket 23 Returning block of 17929 for bucket 10 Sorting block time: 00:00:00 Returning block of 26653 for bucket 21 bucket 30: 40% bucket 37: 20% bucket 38: 20% Getting block 44 of 206 Reserving size (31083) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: Getting block 45 of 206 Reserving size (31083) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Sorting block time: 00:00:00 Returning block of 25781 for bucket 27 Getting block 46 of 206 Reserving size (31083) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: bucket 36: 20% Getting block 47 of 206 Reserving size (31083) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: Reserving size (31083) for bucket 3 Reserving size (31083) for bucket 4 Getting block 6 of 208 Getting block 7 of 208 Getting block 8 of 208 Getting block 9 of 208 Reserving size (31083) for bucket 5 Getting block 10 of 208 Getting block 11 of 208 Getting block 48 of 206 Reserving size (31083) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: bucket 34: 10% bucket 35: 20% bucket 39: 10% bucket 41: 10% bucket 28: 50% bucket 42: 10% bucket 40: 10% Getting block 12 of 208 Getting block 13 of 208 Getting block 14 of 208 Getting block 15 of 208 Getting block 16 of 208 bucket 43: 10% bucket 30: 50% bucket 37: 30% bucket 44: 10% bucket 45: 10% bucket 36: 30% bucket 46: 10% Getting block 49 of 206 Reserving size (31083) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: bucket 47: 10% bucket 48: 10% bucket 35: 30% Getting block 17 of 208 bucket 41: 20% bucket 28: 60% bucket 42: 20% bucket 30: 60% bucket 33: 30% bucket 37: 40% Getting block 18 of 208 Sorting block time: 00:00:00 Returning block of 30809 for bucket 25 bucket 32: 30% Getting block 50 of 206 Reserving size (31083) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 40: 20% bucket 36: 40% Entering block accumulator loop for bucket 1: Getting block 19 of 208 Calculating Z arrays for bucket 2 bucket 45: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 46: 20% bucket 49: 10% Getting block 20 of 208 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 4 Reserving size (31083) for bucket 6 Reserving size (31083) for bucket 7 Reserving size (31083) for bucket 8 Reserving size (31083) for bucket 9 Calculating Z arrays for bucket 5 Reserving size (31083) for bucket 10 Reserving size (31083) for bucket 11 Reserving size (31083) for bucket 12 Reserving size (31083) for bucket 13 Reserving size (31083) for bucket 14 Reserving size (31083) for bucket 15 Reserving size (31083) for bucket 16 Reserving size (31083) for bucket 17 Reserving size (31083) for bucket 18 bucket 29: 40% Getting block 51 of 206 bucket 48: 20% Getting block 21 of 208 Reserving size (31083) for bucket 19 Entering block accumulator loop for bucket 2: Getting block 22 of 208 Getting block 23 of 208 Getting block 24 of 208 Getting block 25 of 208 Getting block 26 of 208 Getting block 27 of 208 Reserving size (31083) for bucket 20 Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 4: Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 9 Entering block accumulator loop for bucket 5: 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 Reserving size (31083) for bucket 21 Calculating Z arrays for bucket 19 bucket 31: 30% bucket 38: 30% Returning block of 23257 for bucket 17 bucket 39: 20% Returning block of 30075 for bucket 16 bucket 47: 20% bucket 34: 20% bucket 28: 70% bucket 30: 70% bucket 37: 50% bucket 50: 10% bucket 36: 50% bucket 42: 30% bucket 45: 30% Reserving size (31083) for bucket 51 Reserving size (31083) for bucket 22 Reserving size (31083) for bucket 23 Reserving size (31083) for bucket 24 Reserving size (31083) for bucket 25 Reserving size (31083) for bucket 26 Reserving size (31083) for bucket 27 bucket 46: 30% Calculating Z arrays for bucket 20 bucket 49: 20% bucket 41: 30% bucket 35: 40% bucket 29: 50% bucket 48: 30% Entering block accumulator loop for bucket 6: Getting block 52 of 206 Entering block accumulator loop for bucket 8: bucket 33: 40% Entering block accumulator loop for bucket 7: 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: Calculating Z arrays for bucket 51 bucket 40: 30% 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: bucket 1: 10% bucket 32: 40% Entering block accumulator loop for bucket 17: Calculating Z arrays for bucket 21 bucket 43: 20% Entering block accumulator loop for bucket 18: bucket 28: 80% Entering block accumulator loop for bucket 19: bucket 31: 40% Calculating Z arrays for bucket 22 bucket 30: 80% Calculating Z arrays for bucket 23 bucket 38: 40% bucket 37: 60% bucket 34: 30% bucket 36: 60% bucket 42: 40% Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 26 Calculating Z arrays for bucket 25 Calculating Z arrays for bucket 27 bucket 2: 10% Entering block accumulator loop for bucket 20: bucket 47: 30% bucket 45: 40% bucket 50: 20% Reserving size (31083) for bucket 52 bucket 46: 40% Entering block accumulator loop for bucket 51: Getting block 53 of 206 bucket 44: 20% bucket 3: 10% bucket 39: 30% bucket 41: 40% bucket 29: 60% bucket 35: 50% bucket 33: 50% bucket 48: 40% bucket 40: 40% bucket 32: 50% bucket 30: 90% bucket 4: 10% bucket 5: 10% bucket 1: 20% bucket 31: 50% bucket 38: 50% bucket 28: 90% bucket 36: 70% bucket 37: 70% bucket 34: 40% bucket 42: 50% bucket 49: 30% Calculating Z arrays for bucket 52 Getting block 54 of 206 Reserving size (31083) for bucket 53 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 26: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 27: bucket 2: 20% bucket 6: 10% bucket 8: 10% bucket 7: 10% bucket 10: 10% bucket 9: 10% bucket 3: 20% bucket 12: 10% bucket 43: 30% bucket 45: 50% bucket 50: 30% bucket 46: 50% bucket 41: 50% bucket 11: 10% bucket 39: 40% bucket 13: 10% bucket 1: 30% bucket 29: 70% bucket 30: 100% bucket 33: 60% bucket 35: 60% bucket 32: 60% bucket 40: 50% bucket 48: 50% Entering block accumulator loop for bucket 52: Reserving size (31083) for bucket 54 Calculating Z arrays for bucket 53 bucket 28: 100% bucket 4: 20% bucket 5: 20% bucket 14: 10% bucket 15: 10% bucket 16: 10% bucket 17: 10% bucket 2: 30% bucket 6: 20% bucket 8: 20% bucket 10: 20% bucket 9: 20% bucket 31: 60% bucket 38: 60% bucket 36: 80% bucket 37: 80% bucket 34: 50% bucket 42: 60% bucket 47: 40% bucket 51: 10% bucket 44: 30% bucket 7: 20% bucket 18: 10% bucket 19: 10% bucket 3: 30% bucket 20: 10% bucket 12: 20% bucket 11: 20% bucket 13: 20% bucket 1: 40% bucket 49: 40% bucket 4: 30% bucket 41: 60% bucket 5: 30% bucket 2: 40% bucket 14: 20% bucket 8: 30% bucket 43: 40% bucket 45: 60% bucket 46: 60% Sorting block of length 10249 for bucket 30 (Using difference cover) bucket 9: 30% bucket 10: 30% bucket 15: 20% bucket 16: 20% Sorting block time: 00:00:00 Calculating Z arrays for bucket 54 bucket 50: 40% Sorting block of length 12820 for bucket 28 (Using difference cover) Entering block accumulator loop for bucket 53: bucket 39: 50% bucket 29: 80% bucket 21: 10% bucket 33: 70% bucket 22: 10% bucket 32: 70% bucket 17: 20% bucket 35: 70% bucket 40: 60% bucket 48: 60% bucket 26: 10% bucket 23: 10% bucket 24: 10% bucket 27: 10% bucket 25: 10% bucket 6: 30% Sorting block time: 00:00:00 bucket 31: 70% bucket 38: 70% bucket 36: 90% bucket 34: 60% bucket 42: 70% bucket 37: 90% bucket 47: 50% bucket 51: 20% bucket 44: 40% Returning block of 10250 for bucket 30 bucket 41: 70% bucket 7: 30% bucket 49: 50% Entering block accumulator loop for bucket 54: bucket 43: 50% bucket 45: 70% bucket 46: 70% Returning block of 12821 for bucket 28 bucket 50: 50% bucket 39: 60% bucket 3: 40% bucket 18: 20% bucket 19: 20% bucket 12: 30% bucket 11: 30% bucket 20: 20% bucket 1: 50% bucket 2: 50% bucket 29: 90% bucket 32: 80% bucket 33: 80% bucket 35: 80% bucket 4: 40% bucket 5: 40% bucket 13: 30% bucket 40: 70% bucket 48: 70% bucket 52: 10% bucket 14: 30% bucket 8: 40% bucket 9: 40% bucket 10: 40% bucket 15: 30% bucket 16: 30% bucket 17: 30% bucket 21: 20% bucket 22: 20% bucket 26: 20% bucket 23: 20% bucket 24: 20% bucket 25: 20% bucket 27: 20% bucket 31: 80% bucket 38: 80% bucket 34: 70% bucket 42: 80% bucket 36: 100% bucket 37: 100% bucket 44: 50% bucket 51: 30% bucket 47: 60% bucket 41: 80% bucket 43: 60% bucket 7: 40% bucket 49: 60% bucket 45: 80% bucket 46: 80% bucket 50: 60% bucket 53: 10% bucket 39: 70% bucket 3: 50% bucket 12: 40% bucket 11: 40% bucket 18: 30% bucket 19: 30% bucket 20: 30% bucket 6: 40% bucket 1: 60% bucket 2: 60% bucket 29: 100% bucket 32: 90% bucket 33: 90% bucket 35: 90% bucket 4: 50% bucket 5: 50% bucket 13: 40% bucket 8: 50% bucket 9: 50% bucket 10: 50% bucket 14: 40% bucket 15: 40% bucket 16: 40% bucket 21: 30% bucket 17: 40% bucket 22: 30% Getting block 55 of 206 bucket 26: 30% bucket 40: 80% bucket 23: 30% bucket 48: 80% Sorting block of length 22433 for bucket 36 (Using difference cover) Sorting block of length 24856 for bucket 37 (Using difference cover) bucket 52: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 56 of 206 bucket 24: 30% bucket 27: 30% bucket 25: 30% bucket 31: 90% bucket 38: 90% bucket 42: 90% bucket 34: 80% bucket 44: 60% bucket 54: 10% bucket 51: 40% bucket 43: 70% bucket 41: 90% bucket 47: 70% bucket 7: 50% bucket 49: 70% bucket 45: 90% bucket 3: 60% bucket 12: 50% bucket 11: 50% bucket 1: 70% bucket 18: 40% bucket 19: 40% bucket 2: 70% bucket 20: 40% bucket 6: 50% bucket 4: 60% bucket 5: 60% bucket 8: 60% bucket 13: 50% bucket 9: 60% bucket 10: 60% bucket 14: 50% bucket 15: 50% bucket 16: 50% bucket 21: 40% bucket 22: 40% bucket 17: 50% bucket 23: 40% bucket 26: 40% bucket 24: 40% Sorting block of length 27101 for bucket 29 bucket 27: 40% (Using difference cover) bucket 25: 40% bucket 46: 90% bucket 50: 70% bucket 39: 80% bucket 53: 20% bucket 32: 100% Sorting block time: 00:00:00 bucket 33: 100% bucket 35: 100% Reserving size (31083) for bucket 55 Returning block of 22434 for bucket 36 Returning block of 24857 for bucket 37 bucket 40: 90% bucket 7: 60% bucket 1: 80% bucket 2: 80% Reserving size (31083) for bucket 56 bucket 48: 90% bucket 52: 30% bucket 4: 70% bucket 3: 70% bucket 5: 70% bucket 12: 60% bucket 11: 60% bucket 6: 60% bucket 18: 50% bucket 19: 50% bucket 20: 50% bucket 31: 100% bucket 43: 80% bucket 44: 70% bucket 8: 70% bucket 9: 70% bucket 10: 70% bucket 13: 60% bucket 14: 60% bucket 15: 60% bucket 16: 60% bucket 21: 50% bucket 38: 100% bucket 42: 100% bucket 41: 100% bucket 47: 80% bucket 22: 50% bucket 17: 60% bucket 26: 50% bucket 23: 50% bucket 24: 50% bucket 27: 50% bucket 25: 50% bucket 51: 50% bucket 54: 20% bucket 34: 90% bucket 1: 90% bucket 49: 80% bucket 2: 90% bucket 45: 100% Sorting block of length 24734 for bucket 32 (Using difference cover) Returning block of 27102 for bucket 29 Sorting block of length 19857 for bucket 33 (Using difference cover) Sorting block of length 28576 for bucket 35 (Using difference cover) Calculating Z arrays for bucket 55 Calculating Z arrays for bucket 56 bucket 39: 90% bucket 46: 100% bucket 50: 80% bucket 40: 100% bucket 7: 70% bucket 52: 40% bucket 48: 100% Sorting block of length 26029 for bucket 31 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 30778 for bucket 38 bucket 4: 80% (Using difference cover) bucket 3: 80% Sorting block of length 19093 for bucket 42 bucket 5: 80% (Using difference cover) bucket 6: 70% Sorting block of length 28090 for bucket 41 bucket 11: 70% (Using difference cover) bucket 12: 70% bucket 18: 60% bucket 19: 60% bucket 20: 60% bucket 53: 30% bucket 43: 90% bucket 44: 80% bucket 47: 90% Sorting block of length 25946 for bucket 45 (Using difference cover) Getting block 57 of 206 Entering block accumulator loop for bucket 55: Entering block accumulator loop for bucket 56: Sorting block of length 27445 for bucket 46 (Using difference cover) Sorting block of length 24124 for bucket 40 (Using difference cover) bucket 8: 80% bucket 9: 80% bucket 10: 80% bucket 14: 70% bucket 34: 100% bucket 13: 70% bucket 15: 70% bucket 21: 60% bucket 16: 70% Sorting block time: 00:00:00 bucket 51: 60% bucket 54: 30% Sorting block of length 29120 for bucket 48 (Using difference cover) Returning block of 19858 for bucket 33 Returning block of 24735 for bucket 32 Returning block of 28577 for bucket 35 bucket 49: 90% bucket 39: 100% bucket 17: 70% bucket 50: 90% bucket 22: 60% bucket 26: 60% 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 Getting block 58 of 206 bucket 52: 50% Reserving size (31083) for bucket 57 Getting block 59 of 206 Sorting block of length 21317 for bucket 34 (Using difference cover) Returning block of 26030 for bucket 31 Sorting block of length 13748 for bucket 39 (Using difference cover) bucket 23: 60% bucket 24: 60% bucket 25: 60% bucket 27: 60% bucket 1: 100% bucket 2: 100% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 43: 100% bucket 47: 100% bucket 53: 40% Returning block of 19094 for bucket 42 Returning block of 24125 for bucket 40 Returning block of 25947 for bucket 45 Returning block of 27446 for bucket 46 Returning block of 28091 for bucket 41 bucket 54: 40% bucket 51: 70% Returning block of 29121 for bucket 48 bucket 7: 80% Returning block of 30779 for bucket 38 bucket 4: 90% bucket 49: 100% bucket 3: 90% bucket 5: 90% bucket 6: 80% bucket 11: 80% bucket 12: 80% bucket 18: 70% bucket 19: 70% bucket 20: 70% Reserving size (31083) for bucket 58 Calculating Z arrays for bucket 57 Reserving size (31083) for bucket 59 Returning block of 13749 for bucket 39 bucket 8: 90% bucket 9: 90% bucket 10: 90% Returning block of 21318 for bucket 34 bucket 14: 80% Getting block 60 of 206 Getting block 61 of 206 bucket 44: 90% bucket 55: 10% bucket 13: 80% bucket 15: 80% bucket 21: 70% bucket 16: 80% bucket 17: 80% Sorting block of length 12825 for bucket 1 (Using difference cover) Sorting block of length 23586 for bucket 2 (Using difference cover) bucket 22: 70% bucket 26: 70% bucket 23: 70% bucket 24: 70% bucket 25: 70% bucket 27: 70% bucket 4: 100% Getting block 62 of 206 Sorting block of length 23477 for bucket 43 (Using difference cover) bucket 56: 10% Sorting block of length 23616 for bucket 47 (Using difference cover) bucket 52: 60% Sorting block of length 23846 for bucket 49 (Using difference cover) Sorting block time: 00:00:00 Calculating Z arrays for bucket 58 Calculating Z arrays for bucket 59 Getting block 63 of 206 Entering block accumulator loop for bucket 57: Reserving size (31083) for bucket 60 Sorting block time: 00:00:00 bucket 7: 90% bucket 3: 100% bucket 5: 100% bucket 6: 90% bucket 11: 90% bucket 12: 90% bucket 18: 80% bucket 19: 80% bucket 20: 80% Sorting block time: 00:00:00 bucket 54: 50% bucket 50: 100% Reserving size (31083) for bucket 61 bucket 51: 80% Sorting block time: 00:00:00 bucket 8: 100% bucket 9: 100% bucket 14: 90% bucket 10: 100% Sorting block time: 00:00:00 bucket 44: 100% bucket 55: 20% bucket 13: 90% Reserving size (31083) for bucket 62 bucket 15: 90% Getting block 64 of 206 bucket 16: 90% Returning block of 23478 for bucket 43 bucket 21: 80% Getting block 65 of 206 Getting block 66 of 206 bucket 17: 90% Getting block 67 of 206 Sorting block of length 3763 for bucket 4 (Using difference cover) bucket 22: 80% Returning block of 23587 for bucket 2 bucket 26: 80% bucket 23: 80% bucket 24: 80% bucket 25: 80% Getting block 68 of 206 Getting block 69 of 206 Getting block 70 of 206 Entering block accumulator loop for bucket 58: Reserving size (31083) for bucket 63 Entering block accumulator loop for bucket 59: Getting block 71 of 206 Calculating Z arrays for bucket 60 Getting block 72 of 206 Returning block of 23617 for bucket 47 bucket 56: 20% bucket 52: 70% Sorting block of length 24067 for bucket 50 (Using difference cover) Calculating Z arrays for bucket 61 Returning block of 23847 for bucket 49 bucket 53: 50% Sorting block of length 24572 for bucket 44 (Using difference cover) Sorting block time: 00:00:00 Sorting block of length 29386 for bucket 3 (Using difference cover) Sorting block of length 27986 for bucket 5 (Using difference cover) bucket 27: 80% Returning block of 12826 for bucket 1 bucket 6: 100% bucket 7: 100% bucket 11: 100% Sorting block of length 10734 for bucket 8 (Using difference cover) Sorting block time: 00:00:00 bucket 54: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 30647 for bucket 9 (Using difference cover) bucket 12: 100% Sorting block of length 20194 for bucket 10 (Using difference cover) bucket 18: 90% bucket 19: 90% bucket 20: 90% bucket 14: 100% Returning block of 3764 for bucket 4 bucket 13: 100% Sorting block time: 00:00:00 bucket 51: 90% bucket 55: 30% bucket 15: 100% bucket 16: 100% bucket 21: 90% bucket 17: 100% bucket 22: 90% bucket 26: 90% bucket 23: 90% bucket 24: 90% bucket 25: 90% Sorting block of length 29884 for bucket 6 (Using difference cover) Sorting block of length 29681 for bucket 7 (Using difference cover) Sorting block of length 29345 for bucket 11 (Using difference cover) Returning block of 10735 for bucket 8 Returning block of 27987 for bucket 5 Sorting block of length 13714 for bucket 12 (Using difference cover) Sorting block of length 7956 for bucket 14 (Using difference cover) Getting block 28 of 208 bucket 27: 90% Sorting block of length 23857 for bucket 13 (Using difference cover) bucket 19: 100% Sorting block of length 30277 for bucket 15 (Using difference cover) Sorting block of length 26996 for bucket 16 (Using difference cover) Sorting block of length 19504 for bucket 17 (Using difference cover) bucket 20: 100% Getting block 29 of 208 bucket 18: 100% Reserving size (31083) for bucket 28 Getting block 30 of 208 Sorting block of length 22188 for bucket 19 (Using difference cover) Sorting block of length 25058 for bucket 20 (Using difference cover) Reserving size (31083) for bucket 29 Sorting block of length 27053 for bucket 18 Calculating Z arrays for bucket 28 (Using difference cover) Getting block 31 of 208 Getting block 32 of 208 Reserving size (31083) for bucket 30 Calculating Z arrays for bucket 29 Reserving size (31083) for bucket 31 Entering block accumulator loop for bucket 28: Reserving size (31083) for bucket 32 Calculating Z arrays for bucket 30 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 29: Calculating Z arrays for bucket 32 Calculating Z arrays for bucket 62 Reserving size (31083) for bucket 64 Reserving size (31083) for bucket 65 Reserving size (31083) for bucket 66 Reserving size (31083) for bucket 67 Reserving size (31083) for bucket 68 Reserving size (31083) for bucket 69 Reserving size (31083) for bucket 70 Calculating Z arrays for bucket 63 Reserving size (31083) for bucket 71 Reserving size (31083) for bucket 72 Entering block accumulator loop for bucket 60: Entering block accumulator loop for bucket 61: Returning block of 24573 for bucket 44 bucket 52: 80% bucket 57: 10% bucket 56: 30% bucket 21: 100% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 30: bucket 22: 100% Returning block of 24068 for bucket 50 bucket 53: 60% bucket 54: 70% bucket 55: 40% Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 31: Entering block accumulator loop for bucket 62: Calculating Z arrays for bucket 65 Calculating Z arrays for bucket 66 Calculating Z arrays for bucket 67 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 32: Calculating Z arrays for bucket 69 Calculating Z arrays for bucket 70 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 63: Calculating Z arrays for bucket 72 Getting block 73 of 206 Getting block 74 of 206 Getting block 75 of 206 bucket 51: 100% bucket 59: 10% bucket 58: 10% bucket 56: 40% bucket 57: 20% bucket 52: 90% Entering block accumulator loop for bucket 64: Entering block accumulator loop for bucket 65: bucket 26: 100% bucket 23: 100% Entering block accumulator loop for bucket 66: Entering block accumulator loop for bucket 67: Entering block accumulator loop for bucket 68: Entering block accumulator loop for bucket 69: Entering block accumulator loop for bucket 70: Entering block accumulator loop for bucket 71: Reserving size (31083) for bucket 73 Entering block accumulator loop for bucket 72: Reserving size (31083) for bucket 74 Reserving size (31083) for bucket 75 Sorting block of length 25993 for bucket 51 (Using difference cover) Getting block 76 of 206 bucket 53: 70% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 25: 100% bucket 54: 80% Getting block 77 of 206 bucket 55: 50% bucket 60: 10% bucket 61: 10% bucket 59: 20% Sorting block time: 00:00:00 bucket 27: 100% Sorting block of length 18346 for bucket 21 (Using difference cover) Sorting block time: 00:00:00 bucket 56: 50% bucket 57: 30% Calculating Z arrays for bucket 73 Calculating Z arrays for bucket 74 Calculating Z arrays for bucket 75 Reserving size (31083) for bucket 76 bucket 52: 100% Reserving size (31083) for bucket 77 bucket 62: 10% Returning block of 25994 for bucket 51 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 28: 10% bucket 63: 10% bucket 53: 80% bucket 58: 20% bucket 54: 90% bucket 64: 10% bucket 55: 60% bucket 60: 20% bucket 61: 20% Sorting block time: 00:00:00 Returning block of 13715 for bucket 12 Returning block of 23858 for bucket 13 bucket 65: 10% bucket 59: 30% Entering block accumulator loop for bucket 73: Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 74: Entering block accumulator loop for bucket 75: Sorting block of length 29578 for bucket 52 (Using difference cover) Calculating Z arrays for bucket 77 bucket 56: 60% bucket 57: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 28839 for bucket 22 (Using difference cover) bucket 24: 100% Sorting block of length 4776 for bucket 26 (Using difference cover) Sorting block of length 24521 for bucket 23 (Using difference cover) Sorting block time: 00:00:00 Returning block of 29346 for bucket 11 bucket 29: 10% Returning block of 19505 for bucket 17 Returning block of 26997 for bucket 16 Sorting block time: 00:00:00 bucket 68: 10% bucket 69: 10% bucket 66: 10% bucket 67: 10% bucket 70: 10% bucket 71: 10% bucket 62: 20% bucket 72: 10% Entering block accumulator loop for bucket 76: Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 29788 for bucket 27 (Using difference cover) Returning block of 30648 for bucket 9 bucket 58: 30% bucket 53: 90% bucket 54: 100% Getting block 78 of 206 Entering block accumulator loop for bucket 77: bucket 63: 20% bucket 64: 20% bucket 55: 70% Sorting block time: 00:00:00 Returning block of 29885 for bucket 6 Sorting block of length 28441 for bucket 25 (Using difference cover) Returning block of 20195 for bucket 10 Returning block of 29387 for bucket 3 bucket 28: 20% Returning block of 18347 for bucket 21 Returning block of 22189 for bucket 19 Sorting block of length 30287 for bucket 24 (Using difference cover) Returning block of 29682 for bucket 7 bucket 31: 10% bucket 60: 30% bucket 61: 30% bucket 59: 40% Returning block of 29579 for bucket 52 bucket 65: 20% bucket 56: 70% bucket 57: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 30: 10% bucket 68: 20% Sorting block of length 21516 for bucket 54 (Using difference cover) Reserving size (31083) for bucket 78 bucket 32: 10% Returning block of 27054 for bucket 18 Sorting block time: 00:00:00 bucket 62: 30% bucket 66: 20% bucket 67: 20% bucket 72: 20% bucket 70: 20% bucket 74: 10% bucket 71: 20% bucket 73: 10% bucket 58: 40% bucket 53: 100% Sorting block time: 00:00:00 Returning block of 4777 for bucket 26 Returning block of 30278 for bucket 15 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 29: 20% bucket 55: 80% Returning block of 7957 for bucket 14 Getting block 33 of 208 Getting block 34 of 208 Returning block of 24522 for bucket 23 bucket 63: 30% Returning block of 25059 for bucket 20 bucket 64: 30% bucket 31: 20% bucket 59: 50% Returning block of 29789 for bucket 27 bucket 61: 40% bucket 28: 30% bucket 56: 80% bucket 57: 60% bucket 76: 10% Calculating Z arrays for bucket 78 bucket 75: 10% bucket 65: 30% bucket 69: 20% Returning block of 21517 for bucket 54 Sorting block of length 26338 for bucket 53 (Using difference cover) Getting block 79 of 206 bucket 60: 40% Getting block 35 of 208 Getting block 36 of 208 Getting block 37 of 208 Returning block of 28840 for bucket 22 bucket 30: 20% bucket 32: 20% Sorting block time: 00:00:00 bucket 68: 30% bucket 58: 50% bucket 62: 40% bucket 66: 30% bucket 72: 30% bucket 67: 30% bucket 70: 30% bucket 73: 20% Entering block accumulator loop for bucket 78: Reserving size (31083) for bucket 79 Returning block of 30288 for bucket 24 Returning block of 28442 for bucket 25 Getting block 38 of 208 bucket 77: 10% bucket 55: 90% bucket 59: 60% bucket 56: 90% Reserving size (31083) for bucket 33 bucket 61: 50% Reserving size (31083) for bucket 34 bucket 63: 40% bucket 64: 40% bucket 74: 20% bucket 76: 20% Returning block of 26339 for bucket 53 bucket 75: 20% bucket 57: 70% Calculating Z arrays for bucket 79 Getting block 80 of 206 bucket 71: 30% Getting block 39 of 208 Getting block 40 of 208 Getting block 41 of 208 Getting block 42 of 208 Getting block 43 of 208 Getting block 44 of 208 bucket 58: 60% bucket 29: 30% bucket 31: 30% bucket 28: 40% bucket 68: 40% bucket 62: 50% bucket 66: 40% bucket 72: 40% bucket 70: 40% bucket 67: 40% bucket 73: 30% Entering block accumulator loop for bucket 79: Reserving size (31083) for bucket 80 bucket 65: 40% bucket 69: 30% bucket 60: 50% Reserving size (31083) for bucket 35 Reserving size (31083) for bucket 36 Reserving size (31083) for bucket 37 bucket 59: 70% bucket 56: 100% bucket 61: 60% bucket 55: 100% Getting block 45 of 208 Getting block 46 of 208 bucket 63: 50% bucket 64: 50% bucket 76: 30% bucket 75: 30% bucket 78: 10% bucket 57: 80% bucket 71: 40% bucket 77: 20% bucket 58: 70% bucket 30: 30% bucket 32: 30% Getting block 47 of 208 Reserving size (31083) for bucket 38 Calculating Z arrays for bucket 33 Calculating Z arrays for bucket 34 Calculating Z arrays for bucket 80 Getting block 81 of 206 bucket 74: 30% Reserving size (31083) for bucket 39 Reserving size (31083) for bucket 40 Reserving size (31083) for bucket 41 Reserving size (31083) for bucket 42 Reserving size (31083) for bucket 43 Reserving size (31083) for bucket 44 Getting block 48 of 208 Getting block 49 of 208 Getting block 50 of 208 bucket 28: 50% Calculating Z arrays for bucket 35 bucket 31: 40% bucket 29: 40% bucket 60: 60% bucket 62: 60% bucket 65: 50% Calculating Z arrays for bucket 36 Calculating Z arrays for bucket 37 bucket 68: 50% Getting block 51 of 208 bucket 72: 50% Reserving size (31083) for bucket 45 bucket 66: 50% bucket 69: 40% Sorting block of length 21204 for bucket 56 (Using difference cover) Reserving size (31083) for bucket 46 Getting block 52 of 208 Reserving size (31083) for bucket 47 Calculating Z arrays for bucket 38 Sorting block of length 15411 for bucket 55 (Using difference cover) bucket 70: 50% bucket 73: 40% bucket 67: 50% Entering block accumulator loop for bucket 33: Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 59: 80% Entering block accumulator loop for bucket 34: bucket 61: 70% bucket 30: 40% bucket 57: 90% bucket 32: 40% bucket 58: 80% bucket 63: 60% bucket 64: 60% bucket 76: 40% bucket 78: 20% bucket 71: 50% bucket 75: 40% bucket 79: 10% Getting block 53 of 208 Getting block 54 of 208 Calculating Z arrays for bucket 39 Calculating Z arrays for bucket 40 Calculating Z arrays for bucket 41 Calculating Z arrays for bucket 42 Calculating Z arrays for bucket 43 Calculating Z arrays for bucket 44 Reserving size (31083) for bucket 48 Reserving size (31083) for bucket 49 Reserving size (31083) for bucket 50 Entering block accumulator loop for bucket 35: bucket 28: 60% bucket 31: 50% bucket 29: 50% Entering block accumulator loop for bucket 80: Reserving size (31083) for bucket 81 bucket 74: 40% bucket 77: 30% bucket 60: 70% bucket 62: 70% Returning block of 21205 for bucket 56 Entering block accumulator loop for bucket 36: Entering block accumulator loop for bucket 37: Reserving size (31083) for bucket 51 Calculating Z arrays for bucket 45 Calculating Z arrays for bucket 46 Reserving size (31083) for bucket 52 Returning block of 15412 for bucket 55 bucket 68: 60% bucket 72: 60% bucket 69: 50% bucket 66: 60% bucket 67: 60% bucket 70: 60% bucket 73: 50% Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 38: Reserving size (31083) for bucket 53 Reserving size (31083) for bucket 54 bucket 59: 90% bucket 30: 50% bucket 57: 100% bucket 58: 90% bucket 61: 80% bucket 65: 60% bucket 63: 70% bucket 64: 70% bucket 76: 50% bucket 78: 30% bucket 71: 60% bucket 75: 50% bucket 79: 20% Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 39: Entering block accumulator loop for bucket 40: Entering block accumulator loop for bucket 41: Entering block accumulator loop for bucket 42: Entering block accumulator loop for bucket 43: Calculating Z arrays for bucket 48 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 44: Calculating Z arrays for bucket 50 bucket 31: 60% bucket 60: 80% bucket 62: 80% bucket 74: 50% bucket 29: 60% Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 45: bucket 32: 50% bucket 28: 70% Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 46: bucket 68: 70% bucket 69: 60% bucket 72: 70% bucket 66: 70% Sorting block of length 16378 for bucket 57 (Using difference cover) bucket 67: 70% bucket 70: 70% bucket 73: 60% Getting block 82 of 206 Entering block accumulator loop for bucket 81: bucket 77: 40% Entering block accumulator loop for bucket 47: Calculating Z arrays for bucket 53 Calculating Z arrays for bucket 54 Sorting block time: 00:00:00 bucket 59: 100% bucket 58: 100% bucket 33: 10% bucket 61: 90% bucket 34: 10% bucket 63: 80% bucket 64: 80% bucket 78: 40% bucket 71: 70% bucket 76: 60% bucket 75: 60% bucket 65: 70% bucket 80: 10% Entering block accumulator loop for bucket 48: Entering block accumulator loop for bucket 49: Entering block accumulator loop for bucket 50: bucket 31: 70% bucket 60: 90% bucket 62: 90% Entering block accumulator loop for bucket 51: bucket 35: 10% Entering block accumulator loop for bucket 52: bucket 29: 70% bucket 30: 60% Entering block accumulator loop for bucket 53: Entering block accumulator loop for bucket 54: bucket 32: 60% bucket 28: 80% bucket 37: 10% bucket 36: 10% bucket 38: 10% bucket 41: 10% Getting block 83 of 206 Reserving size (31083) for bucket 82 bucket 40: 10% bucket 39: 10% bucket 33: 20% bucket 34: 20% bucket 74: 60% bucket 79: 30% Returning block of 16379 for bucket 57 bucket 68: 80% bucket 66: 80% bucket 69: 70% bucket 31: 80% bucket 42: 10% bucket 43: 10% bucket 44: 10% bucket 45: 10% bucket 29: 80% Sorting block of length 28804 for bucket 59 bucket 35: 20% (Using difference cover) bucket 72: 80% Sorting block of length 24027 for bucket 58 (Using difference cover) bucket 67: 80% bucket 70: 80% bucket 73: 70% Sorting block time: 00:00:00 bucket 61: 100% bucket 65: 80% bucket 64: 90% bucket 28: 90% bucket 30: 70% bucket 32: 70% bucket 37: 20% bucket 41: 20% bucket 36: 20% bucket 46: 10% bucket 47: 10% bucket 38: 20% bucket 33: 30% Sorting block time: 00:00:00 bucket 63: 90% bucket 80: 20% bucket 78: 50% bucket 71: 80% bucket 76: 70% bucket 75: 70% bucket 77: 50% bucket 40: 20% bucket 34: 30% bucket 60: 100% bucket 62: 100% Reserving size (31083) for bucket 83 Calculating Z arrays for bucket 82 bucket 81: 10% bucket 68: 90% bucket 66: 90% bucket 69: 80% bucket 74: 70% bucket 79: 40% bucket 39: 20% bucket 48: 10% bucket 31: 90% bucket 42: 20% bucket 43: 20% bucket 45: 20% bucket 44: 20% bucket 49: 10% bucket 51: 10% bucket 50: 10% bucket 52: 10% bucket 29: 90% bucket 35: 30% bucket 54: 10% bucket 53: 10% Returning block of 28805 for bucket 59 Sorting block of length 22483 for bucket 61 (Using difference cover) bucket 72: 90% Returning block of 24028 for bucket 58 bucket 64: 100% bucket 67: 90% bucket 70: 90% bucket 73: 80% bucket 65: 90% Sorting block of length 23207 for bucket 60 (Using difference cover) Sorting block of length 21761 for bucket 62 (Using difference cover) Calculating Z arrays for bucket 83 Getting block 84 of 206 bucket 28: 100% bucket 30: 80% Entering block accumulator loop for bucket 82: bucket 32: 80% bucket 33: 40% bucket 41: 30% bucket 36: 30% bucket 46: 20% bucket 38: 30% bucket 47: 20% bucket 34: 40% bucket 40: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 63: 100% bucket 80: 30% bucket 78: 60% bucket 71: 90% bucket 76: 80% bucket 75: 80% bucket 77: 60% bucket 68: 100% bucket 81: 20% bucket 69: 90% bucket 37: 30% bucket 31: 100% bucket 43: 30% bucket 42: 30% bucket 45: 30% bucket 74: 80% bucket 66: 100% bucket 79: 50% Sorting block of length 22946 for bucket 64 (Using difference cover) Entering block accumulator loop for bucket 83: Reserving size (31083) for bucket 84 Returning block of 22484 for bucket 61 Returning block of 23208 for bucket 60 Returning block of 21762 for bucket 62 bucket 72: 100% bucket 67: 100% bucket 39: 30% bucket 48: 20% bucket 44: 30% bucket 51: 20% bucket 52: 20% bucket 49: 20% bucket 50: 20% bucket 29: 100% bucket 35: 40% bucket 70: 100% Sorting block of length 28627 for bucket 63 (Using difference cover) Sorting block of length 22379 for bucket 68 (Using difference cover) bucket 73: 90% bucket 65: 100% Sorting block of length 27267 for bucket 66 (Using difference cover) Getting block 85 of 206 Sorting block time: 00:00:00 bucket 80: 40% Calculating Z arrays for bucket 84 Getting block 86 of 206 Sorting block of length 4335 for bucket 72 (Using difference cover) Sorting block of length 19106 for bucket 28 (Using difference cover) bucket 54: 20% bucket 53: 20% bucket 30: 90% bucket 32: 90% bucket 33: 50% bucket 41: 40% bucket 34: 50% bucket 36: 40% bucket 40: 40% 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 of length 29241 for bucket 67 (Using difference cover) bucket 69: 100% Sorting block time: 00:00:00 Sorting block of length 10701 for bucket 31 (Using difference cover) bucket 46: 30% bucket 38: 40% bucket 47: 30% bucket 81: 30% bucket 78: 70% bucket 71: 100% bucket 76: 90% bucket 77: 70% Sorting block of length 17460 for bucket 70 (Using difference cover) Sorting block of length 15797 for bucket 65 (Using difference cover) Reserving size (31083) for bucket 85 Returning block of 22947 for bucket 64 bucket 37: 40% bucket 42: 40% Sorting block of length 19505 for bucket 29 (Using difference cover) bucket 43: 40% bucket 45: 40% Sorting block time: 00:00:00 bucket 74: 90% bucket 75: 90% bucket 82: 10% bucket 79: 60% Reserving size (31083) for bucket 86 Entering block accumulator loop for bucket 84: Returning block of 4336 for bucket 72 Returning block of 22380 for bucket 68 Returning block of 27268 for bucket 66 Returning block of 28628 for bucket 63 Sorting block of length 13922 for bucket 69 (Using difference cover) bucket 73: 100% bucket 83: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 39: 40% bucket 44: 40% bucket 48: 30% bucket 51: 30% bucket 52: 30% bucket 35: 50% bucket 49: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 80: 50% Sorting block of length 30974 for bucket 71 (Using difference cover) Getting block 87 of 206 Calculating Z arrays for bucket 85 Returning block of 29242 for bucket 67 Getting block 88 of 206 Returning block of 19107 for bucket 28 bucket 50: 30% bucket 30: 100% bucket 32: 100% bucket 33: 60% bucket 34: 60% bucket 41: 50% bucket 36: 50% bucket 54: 30% bucket 40: 50% bucket 53: 30% Getting block 89 of 206 Calculating Z arrays for bucket 86 Returning block of 10702 for bucket 31 Returning block of 19506 for bucket 29 bucket 38: 50% bucket 42: 50% bucket 43: 50% bucket 37: 50% Sorting block time: 00:00:00 Sorting block of length 28526 for bucket 73 bucket 46: 40% (Using difference cover) bucket 47: 40% bucket 81: 40% bucket 45: 50% bucket 78: 80% bucket 76: 100% Returning block of 15798 for bucket 65 bucket 39: 50% Sorting block time: 00:00:00 Returning block of 17461 for bucket 70 Returning block of 13923 for bucket 69 bucket 82: 20% bucket 48: 40% bucket 44: 50% bucket 35: 60% Sorting block of length 28198 for bucket 30 (Using difference cover) Sorting block of length 21686 for bucket 32 (Using difference cover) bucket 49: 40% bucket 51: 40% bucket 52: 40% bucket 74: 100% bucket 34: 70% bucket 33: 70% bucket 41: 60% bucket 36: 60% bucket 54: 40% bucket 75: 100% bucket 79: 70% bucket 77: 80% bucket 83: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 53: 40% bucket 42: 60% bucket 43: 60% bucket 38: 60% bucket 45: 60% bucket 46: 50% Reserving size (31083) for bucket 87 Getting block 90 of 206 Entering block accumulator loop for bucket 85: bucket 39: 60% bucket 50: 40% bucket 47: 50% Reserving size (31083) for bucket 88 Reserving size (31083) for bucket 89 Returning block of 30975 for bucket 71 Entering block accumulator loop for bucket 86: bucket 80: 60% Getting block 91 of 206 Getting block 92 of 206 Getting block 93 of 206 Sorting block of length 27323 for bucket 76 (Using difference cover) Getting block 94 of 206 bucket 44: 60% bucket 48: 50% bucket 35: 70% Returning block of 28527 for bucket 73 bucket 81: 50% bucket 78: 90% bucket 84: 10% Sorting block of length 22437 for bucket 74 (Using difference cover) Sorting block of length 23507 for bucket 75 (Using difference cover) bucket 82: 30% bucket 83: 30% Calculating Z arrays for bucket 87 Reserving size (31083) for bucket 90 Getting block 55 of 208 bucket 49: 50% Sorting block time: 00:00:00 bucket 79: 80% bucket 77: 90% Calculating Z arrays for bucket 88 Calculating Z arrays for bucket 89 Getting block 95 of 206 Reserving size (31083) for bucket 91 Reserving size (31083) for bucket 92 bucket 51: 50% bucket 52: 50% Returning block of 28199 for bucket 30 Returning block of 21687 for bucket 32 bucket 40: 60% bucket 34: 80% bucket 33: 80% bucket 41: 70% bucket 36: 70% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (31083) for bucket 93 Reserving size (31083) for bucket 94 Getting block 96 of 206 Getting block 97 of 206 Getting block 98 of 206 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 87: Returning block of 27324 for bucket 76 Getting block 56 of 208 Getting block 57 of 208 bucket 54: 50% bucket 37: 60% bucket 42: 70% bucket 43: 70% bucket 45: 70% bucket 38: 70% bucket 53: 50% bucket 39: 70% bucket 47: 60% bucket 46: 60% bucket 80: 70% bucket 44: 70% bucket 35: 80% Entering block accumulator loop for bucket 88: Entering block accumulator loop for bucket 89: Reserving size (31083) for bucket 95 Calculating Z arrays for bucket 91 Calculating Z arrays for bucket 92 Returning block of 23508 for bucket 75 bucket 81: 60% Returning block of 22438 for bucket 74 bucket 78: 100% bucket 84: 20% bucket 83: 40% Reserving size (31083) for bucket 55 bucket 48: 60% bucket 49: 60% bucket 85: 10% bucket 50: 50% bucket 34: 90% bucket 33: 90% bucket 41: 80% bucket 51: 60% bucket 36: 80% Reserving size (31083) for bucket 56 Reserving size (31083) for bucket 57 bucket 52: 60% bucket 42: 80% bucket 43: 80% bucket 54: 60% bucket 45: 80% bucket 38: 80% bucket 39: 80% bucket 46: 70% bucket 53: 60% bucket 35: 90% Calculating Z arrays for bucket 93 Calculating Z arrays for bucket 94 Reserving size (31083) for bucket 96 Calculating Z arrays for bucket 55 Getting block 58 of 208 Getting block 59 of 208 bucket 44: 80% Reserving size (31083) for bucket 97 bucket 40: 70% Reserving size (31083) for bucket 98 Entering block accumulator loop for bucket 90: Getting block 99 of 206 bucket 37: 70% bucket 47: 70% bucket 49: 70% bucket 48: 70% bucket 34: 100% bucket 33: 100% bucket 41: 90% bucket 36: 90% bucket 82: 40% bucket 86: 10% bucket 77: 100% bucket 79: 90% Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 91: Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 92: Sorting block of length 13871 for bucket 78 (Using difference cover) Calculating Z arrays for bucket 57 bucket 50: 60% bucket 51: 70% bucket 42: 90% bucket 35: 100% Entering block accumulator loop for bucket 55: Reserving size (31083) for bucket 58 Reserving size (31083) for bucket 59 bucket 43: 90% bucket 38: 90% bucket 39: 90% bucket 45: 90% bucket 54: 70% bucket 46: 80% bucket 52: 70% bucket 80: 80% Sorting block of length 27649 for bucket 34 (Using difference cover) Sorting block of length 18501 for bucket 33 (Using difference cover) bucket 53: 70% bucket 44: 90% bucket 41: 100% bucket 36: 100% Entering block accumulator loop for bucket 56: bucket 49: 80% Sorting block time: 00:00:00 bucket 83: 50% Sorting block time: 00:00:00 bucket 47: 80% bucket 48: 80% Entering block accumulator loop for bucket 57: Sorting block of length 16016 for bucket 35 (Using difference cover) Calculating Z arrays for bucket 58 Calculating Z arrays for bucket 59 bucket 37: 80% Sorting block time: 00:00:00 bucket 42: 100% bucket 43: 100% bucket 45: 100% bucket 38: 100% Sorting block of length 22022 for bucket 41 (Using difference cover) Sorting block of length 18784 for bucket 36 (Using difference cover) bucket 39: 100% bucket 46: 90% bucket 54: 80% bucket 40: 80% bucket 51: 80% bucket 50: 70% bucket 52: 80% Returning block of 18502 for bucket 33 Entering block accumulator loop for bucket 58: Entering block accumulator loop for bucket 59: Returning block of 27650 for bucket 34 Sorting block of length 15333 for bucket 42 (Using difference cover) Sorting block of length 18459 for bucket 43 (Using difference cover) Sorting block of length 9297 for bucket 45 (Using difference cover) bucket 44: 100% Sorting block of length 29837 for bucket 38 (Using difference cover) Sorting block of length 28342 for bucket 39 (Using difference cover) bucket 49: 90% Getting block 100 of 206 bucket 53: 80% bucket 81: 70% bucket 84: 30% bucket 85: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 23070 for bucket 44 (Using difference cover) 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 55: 10% bucket 46: 100% bucket 56: 10% bucket 54: 90% bucket 57: 10% bucket 51: 90% bucket 49: 100% bucket 52: 90% bucket 47: 90% Entering block accumulator loop for bucket 93: Sorting block time: 00:00:00 bucket 50: 80% bucket 48: 90% Returning block of 9298 for bucket 45 Sorting block time: 00:00:00 bucket 37: 90% Returning block of 15334 for bucket 42 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 94: Calculating Z arrays for bucket 97 Calculating Z arrays for bucket 98 Returning block of 16017 for bucket 35 bucket 58: 10% Getting block 60 of 208 Returning block of 18785 for bucket 36 bucket 53: 90% Returning block of 28343 for bucket 39 Returning block of 22023 for bucket 41 Returning block of 29838 for bucket 38 Getting block 61 of 208 Sorting block of length 26604 for bucket 46 (Using difference cover) Sorting block of length 6196 for bucket 49 (Using difference cover) Returning block of 18460 for bucket 43 Reserving size (31083) for bucket 99 Getting block 101 of 206 Sorting block of length 19692 for bucket 77 (Using difference cover) Entering block accumulator loop for bucket 95: bucket 87: 10% Sorting block time: 00:00:00 bucket 40: 90% Returning block of 23071 for bucket 44 bucket 59: 10% bucket 47: 100% bucket 54: 100% bucket 55: 20% bucket 51: 100% bucket 57: 20% Reserving size (31083) for bucket 60 bucket 52: 100% bucket 56: 20% Reserving size (31083) for bucket 61 Sorting block time: 00:00:00 bucket 88: 10% bucket 86: 20% bucket 82: 50% bucket 89: 10% bucket 79: 100% Returning block of 13872 for bucket 78 Getting block 102 of 206 Getting block 103 of 206 bucket 80: 90% bucket 83: 60% bucket 48: 100% Reserving size (31083) for bucket 100 bucket 81: 80% bucket 85: 30% bucket 84: 40% Sorting block time: 00:00:00 Returning block of 6197 for bucket 49 Entering block accumulator loop for bucket 96: Entering block accumulator loop for bucket 97: bucket 50: 90% Getting block 62 of 208 bucket 58: 20% Getting block 63 of 208 Sorting block of length 9618 for bucket 47 (Using difference cover) Sorting block of length 24316 for bucket 54 (Using difference cover) Sorting block of length 28049 for bucket 51 (Using difference cover) bucket 53: 100% Calculating Z arrays for bucket 60 Sorting block of length 23570 for bucket 52 (Using difference cover) Calculating Z arrays for bucket 61 bucket 57: 30% bucket 55: 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 Getting block 64 of 208 bucket 59: 20% Getting block 65 of 208 Sorting block of length 25126 for bucket 48 (Using difference cover) Getting block 66 of 208 bucket 37: 100% bucket 40: 100% bucket 56: 30% Returning block of 26605 for bucket 46 Getting block 67 of 208 Getting block 68 of 208 Getting block 69 of 208 Reserving size (31083) for bucket 62 Getting block 70 of 208 Reserving size (31083) for bucket 63 Sorting block of length 26577 for bucket 53 (Using difference cover) Entering block accumulator loop for bucket 60: Entering block accumulator loop for bucket 61: Returning block of 9619 for bucket 47 Returning block of 24317 for bucket 54 Returning block of 23571 for bucket 52 Entering block accumulator loop for bucket 98: Calculating Z arrays for bucket 99 Reserving size (31083) for bucket 101 Returning block of 19693 for bucket 77 bucket 90: 10% bucket 91: 10% bucket 87: 20% Sorting block of length 30930 for bucket 79 (Using difference cover) Reserving size (31083) for bucket 102 Reserving size (31083) for bucket 103 Returning block of 28050 for bucket 51 bucket 50: 100% bucket 57: 40% Sorting block time: 00:00:00 bucket 55: 40% Sorting block time: 00:00:00 bucket 92: 10% bucket 80: 100% bucket 86: 30% bucket 83: 70% Sorting block time: 00:00:00 Reserving size (31083) for bucket 64 bucket 58: 30% Reserving size (31083) for bucket 65 Reserving size (31083) for bucket 66 Sorting block of length 18116 for bucket 37 (Using difference cover) Sorting block time: 00:00:00 Sorting block of length 13256 for bucket 40 (Using difference cover) Reserving size (31083) for bucket 67 Reserving size (31083) for bucket 68 Reserving size (31083) for bucket 69 Getting block 71 of 208 Calculating Z arrays for bucket 62 Reserving size (31083) for bucket 70 Calculating Z arrays for bucket 63 Sorting block of length 29535 for bucket 50 (Using difference cover) Returning block of 25127 for bucket 48 Returning block of 26578 for bucket 53 Calculating Z arrays for bucket 100 bucket 89: 20% bucket 82: 60% bucket 85: 40% Sorting block time: 00:00:00 bucket 59: 30% bucket 57: 50% bucket 55: 50% bucket 56: 40% bucket 84: 50% bucket 81: 90% bucket 88: 20% bucket 93: 10% bucket 94: 10% Sorting block time: 00:00:00 Calculating Z arrays for bucket 64 Calculating Z arrays for bucket 65 Calculating Z arrays for bucket 66 Returning block of 18117 for bucket 37 Calculating Z arrays for bucket 67 Calculating Z arrays for bucket 68 Calculating Z arrays for bucket 69 Reserving size (31083) for bucket 71 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 62: Getting block 72 of 208 Getting block 73 of 208 Getting block 74 of 208 Getting block 75 of 208 Entering block accumulator loop for bucket 63: Getting block 76 of 208 Returning block of 13257 for bucket 40 bucket 58: 40% Returning block of 29536 for bucket 50 bucket 60: 10% bucket 61: 10% bucket 57: 60% bucket 55: 60% Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 99: Calculating Z arrays for bucket 102 Calculating Z arrays for bucket 103 Getting block 104 of 206 Returning block of 30931 for bucket 79 bucket 87: 30% Sorting block of length 29866 for bucket 80 (Using difference cover) bucket 90: 20% bucket 91: 20% bucket 95: 10% bucket 83: 80% Entering block accumulator loop for bucket 64: Entering block accumulator loop for bucket 65: Entering block accumulator loop for bucket 66: Entering block accumulator loop for bucket 67: bucket 59: 40% Entering block accumulator loop for bucket 68: Entering block accumulator loop for bucket 69: Sorting block time: 00:00:00 Entering block accumulator loop for bucket 100: bucket 86: 40% bucket 92: 20% bucket 89: 30% bucket 85: 50% bucket 82: 70% bucket 96: 10% bucket 97: 10% Calculating Z arrays for bucket 71 bucket 88: 30% bucket 81: 100% bucket 84: 60% bucket 93: 20% bucket 94: 20% Entering block accumulator loop for bucket 101: Entering block accumulator loop for bucket 102: Reserving size (31083) for bucket 104 Getting block 105 of 206 Entering block accumulator loop for bucket 103: Returning block of 29867 for bucket 80 bucket 87: 40% bucket 90: 30% Entering block accumulator loop for bucket 70: Reserving size (31083) for bucket 72 Reserving size (31083) for bucket 73 Reserving size (31083) for bucket 74 Reserving size (31083) for bucket 75 Reserving size (31083) for bucket 76 Getting block 77 of 208 bucket 98: 10% Getting block 78 of 208 bucket 83: 90% bucket 57: 70% bucket 60: 20% bucket 58: 50% bucket 55: 70% bucket 91: 30% bucket 95: 20% Sorting block of length 28113 for bucket 81 (Using difference cover) bucket 86: 50% bucket 85: 60% bucket 89: 40% Sorting block time: 00:00:00 Calculating Z arrays for bucket 104 Reserving size (31083) for bucket 105 Getting block 106 of 206 bucket 88: 40% bucket 92: 30% bucket 84: 70% bucket 97: 20% bucket 96: 20% bucket 82: 80% bucket 61: 20% Getting block 79 of 208 Entering block accumulator loop for bucket 71: bucket 59: 50% bucket 56: 50% bucket 87: 50% bucket 93: 30% bucket 99: 10% bucket 94: 30% bucket 90: 40% bucket 83: 100% Calculating Z arrays for bucket 72 Calculating Z arrays for bucket 73 Calculating Z arrays for bucket 74 Calculating Z arrays for bucket 75 Calculating Z arrays for bucket 76 Reserving size (31083) for bucket 77 Reserving size (31083) for bucket 78 bucket 98: 20% Getting block 80 of 208 Returning block of 28114 for bucket 81 Getting block 81 of 208 bucket 85: 70% bucket 62: 10% bucket 89: 50% bucket 63: 10% bucket 86: 60% bucket 57: 80% bucket 91: 40% bucket 55: 80% bucket 95: 30% bucket 58: 60% Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 104: bucket 100: 10% Reserving size (31083) for bucket 106 Getting block 107 of 206 bucket 102: 10% bucket 60: 30% bucket 66: 10% bucket 64: 10% bucket 65: 10% bucket 101: 10% bucket 88: 50% bucket 84: 80% bucket 82: 90% bucket 92: 40% bucket 67: 10% bucket 68: 10% bucket 69: 10% Reserving size (31083) for bucket 79 Sorting block of length 17326 for bucket 83 (Using difference cover) Sorting block time: 00:00:00 bucket 103: 10% bucket 96: 30% bucket 97: 30% bucket 87: 60% bucket 90: 50% bucket 93: 40% bucket 99: 20% bucket 94: 40% bucket 61: 30% Entering block accumulator loop for bucket 72: bucket 85: 80% Entering block accumulator loop for bucket 73: Entering block accumulator loop for bucket 74: bucket 89: 60% Entering block accumulator loop for bucket 75: bucket 86: 70% Entering block accumulator loop for bucket 76: bucket 59: 60% bucket 56: 60% bucket 70: 10% Calculating Z arrays for bucket 77 Calculating Z arrays for bucket 78 Reserving size (31083) for bucket 80 Reserving size (31083) for bucket 81 bucket 57: 90% bucket 55: 90% bucket 58: 70% bucket 62: 20% bucket 63: 20% bucket 66: 20% Calculating Z arrays for bucket 79 bucket 60: 40% bucket 64: 20% bucket 65: 20% Entering block accumulator loop for bucket 105: Calculating Z arrays for bucket 106 Reserving size (31083) for bucket 107 bucket 67: 20% bucket 68: 20% bucket 69: 20% bucket 91: 50% bucket 98: 30% bucket 95: 40% bucket 88: 60% bucket 84: 90% bucket 102: 20% bucket 100: 20% bucket 82: 100% bucket 92: 50% bucket 101: 20% bucket 61: 40% bucket 71: 10% Returning block of 17327 for bucket 83 Entering block accumulator loop for bucket 77: Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 78: Calculating Z arrays for bucket 81 bucket 59: 70% bucket 56: 70% bucket 57: 100% bucket 55: 100% bucket 70: 20% Entering block accumulator loop for bucket 79: bucket 66: 30% Getting block 108 of 206 bucket 87: 70% bucket 90: 60% bucket 96: 40% bucket 93: 50% bucket 94: 50% bucket 97: 40% bucket 103: 20% bucket 99: 30% bucket 58: 80% bucket 85: 90% bucket 89: 70% bucket 86: 80% bucket 62: 30% bucket 60: 50% bucket 63: 30% bucket 64: 30% bucket 65: 30% bucket 67: 30% bucket 68: 30% bucket 69: 30% Entering block accumulator loop for bucket 106: Calculating Z arrays for bucket 107 bucket 104: 10% Sorting block of length 25496 for bucket 82 (Using difference cover) bucket 88: 70% bucket 84: 100% bucket 91: 60% bucket 92: 60% bucket 98: 40% bucket 102: 30% bucket 100: 30% bucket 61: 50% bucket 71: 20% Entering block accumulator loop for bucket 80: Entering block accumulator loop for bucket 81: Sorting block of length 24927 for bucket 57 (Using difference cover) bucket 73: 10% Sorting block of length 28695 for bucket 55 (Using difference cover) bucket 72: 10% bucket 74: 10% bucket 66: 40% bucket 70: 30% bucket 59: 80% bucket 56: 80% Sorting block time: 00:00:00 bucket 101: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 75: 10% bucket 76: 10% bucket 58: 90% bucket 60: 60% bucket 63: 40% bucket 62: 40% bucket 64: 40% bucket 65: 40% bucket 67: 40% bucket 68: 40% bucket 69: 40% Reserving size (31083) for bucket 108 bucket 95: 50% bucket 87: 80% bucket 90: 70% bucket 93: 60% bucket 94: 60% bucket 96: 50% bucket 61: 60% Returning block of 24928 for bucket 57 bucket 97: 50% bucket 99: 40% bucket 103: 30% bucket 89: 80% Returning block of 28696 for bucket 55 bucket 85: 100% bucket 86: 90% bucket 66: 50% bucket 71: 30% bucket 70: 40% bucket 59: 90% bucket 56: 90% bucket 72: 20% bucket 73: 20% bucket 74: 20% bucket 77: 10% bucket 79: 10% bucket 78: 10% Entering block accumulator loop for bucket 107: Sorting block of length 26068 for bucket 84 (Using difference cover) bucket 67: 50% bucket 69: 50% bucket 68: 50% bucket 60: 70% bucket 75: 20% bucket 58: 100% bucket 62: 50% bucket 63: 50% bucket 65: 50% bucket 64: 50% bucket 76: 20% Returning block of 25497 for bucket 82 bucket 105: 10% Sorting block time: 00:00:00 bucket 88: 80% bucket 91: 70% bucket 92: 70% bucket 98: 50% bucket 104: 20% bucket 81: 10% bucket 80: 10% bucket 102: 40% bucket 100: 40% bucket 61: 70% bucket 66: 60% bucket 56: 100% bucket 70: 50% bucket 71: 40% bucket 59: 100% Sorting block of length 30794 for bucket 58 (Using difference cover) bucket 72: 30% Getting block 82 of 208 bucket 73: 30% bucket 74: 30% bucket 77: 20% bucket 79: 20% bucket 78: 20% bucket 67: 60% bucket 68: 60% bucket 60: 80% Getting block 109 of 206 Sorting block time: 00:00:00 bucket 75: 30% bucket 63: 60% bucket 65: 60% bucket 62: 60% bucket 64: 60% Calculating Z arrays for bucket 108 bucket 101: 40% bucket 87: 90% bucket 90: 80% bucket 94: 70% bucket 93: 70% Getting block 83 of 208 bucket 76: 30% bucket 69: 60% Sorting block of length 24558 for bucket 56 (Using difference cover) bucket 81: 20% Sorting block of length 2379 for bucket 59 (Using difference cover) Reserving size (31083) for bucket 82 bucket 80: 20% bucket 66: 70% bucket 70: 60% Sorting block of length 19685 for bucket 85 (Using difference cover) bucket 95: 60% bucket 96: 60% bucket 89: 90% bucket 97: 60% bucket 99: 50% bucket 103: 40% bucket 106: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 61: 80% Returning block of 30795 for bucket 58 Sorting block time: 00:00:00 bucket 86: 100% Returning block of 26069 for bucket 84 bucket 105: 20% bucket 88: 90% bucket 91: 80% bucket 92: 80% bucket 98: 60% bucket 104: 30% bucket 102: 50% bucket 100: 50% bucket 67: 70% bucket 71: 50% bucket 73: 40% bucket 72: 40% bucket 74: 40% bucket 68: 70% bucket 79: 30% bucket 77: 30% bucket 60: 90% bucket 78: 30% bucket 63: 70% Reserving size (31083) for bucket 109 bucket 75: 40% bucket 62: 70% bucket 64: 70% Entering block accumulator loop for bucket 108: bucket 87: 100% bucket 90: 90% bucket 94: 80% bucket 93: 80% bucket 101: 50% Reserving size (31083) for bucket 83 Calculating Z arrays for bucket 82 Returning block of 2380 for bucket 59 Returning block of 24559 for bucket 56 bucket 69: 70% bucket 70: 70% bucket 81: 30% bucket 76: 40% bucket 80: 30% bucket 65: 70% bucket 66: 80% bucket 61: 90% bucket 67: 80% bucket 71: 60% bucket 73: 50% Returning block of 19686 for bucket 85 bucket 68: 80% bucket 72: 50% bucket 74: 50% bucket 63: 80% bucket 79: 40% bucket 60: 100% bucket 77: 40% bucket 78: 40% Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 82: Getting block 84 of 208 bucket 89: 100% bucket 106: 20% bucket 75: 50% Sorting block of length 16407 for bucket 86 bucket 62: 80% (Using difference cover) bucket 69: 80% bucket 70: 80% bucket 64: 80% bucket 80: 40% Sorting block of length 29831 for bucket 60 (Using difference cover) bucket 76: 50% bucket 81: 40% Sorting block time: 00:00:01 Getting block 110 of 206 bucket 99: 60% bucket 97: 70% bucket 96: 70% bucket 95: 70% bucket 103: 50% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 83: Reserving size (31083) for bucket 84 Getting block 85 of 208 Getting block 86 of 208 bucket 105: 30% bucket 88: 100% bucket 107: 10% bucket 91: 90% bucket 92: 90% bucket 98: 70% bucket 102: 60% bucket 100: 60% bucket 67: 90% bucket 73: 60% bucket 71: 70% bucket 74: 60% bucket 68: 90% bucket 63: 90% Calculating Z arrays for bucket 109 bucket 104: 40% bucket 66: 90% Sorting block of length 28577 for bucket 87 bucket 61: 100% (Using difference cover) bucket 72: 60% bucket 90: 100% bucket 79: 50% bucket 94: 90% bucket 65: 80% bucket 93: 90% bucket 77: 50% bucket 101: 60% bucket 78: 50% bucket 75: 60% bucket 62: 90% Returning block of 29832 for bucket 60 bucket 69: 90% bucket 70: 90% bucket 64: 90% Sorting block of length 12513 for bucket 89 (Using difference cover) Returning block of 16408 for bucket 86 Calculating Z arrays for bucket 84 Reserving size (31083) for bucket 85 Reserving size (31083) for bucket 110 bucket 106: 30% Getting block 111 of 206 Sorting block of length 5419 for bucket 88 (Using difference cover) bucket 99: 70% Reserving size (31083) for bucket 86 bucket 80: 50% bucket 76: 60% bucket 97: 80% bucket 96: 80% bucket 95: 80% bucket 103: 60% bucket 105: 40% bucket 81: 50% bucket 82: 10% Sorting block time: 00:00:01 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 107: 20% bucket 91: 100% bucket 92: 100% bucket 98: 80% bucket 102: 70% bucket 100: 70% bucket 67: 100% bucket 73: 70% bucket 68: 100% bucket 74: 70% Sorting block of length 3476 for bucket 61 (Using difference cover) bucket 63: 100% bucket 71: 80% bucket 66: 100% bucket 72: 70% bucket 70: 100% bucket 62: 100% bucket 79: 60% bucket 64: 100% Entering block accumulator loop for bucket 84: Calculating Z arrays for bucket 85 bucket 77: 60% Sorting block time: 00:00:00 bucket 69: 100% Entering block accumulator loop for bucket 109: Sorting block of length 19745 for bucket 90 (Using difference cover) bucket 104: 50% Getting block 112 of 206 Calculating Z arrays for bucket 110 Reserving size (31083) for bucket 111 bucket 108: 10% bucket 93: 100% bucket 94: 100% Returning block of 28578 for bucket 87 Returning block of 12514 for bucket 89 Sorting block time: 00:00:00 bucket 101: 70% Returning block of 5420 for bucket 88 bucket 106: 40% Sorting block of length 20343 for bucket 91 (Using difference cover) Sorting block of length 30185 for bucket 92 (Using difference cover) bucket 99: 80% bucket 97: 90% bucket 103: 70% bucket 95: 90% bucket 96: 90% bucket 105: 50% bucket 75: 70% bucket 78: 60% bucket 65: 90% Calculating Z arrays for bucket 86 bucket 83: 10% bucket 80: 60% bucket 76: 70% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 107: 30% Sorting block of length 23776 for bucket 67 (Using difference cover) Sorting block of length 29937 for bucket 68 (Using difference cover) Sorting block of length 20523 for bucket 63 (Using difference cover) Getting block 87 of 208 Sorting block of length 29881 for bucket 66 (Using difference cover) Sorting block of length 28443 for bucket 70 (Using difference cover) Sorting block of length 30589 for bucket 62 (Using difference cover) Sorting block of length 16008 for bucket 64 (Using difference cover) bucket 102: 80% bucket 98: 90% bucket 100: 80% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 85: Returning block of 3477 for bucket 61 Sorting block of length 6865 for bucket 69 (Using difference cover) bucket 81: 60% bucket 82: 20% bucket 73: 80% bucket 71: 90% bucket 74: 80% bucket 72: 80% bucket 79: 70% bucket 77: 70% bucket 65: 100% Entering block accumulator loop for bucket 86: bucket 78: 70% Reserving size (31083) for bucket 87 Reserving size (31083) for bucket 112 Calculating Z arrays for bucket 111 Getting block 113 of 206 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 80: 70% bucket 83: 20% bucket 76: 80% Entering block accumulator loop for bucket 110: Sorting block of length 23555 for bucket 93 (Using difference cover) Sorting block of length 19832 for bucket 94 (Using difference cover) Returning block of 19746 for bucket 90 bucket 108: 20% bucket 104: 60% Returning block of 20344 for bucket 91 Returning block of 30186 for bucket 92 bucket 105: 60% bucket 106: 50% bucket 99: 90% bucket 97: 100% bucket 103: 80% bucket 95: 100% Returning block of 23777 for bucket 67 bucket 96: 100% bucket 75: 80% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 20524 for bucket 63 bucket 84: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 101: 80% bucket 107: 40% bucket 102: 90% bucket 100: 90% Calculating Z arrays for bucket 112 bucket 98: 100% Reserving size (31083) for bucket 113 Entering block accumulator loop for bucket 111: Getting block 114 of 206 Getting block 115 of 206 Getting block 116 of 206 Sorting block of length 8692 for bucket 97 (Using difference cover) Sorting block of length 30593 for bucket 95 (Using difference cover) Sorting block of length 29626 for bucket 96 (Using difference cover) Sorting block of length 30562 for bucket 65 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 109: 10% Returning block of 19833 for bucket 94 Returning block of 23556 for bucket 93 bucket 108: 30% bucket 105: 70% bucket 106: 60% Sorting block of length 24583 for bucket 98 (Using difference cover) Entering block accumulator loop for bucket 112: Sorting block time: 00:00:00 Calculating Z arrays for bucket 87 Returning block of 16009 for bucket 64 Returning block of 30590 for bucket 62 Returning block of 6866 for bucket 69 bucket 73: 90% bucket 72: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Calculating Z arrays for bucket 113 Reserving size (31083) for bucket 114 Reserving size (31083) for bucket 115 bucket 74: 90% Reserving size (31083) for bucket 116 bucket 71: 100% bucket 103: 90% bucket 99: 100% bucket 104: 70% Returning block of 8693 for bucket 97 bucket 101: 90% Returning block of 30594 for bucket 95 bucket 110: 10% bucket 107: 50% bucket 102: 100% bucket 100: 100% Getting block 117 of 206 Getting block 118 of 206 Getting block 119 of 206 bucket 81: 70% bucket 79: 80% bucket 82: 30% bucket 77: 80% bucket 78: 80% Returning block of 28444 for bucket 70 Returning block of 29882 for bucket 66 Returning block of 29938 for bucket 68 bucket 75: 90% Returning block of 29627 for bucket 96 Returning block of 24584 for bucket 98 bucket 105: 80% Calculating Z arrays for bucket 114 bucket 108: 40% bucket 80: 80% bucket 76: 90% bucket 84: 20% bucket 83: 30% Returning block of 30563 for bucket 65 Entering block accumulator loop for bucket 87: Getting block 88 of 208 Entering block accumulator loop for bucket 113: Calculating Z arrays for bucket 115 Calculating Z arrays for bucket 116 Sorting block of length 27876 for bucket 99 (Using difference cover) bucket 106: 70% bucket 85: 10% Sorting block of length 30812 for bucket 71 (Using difference cover) bucket 73: 100% bucket 86: 10% bucket 74: 100% Getting block 89 of 208 bucket 79: 90% Sorting block of length 23196 for bucket 102 (Using difference cover) bucket 109: 20% bucket 77: 90% Getting block 90 of 208 Reserving size (31083) for bucket 88 bucket 78: 90% bucket 81: 80% bucket 82: 40% bucket 75: 100% Sorting block time: 00:00:00 bucket 84: 30% Sorting block time: 00:00:00 Sorting block of length 27559 for bucket 100 (Using difference cover) Reserving size (31083) for bucket 117 Reserving size (31083) for bucket 118 Reserving size (31083) for bucket 119 Getting block 120 of 206 bucket 111: 10% bucket 110: 20% bucket 103: 100% bucket 101: 100% bucket 104: 80% bucket 107: 60% bucket 112: 10% bucket 83: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 121 of 206 Entering block accumulator loop for bucket 114: bucket 105: 90% Getting block 91 of 208 Getting block 92 of 208 Getting block 93 of 208 Sorting block of length 27409 for bucket 73 (Using difference cover) Sorting block of length 12567 for bucket 74 (Using difference cover) bucket 80: 90% Reserving size (31083) for bucket 89 Getting block 94 of 208 Getting block 95 of 208 Getting block 96 of 208 bucket 76: 100% Reserving size (31083) for bucket 90 Calculating Z arrays for bucket 88 Sorting block of length 27095 for bucket 75 (Using difference cover) bucket 72: 100% Returning block of 30813 for bucket 71 bucket 85: 20% bucket 86: 20% Entering block accumulator loop for bucket 115: Entering block accumulator loop for bucket 116: bucket 108: 50% Getting block 122 of 206 bucket 106: 80% Returning block of 27877 for bucket 99 bucket 109: 30% Calculating Z arrays for bucket 117 Calculating Z arrays for bucket 118 Calculating Z arrays for bucket 119 Reserving size (31083) for bucket 120 Getting block 123 of 206 Sorting block of length 28528 for bucket 103 (Using difference cover) Getting block 97 of 208 Sorting block of length 8457 for bucket 101 (Using difference cover) Returning block of 23197 for bucket 102 bucket 79: 100% bucket 78: 100% bucket 81: 90% bucket 77: 100% bucket 82: 50% bucket 87: 10% bucket 84: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 27560 for bucket 100 bucket 110: 30% Sorting block time: 00:00:00 bucket 83: 50% bucket 111: 20% bucket 107: 70% bucket 104: 90% bucket 112: 20% Reserving size (31083) for bucket 121 Getting block 124 of 206 Getting block 125 of 206 bucket 105: 100% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (31083) for bucket 91 Reserving size (31083) for bucket 92 Reserving size (31083) for bucket 93 Calculating Z arrays for bucket 89 Reserving size (31083) for bucket 94 Reserving size (31083) for bucket 95 Reserving size (31083) for bucket 96 Sorting block of length 29835 for bucket 76 (Using difference cover) Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 88: Sorting block of length 6236 for bucket 72 (Using difference cover) Reserving size (31083) for bucket 97 bucket 85: 30% bucket 86: 30% bucket 80: 100% Sorting block of length 8778 for bucket 79 (Using difference cover) Sorting block of length 26793 for bucket 78 (Using difference cover) Sorting block of length 25495 for bucket 77 (Using difference cover) Returning block of 12568 for bucket 74 Reserving size (31083) for bucket 122 Entering block accumulator loop for bucket 117: Entering block accumulator loop for bucket 118: Entering block accumulator loop for bucket 119: Calculating Z arrays for bucket 120 Reserving size (31083) for bucket 123 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 84: 50% bucket 87: 20% bucket 81: 100% bucket 82: 60% Returning block of 27096 for bucket 75 Returning block of 27410 for bucket 73 Returning block of 8458 for bucket 101 Returning block of 28529 for bucket 103 bucket 113: 10% bucket 108: 60% bucket 109: 40% bucket 106: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 83: 60% bucket 110: 40% Calculating Z arrays for bucket 121 Reserving size (31083) for bucket 124 Reserving size (31083) for bucket 125 Sorting block of length 24947 for bucket 105 (Using difference cover) bucket 111: 30% bucket 107: 80% bucket 104: 100% bucket 114: 10% Calculating Z arrays for bucket 122 bucket 115: 10% Calculating Z arrays for bucket 91 Calculating Z arrays for bucket 92 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 89: Calculating Z arrays for bucket 94 Calculating Z arrays for bucket 95 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 90: Getting block 98 of 208 Calculating Z arrays for bucket 97 Sorting block of length 29310 for bucket 80 (Using difference cover) Returning block of 6237 for bucket 72 Sorting block time: 00:00:00 bucket 112: 30% Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 120: Getting block 126 of 206 Getting block 127 of 206 bucket 116: 10% bucket 113: 20% bucket 108: 70% bucket 106: 100% bucket 109: 50% Sorting block time: 00:00:00 Returning block of 8779 for bucket 79 bucket 85: 40% Sorting block of length 15049 for bucket 81 bucket 86: 40% (Using difference cover) Returning block of 25496 for bucket 77 Returning block of 26794 for bucket 78 Returning block of 29836 for bucket 76 Getting block 128 of 206 Entering block accumulator loop for bucket 121: Calculating Z arrays for bucket 124 Calculating Z arrays for bucket 125 Sorting block of length 27813 for bucket 104 (Using difference cover) Entering block accumulator loop for bucket 122: Returning block of 24948 for bucket 105 bucket 110: 50% bucket 111: 40% bucket 107: 90% bucket 114: 20% bucket 117: 10% bucket 115: 20% Entering block accumulator loop for bucket 123: Reserving size (31083) for bucket 126 Reserving size (31083) for bucket 127 Getting block 129 of 206 Getting block 130 of 206 bucket 84: 60% Sorting block time: 00:00:00 bucket 87: 30% Sorting block time: 00:00:00 Sorting block of length 25058 for bucket 106 bucket 82: 70% (Using difference cover) bucket 83: 70% bucket 119: 10% bucket 112: 40% bucket 113: 30% bucket 108: 80% bucket 116: 20% bucket 109: 60% Entering block accumulator loop for bucket 91: Entering block accumulator loop for bucket 92: Entering block accumulator loop for bucket 93: Entering block accumulator loop for bucket 94: Entering block accumulator loop for bucket 95: Entering block accumulator loop for bucket 96: Reserving size (31083) for bucket 98 Getting block 99 of 208 Entering block accumulator loop for bucket 97: Sorting block time: 00:00:00 Reserving size (31083) for bucket 128 bucket 118: 10% Entering block accumulator loop for bucket 124: Entering block accumulator loop for bucket 125: Returning block of 29311 for bucket 80 Calculating Z arrays for bucket 126 Getting block 100 of 208 Calculating Z arrays for bucket 127 Getting block 101 of 208 Reserving size (31083) for bucket 129 bucket 88: 10% Reserving size (31083) for bucket 130 bucket 86: 50% Returning block of 27814 for bucket 104 bucket 85: 50% bucket 120: 10% bucket 110: 60% bucket 111: 50% bucket 114: 30% bucket 117: 20% bucket 107: 100% bucket 115: 30% Returning block of 25059 for bucket 106 bucket 119: 20% bucket 112: 50% bucket 113: 40% bucket 108: 90% Returning block of 15050 for bucket 81 bucket 84: 70% bucket 116: 30% bucket 109: 70% bucket 87: 40% bucket 83: 80% bucket 82: 80% Calculating Z arrays for bucket 128 Calculating Z arrays for bucket 98 Reserving size (31083) for bucket 99 Entering block accumulator loop for bucket 126: bucket 90: 10% bucket 89: 10% Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 127: Calculating Z arrays for bucket 130 Getting block 131 of 206 Sorting block of length 21271 for bucket 107 (Using difference cover) bucket 121: 10% bucket 122: 10% bucket 118: 20% Getting block 102 of 208 Reserving size (31083) for bucket 100 Reserving size (31083) for bucket 101 Getting block 103 of 208 Getting block 104 of 208 Getting block 105 of 208 Getting block 106 of 208 bucket 85: 60% bucket 86: 60% bucket 88: 20% Sorting block time: 00:00:00 bucket 120: 20% bucket 110: 70% bucket 114: 40% bucket 117: 30% bucket 111: 60% bucket 119: 30% bucket 84: 80% bucket 112: 60% bucket 108: 100% bucket 113: 50% bucket 115: 40% bucket 123: 10% bucket 87: 50% Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 98: bucket 116: 40% bucket 82: 90% bucket 109: 80% bucket 92: 10% bucket 95: 10% bucket 91: 10% bucket 93: 10% bucket 96: 10% bucket 90: 20% bucket 97: 10% bucket 89: 20% Reserving size (31083) for bucket 102 Calculating Z arrays for bucket 100 Calculating Z arrays for bucket 101 Reserving size (31083) for bucket 103 Reserving size (31083) for bucket 104 Reserving size (31083) for bucket 105 Entering block accumulator loop for bucket 128: Reserving size (31083) for bucket 106 Getting block 107 of 208 bucket 124: 10% bucket 94: 10% bucket 83: 90% bucket 85: 70% bucket 86: 70% Entering block accumulator loop for bucket 129: bucket 125: 10% Reserving size (31083) for bucket 131 Entering block accumulator loop for bucket 130: Getting block 132 of 206 Returning block of 21272 for bucket 107 Getting block 133 of 206 bucket 121: 20% Sorting block of length 9911 for bucket 108 (Using difference cover) bucket 122: 20% bucket 118: 30% Getting block 108 of 208 bucket 88: 30% Entering block accumulator loop for bucket 99: bucket 84: 90% bucket 87: 60% bucket 82: 100% Sorting block time: 00:00:00 bucket 120: 30% bucket 110: 80% bucket 119: 40% bucket 111: 70% bucket 117: 40% bucket 114: 50% bucket 112: 70% bucket 113: 60% bucket 123: 20% bucket 115: 50% bucket 92: 20% bucket 91: 20% bucket 95: 20% bucket 96: 20% Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 100: Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 101: Calculating Z arrays for bucket 104 Calculating Z arrays for bucket 105 Calculating Z arrays for bucket 106 Reserving size (31083) for bucket 107 bucket 93: 20% bucket 90: 30% bucket 89: 30% bucket 97: 20% bucket 94: 20% bucket 85: 80% bucket 86: 80% bucket 116: 50% bucket 109: 90% Reserving size (31083) for bucket 108 bucket 83: 100% Sorting block of length 30080 for bucket 82 (Using difference cover) bucket 87: 70% bucket 88: 40% bucket 84: 100% bucket 124: 20% bucket 126: 10% Calculating Z arrays for bucket 131 Reserving size (31083) for bucket 132 bucket 127: 10% Reserving size (31083) for bucket 133 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 102: Returning block of 9912 for bucket 108 bucket 125: 20% bucket 121: 30% bucket 122: 30% bucket 118: 40% Entering block accumulator loop for bucket 103: bucket 98: 10% Entering block accumulator loop for bucket 104: Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 105: Entering block accumulator loop for bucket 106: bucket 92: 30% bucket 91: 30% bucket 95: 30% bucket 96: 30% bucket 93: 30% bucket 90: 40% bucket 85: 90% bucket 86: 90% bucket 120: 40% bucket 110: 90% bucket 111: 80% bucket 119: 50% bucket 123: 30% bucket 112: 80% bucket 113: 70% bucket 117: 50% bucket 114: 60% bucket 115: 60% Calculating Z arrays for bucket 108 Sorting block of length 26204 for bucket 83 (Using difference cover) Sorting block of length 29981 for bucket 84 (Using difference cover) bucket 97: 30% bucket 94: 30% bucket 89: 40% Returning block of 30081 for bucket 82 bucket 88: 50% bucket 87: 80% bucket 116: 60% bucket 99: 10% bucket 109: 100% bucket 100: 10% Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 131: Calculating Z arrays for bucket 133 Getting block 134 of 206 bucket 124: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 107: bucket 98: 20% bucket 92: 40% bucket 95: 40% bucket 93: 40% bucket 101: 10% bucket 96: 40% bucket 85: 100% bucket 86: 100% Entering block accumulator loop for bucket 108: Returning block of 26205 for bucket 83 bucket 91: 40% Returning block of 29982 for bucket 84 bucket 126: 20% bucket 128: 10% bucket 129: 10% bucket 130: 10% bucket 90: 50% bucket 127: 20% bucket 125: 30% bucket 121: 40% bucket 122: 40% bucket 118: 50% bucket 94: 40% bucket 97: 40% bucket 89: 50% bucket 88: 60% bucket 87: 90% bucket 99: 20% bucket 102: 10% bucket 103: 10% bucket 120: 50% bucket 110: 100% bucket 111: 90% bucket 123: 40% bucket 112: 90% bucket 119: 60% bucket 113: 80% bucket 117: 60% bucket 114: 70% Sorting block of length 28654 for bucket 109 (Using difference cover) bucket 104: 10% Sorting block of length 21405 for bucket 85 (Using difference cover) Sorting block of length 18671 for bucket 86 (Using difference cover) bucket 105: 10% bucket 100: 20% bucket 106: 10% bucket 92: 50% bucket 98: 30% bucket 95: 50% bucket 96: 50% bucket 93: 50% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 132: bucket 115: 70% Entering block accumulator loop for bucket 133: Reserving size (31083) for bucket 134 bucket 124: 40% bucket 116: 70% Getting block 135 of 206 bucket 101: 20% bucket 94: 50% bucket 88: 70% bucket 87: 100% bucket 97: 50% bucket 99: 30% bucket 103: 20% bucket 102: 20% bucket 126: 30% bucket 128: 20% bucket 129: 20% bucket 130: 20% bucket 125: 40% Sorting block of length 24529 for bucket 110 (Using difference cover) bucket 121: 50% bucket 122: 50% bucket 127: 30% bucket 118: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 109 of 208 Getting block 110 of 208 bucket 90: 60% Returning block of 28655 for bucket 109 Sorting block time: 00:00:00 bucket 120: 60% bucket 111: 100% bucket 123: 50% bucket 112: 100% bucket 113: 90% bucket 119: 70% bucket 117: 70% bucket 114: 80% bucket 91: 50% bucket 89: 60% bucket 107: 10% bucket 106: 20% bucket 92: 60% bucket 108: 10% bucket 95: 60% bucket 96: 60% bucket 98: 40% bucket 100: 30% Getting block 111 of 208 Sorting block of length 29503 for bucket 87 (Using difference cover) bucket 104: 20% bucket 105: 20% Calculating Z arrays for bucket 134 Reserving size (31083) for bucket 135 bucket 131: 10% bucket 124: 50% bucket 116: 80% bucket 115: 80% Sorting block time: 00:00:00 Returning block of 18672 for bucket 86 Returning block of 21406 for bucket 85 bucket 93: 60% bucket 88: 80% bucket 97: 60% bucket 94: 60% bucket 99: 40% bucket 101: 30% bucket 103: 30% bucket 102: 30% bucket 126: 40% bucket 128: 30% Reserving size (31083) for bucket 109 Reserving size (31083) for bucket 110 bucket 90: 70% Returning block of 24530 for bucket 110 bucket 125: 50% bucket 122: 60% Sorting block of length 14986 for bucket 111 (Using difference cover) bucket 121: 60% bucket 91: 60% Sorting block time: 00:00:00 Sorting block of length 24181 for bucket 112 (Using difference cover) bucket 129: 30% bucket 127: 40% bucket 130: 30% bucket 118: 70% bucket 120: 70% bucket 123: 60% bucket 113: 100% bucket 119: 80% bucket 132: 10% bucket 114: 90% bucket 117: 80% bucket 133: 10% Calculating Z arrays for bucket 135 Reserving size (31083) for bucket 111 Returning block of 29504 for bucket 87 bucket 89: 70% bucket 106: 30% bucket 107: 20% bucket 92: 70% bucket 96: 70% bucket 95: 70% bucket 108: 20% bucket 98: 50% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 134: bucket 131: 20% bucket 104: 30% bucket 105: 30% bucket 88: 90% bucket 97: 70% bucket 93: 70% bucket 99: 50% bucket 94: 70% bucket 100: 40% bucket 103: 40% bucket 124: 60% bucket 102: 40% bucket 116: 90% bucket 115: 90% bucket 126: 50% bucket 128: 40% Calculating Z arrays for bucket 109 Calculating Z arrays for bucket 110 bucket 101: 40% bucket 90: 80% Getting block 136 of 206 Returning block of 14987 for bucket 111 bucket 125: 60% bucket 122: 70% bucket 121: 70% Sorting block of length 30460 for bucket 113 (Using difference cover) Entering block accumulator loop for bucket 135: bucket 91: 70% Calculating Z arrays for bucket 111 Getting block 112 of 208 Getting block 113 of 208 bucket 106: 40% bucket 107: 30% bucket 89: 80% bucket 98: 60% bucket 92: 80% bucket 96: 80% bucket 95: 80% bucket 108: 30% bucket 104: 40% bucket 105: 40% Sorting block time: 00:00:00 Returning block of 24182 for bucket 112 bucket 120: 80% bucket 123: 70% bucket 129: 40% bucket 130: 40% bucket 114: 100% bucket 127: 50% bucket 117: 90% bucket 132: 20% bucket 118: 80% bucket 133: 20% bucket 119: 90% bucket 88: 100% bucket 99: 60% bucket 97: 80% bucket 94: 80% bucket 100: 50% bucket 103: 50% bucket 102: 50% bucket 131: 30% bucket 124: 70% bucket 116: 100% bucket 115: 100% bucket 126: 60% bucket 128: 50% Entering block accumulator loop for bucket 109: Entering block accumulator loop for bucket 110: bucket 93: 80% bucket 90: 90% Reserving size (31083) for bucket 112 Reserving size (31083) for bucket 113 Entering block accumulator loop for bucket 111: Getting block 114 of 208 bucket 101: 50% bucket 106: 50% bucket 98: 70% bucket 107: 40% Reserving size (31083) for bucket 136 Getting block 137 of 206 Returning block of 30461 for bucket 113 bucket 125: 70% bucket 121: 80% bucket 122: 80% bucket 91: 80% bucket 92: 90% Sorting block of length 24632 for bucket 114 (Using difference cover) bucket 120: 90% bucket 123: 80% bucket 130: 50% bucket 129: 50% Sorting block of length 25314 for bucket 88 (Using difference cover) bucket 108: 40% bucket 95: 90% bucket 104: 50% bucket 105: 50% Sorting block time: 00:00:00 Sorting block of length 19220 for bucket 116 (Using difference cover) bucket 119: 100% bucket 117: 100% bucket 127: 60% bucket 132: 30% bucket 118: 90% bucket 89: 90% bucket 99: 70% bucket 96: 90% bucket 97: 90% bucket 100: 60% bucket 102: 60% Sorting block time: 00:00:00 Sorting block of length 29116 for bucket 115 (Using difference cover) bucket 134: 10% bucket 124: 80% bucket 131: 40% Sorting block time: 00:00:00 Calculating Z arrays for bucket 112 bucket 103: 60% Sorting block time: 00:00:00 bucket 133: 30% bucket 126: 70% bucket 128: 60% Calculating Z arrays for bucket 113 Reserving size (31083) for bucket 114 bucket 94: 90% bucket 90: 100% bucket 106: 60% bucket 107: 50% bucket 98: 80% bucket 93: 90% bucket 101: 60% bucket 91: 90% bucket 92: 100% Returning block of 25315 for bucket 88 bucket 108: 50% bucket 95: 100% bucket 104: 60% bucket 105: 60% bucket 89: 100% bucket 99: 80% bucket 97: 100% Calculating Z arrays for bucket 136 Reserving size (31083) for bucket 137 Getting block 138 of 206 bucket 100: 70% bucket 102: 70% Entering block accumulator loop for bucket 112: bucket 96: 100% bucket 135: 10% bucket 125: 80% bucket 121: 90% bucket 109: 10% bucket 110: 10% Calculating Z arrays for bucket 114 Getting block 139 of 206 bucket 122: 90% Returning block of 24633 for bucket 114 Sorting block of length 18290 for bucket 119 (Using difference cover) Sorting block of length 21534 for bucket 117 (Using difference cover) bucket 120: 100% bucket 123: 90% bucket 129: 60% bucket 130: 60% Returning block of 19221 for bucket 116 bucket 132: 40% bucket 118: 100% bucket 127: 70% Returning block of 29117 for bucket 115 bucket 124: 90% bucket 134: 20% bucket 131: 50% bucket 126: 80% Entering block accumulator loop for bucket 113: Sorting block of length 7957 for bucket 90 (Using difference cover) bucket 103: 70% Sorting block of length 26712 for bucket 92 (Using difference cover) Sorting block of length 27177 for bucket 95 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 133: 40% bucket 128: 70% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 24232 for bucket 89 (Using difference cover) Sorting block of length 20022 for bucket 97 (Using difference cover) bucket 106: 70% bucket 111: 10% bucket 94: 100% Sorting block time: 00:00:00 bucket 107: 60% bucket 98: 90% bucket 108: 60% bucket 93: 100% bucket 91: 100% bucket 104: 70% bucket 101: 70% Entering block accumulator loop for bucket 136: Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 12614 for bucket 96 (Using difference cover) bucket 99: 90% bucket 105: 70% bucket 100: 80% bucket 102: 80% Entering block accumulator loop for bucket 114: Calculating Z arrays for bucket 137 Reserving size (31083) for bucket 138 Getting block 140 of 206 bucket 135: 20% bucket 121: 100% Reserving size (31083) for bucket 139 bucket 125: 90% Sorting block time: 00:00:00 bucket 109: 20% bucket 110: 20% Sorting block of length 25085 for bucket 120 (Using difference cover) Sorting block of length 27492 for bucket 118 (Using difference cover) Returning block of 18291 for bucket 119 Returning block of 21535 for bucket 117 bucket 122: 100% bucket 124: 100% bucket 126: 90% bucket 123: 100% bucket 129: 70% bucket 132: 50% bucket 130: 70% bucket 134: 30% bucket 131: 60% bucket 127: 80% bucket 128: 80% Returning block of 7958 for bucket 90 Returning block of 26713 for bucket 92 Getting block 115 of 208 Sorting block of length 24559 for bucket 94 (Using difference cover) Returning block of 27178 for bucket 95 bucket 103: 80% Sorting block of length 20474 for bucket 93 (Using difference cover) Sorting block of length 19807 for bucket 91 (Using difference cover) Returning block of 20023 for bucket 97 Returning block of 24233 for bucket 89 bucket 106: 80% bucket 111: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 133: 50% Entering block accumulator loop for bucket 137: Calculating Z arrays for bucket 138 Reserving size (31083) for bucket 140 Sorting block of length 11752 for bucket 121 (Using difference cover) Calculating Z arrays for bucket 139 bucket 135: 30% bucket 125: 100% Getting block 141 of 206 Getting block 142 of 206 Getting block 143 of 206 Sorting block of length 29495 for bucket 122 (Using difference cover) Sorting block of length 30031 for bucket 124 (Using difference cover) Sorting block of length 13717 for bucket 123 (Using difference cover) bucket 107: 70% bucket 108: 70% bucket 98: 100% bucket 101: 80% bucket 104: 80% Returning block of 12615 for bucket 96 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 25086 for bucket 120 Returning block of 27493 for bucket 118 bucket 126: 100% bucket 128: 90% bucket 129: 80% bucket 127: 90% bucket 131: 70% bucket 132: 60% bucket 134: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 112: 10% bucket 99: 100% bucket 100: 90% bucket 102: 90% bucket 105: 80% bucket 110: 30% Reserving size (31083) for bucket 115 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 138: Entering block accumulator loop for bucket 139: Sorting block of length 17240 for bucket 125 (Using difference cover) Reserving size (31083) for bucket 141 Reserving size (31083) for bucket 142 Reserving size (31083) for bucket 143 Returning block of 11753 for bucket 121 Getting block 144 of 206 Returning block of 13718 for bucket 123 bucket 130: 80% bucket 136: 10% Returning block of 30032 for bucket 124 Returning block of 29496 for bucket 122 bucket 135: 40% bucket 133: 60% Getting block 145 of 206 bucket 109: 30% bucket 113: 10% bucket 103: 90% Sorting block of length 29564 for bucket 98 (Using difference cover) Returning block of 20475 for bucket 93 Returning block of 19808 for bucket 91 Returning block of 24560 for bucket 94 bucket 106: 90% bucket 111: 30% bucket 114: 10% Sorting block time: 00:00:00 Sorting block of length 30439 for bucket 126 (Using difference cover) bucket 128: 100% Sorting block time: 00:00:00 bucket 127: 100% bucket 129: 90% bucket 131: 80% Sorting block time: 00:00:00 bucket 107: 80% bucket 108: 80% Sorting block of length 26565 for bucket 99 (Using difference cover) bucket 104: 90% Sorting block time: 00:00:00 bucket 101: 90% Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 140: bucket 132: 70% Calculating Z arrays for bucket 141 Calculating Z arrays for bucket 142 Calculating Z arrays for bucket 143 Reserving size (31083) for bucket 144 bucket 112: 20% Getting block 116 of 208 Getting block 117 of 208 Getting block 118 of 208 bucket 110: 40% Getting block 119 of 208 Getting block 120 of 208 bucket 137: 10% bucket 134: 50% Reserving size (31083) for bucket 145 Getting block 121 of 208 bucket 105: 90% bucket 109: 40% Returning block of 17241 for bucket 125 Getting block 146 of 206 Getting block 147 of 206 bucket 135: 50% bucket 136: 20% Returning block of 29565 for bucket 98 bucket 113: 20% bucket 106: 100% bucket 114: 20% bucket 103: 100% bucket 111: 40% bucket 102: 100% Sorting block of length 27019 for bucket 128 (Using difference cover) bucket 133: 70% Returning block of 26566 for bucket 99 Returning block of 30440 for bucket 126 bucket 100: 100% Sorting block of length 30813 for bucket 127 Entering block accumulator loop for bucket 115: (Using difference cover) bucket 107: 90% bucket 108: 90% bucket 130: 90% Reserving size (31083) for bucket 116 bucket 129: 100% Reserving size (31083) for bucket 117 bucket 131: 90% Reserving size (31083) for bucket 118 Reserving size (31083) for bucket 119 Reserving size (31083) for bucket 120 bucket 104: 100% Reserving size (31083) for bucket 121 Getting block 122 of 208 Getting block 123 of 208 Entering block accumulator loop for bucket 141: Entering block accumulator loop for bucket 142: Entering block accumulator loop for bucket 143: Calculating Z arrays for bucket 144 Getting block 124 of 208 bucket 101: 100% Calculating Z arrays for bucket 145 bucket 139: 10% bucket 112: 30% bucket 110: 50% Sorting block of length 29285 for bucket 106 (Using difference cover) Sorting block of length 26979 for bucket 103 (Using difference cover) bucket 109: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 148 of 206 Getting block 149 of 206 Getting block 150 of 206 Getting block 151 of 206 Reserving size (31083) for bucket 146 Reserving size (31083) for bucket 147 bucket 132: 80% bucket 137: 20% bucket 134: 60% bucket 136: 30% bucket 135: 60% Sorting block of length 13213 for bucket 129 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 26016 for bucket 102 (Using difference cover) bucket 105: 100% Sorting block of length 25519 for bucket 100 (Using difference cover) Calculating Z arrays for bucket 116 Calculating Z arrays for bucket 117 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 144: Entering block accumulator loop for bucket 145: bucket 138: 10% Returning block of 27020 for bucket 128 Returning block of 30814 for bucket 127 bucket 140: 10% bucket 130: 100% bucket 133: 80% bucket 139: 20% Reserving size (31083) for bucket 148 Reserving size (31083) for bucket 149 Reserving size (31083) for bucket 150 Reserving size (31083) for bucket 151 Calculating Z arrays for bucket 146 Calculating Z arrays for bucket 147 Getting block 152 of 206 Returning block of 13214 for bucket 129 Sorting block time: 00:00:00 Calculating Z arrays for bucket 118 Calculating Z arrays for bucket 119 Calculating Z arrays for bucket 120 Sorting block of length 28525 for bucket 104 (Using difference cover) Calculating Z arrays for bucket 121 Reserving size (31083) for bucket 122 Reserving size (31083) for bucket 123 Reserving size (31083) for bucket 124 bucket 131: 100% bucket 142: 10% bucket 141: 10% Getting block 153 of 206 Sorting block time: 00:00:00 Sorting block of length 24237 for bucket 101 (Using difference cover) bucket 114: 30% bucket 113: 30% bucket 111: 50% bucket 107: 100% bucket 108: 100% Getting block 125 of 208 Returning block of 29286 for bucket 106 Returning block of 26980 for bucket 103 bucket 109: 60% Sorting block of length 19063 for bucket 105 (Using difference cover) bucket 112: 40% Entering block accumulator loop for bucket 116: Entering block accumulator loop for bucket 117: bucket 137: 30% bucket 135: 70% bucket 134: 70% bucket 136: 40% Sorting block of length 23060 for bucket 130 (Using difference cover) bucket 132: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 110: 60% Returning block of 26017 for bucket 102 bucket 115: 10% Sorting block time: 00:00:00 Calculating Z arrays for bucket 148 Calculating Z arrays for bucket 149 Calculating Z arrays for bucket 150 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 146: Reserving size (31083) for bucket 152 Entering block accumulator loop for bucket 147: bucket 143: 10% bucket 140: 20% Entering block accumulator loop for bucket 118: Entering block accumulator loop for bucket 119: Entering block accumulator loop for bucket 120: Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 121: Calculating Z arrays for bucket 123 Calculating Z arrays for bucket 124 Returning block of 25520 for bucket 100 Getting block 126 of 208 Sorting block of length 23058 for bucket 107 (Using difference cover) Sorting block of length 23937 for bucket 108 (Using difference cover) Reserving size (31083) for bucket 125 Returning block of 19064 for bucket 105 Returning block of 28526 for bucket 104 Returning block of 24238 for bucket 101 bucket 114: 40% bucket 109: 70% bucket 113: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 112: 50% bucket 111: 60% Sorting block of length 13790 for bucket 131 (Using difference cover) Reserving size (31083) for bucket 153 bucket 133: 90% bucket 139: 30% bucket 142: 20% bucket 144: 10% bucket 141: 20% bucket 137: 40% bucket 138: 20% Returning block of 23061 for bucket 130 bucket 145: 10% bucket 135: 80% bucket 136: 50% bucket 115: 20% Sorting block time: 00:00:00 Getting block 154 of 206 Getting block 155 of 206 Entering block accumulator loop for bucket 148: Entering block accumulator loop for bucket 149: Entering block accumulator loop for bucket 150: Entering block accumulator loop for bucket 151: bucket 110: 70% Entering block accumulator loop for bucket 122: Calculating Z arrays for bucket 152 Getting block 156 of 206 bucket 134: 80% bucket 132: 100% bucket 143: 20% bucket 140: 30% Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 123: Entering block accumulator loop for bucket 124: Reserving size (31083) for bucket 126 Calculating Z arrays for bucket 125 Getting block 127 of 208 Getting block 128 of 208 Returning block of 23059 for bucket 107 Returning block of 23938 for bucket 108 bucket 114: 50% bucket 116: 10% bucket 117: 10% bucket 109: 80% Returning block of 13791 for bucket 131 Getting block 129 of 208 bucket 113: 50% bucket 112: 60% bucket 111: 70% bucket 115: 30% bucket 142: 30% bucket 139: 40% bucket 144: 20% bucket 141: 30% bucket 133: 100% bucket 145: 20% bucket 135: 90% bucket 118: 10% bucket 136: 60% bucket 120: 10% bucket 119: 10% bucket 110: 80% Calculating Z arrays for bucket 126 Reserving size (31083) for bucket 127 Entering block accumulator loop for bucket 125: Reserving size (31083) for bucket 128 Getting block 130 of 208 Getting block 131 of 208 Getting block 132 of 208 Getting block 133 of 208 Reserving size (31083) for bucket 154 Reserving size (31083) for bucket 155 Reserving size (31083) for bucket 129 bucket 114: 60% bucket 121: 10% bucket 116: 20% bucket 117: 20% bucket 122: 10% bucket 112: 70% bucket 115: 40% bucket 113: 60% bucket 111: 80% Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 126: Calculating Z arrays for bucket 128 Reserving size (31083) for bucket 130 Reserving size (31083) for bucket 131 Reserving size (31083) for bucket 132 Reserving size (31083) for bucket 133 bucket 146: 10% Getting block 134 of 208 Getting block 135 of 208 bucket 118: 20% bucket 120: 20% bucket 119: 20% bucket 124: 10% bucket 110: 90% Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 127: Calculating Z arrays for bucket 130 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 128: Calculating Z arrays for bucket 132 Calculating Z arrays for bucket 133 bucket 123: 10% bucket 114: 70% bucket 122: 20% Entering block accumulator loop for bucket 152: bucket 115: 50% bucket 112: 80% Reserving size (31083) for bucket 156 Sorting block of length 24813 for bucket 132 (Using difference cover) Getting block 157 of 206 Entering block accumulator loop for bucket 153: bucket 138: 30% bucket 137: 50% bucket 147: 10% bucket 143: 30% bucket 140: 40% bucket 134: 90% Reserving size (31083) for bucket 134 Reserving size (31083) for bucket 135 bucket 125: 10% bucket 111: 90% bucket 116: 30% bucket 113: 70% bucket 117: 30% Entering block accumulator loop for bucket 129: Entering block accumulator loop for bucket 130: Entering block accumulator loop for bucket 131: Entering block accumulator loop for bucket 132: Entering block accumulator loop for bucket 133: bucket 121: 20% Sorting block time: 00:00:00 Sorting block of length 12500 for bucket 133 bucket 109: 90% (Using difference cover) bucket 118: 30% bucket 142: 40% bucket 120: 30% bucket 139: 50% bucket 119: 30% bucket 144: 30% bucket 124: 20% bucket 145: 30% bucket 135: 100% bucket 141: 40% bucket 136: 70% bucket 110: 100% bucket 126: 10% bucket 123: 20% bucket 114: 80% bucket 122: 30% Sorting block time: 00:00:00 Calculating Z arrays for bucket 154 Calculating Z arrays for bucket 155 bucket 148: 10% bucket 115: 60% bucket 112: 90% bucket 149: 10% bucket 150: 10% bucket 146: 20% Calculating Z arrays for bucket 134 Calculating Z arrays for bucket 135 bucket 151: 10% Calculating Z arrays for bucket 156 Reserving size (31083) for bucket 157 bucket 111: 100% bucket 125: 20% bucket 116: 40% bucket 113: 80% Getting block 158 of 206 Returning block of 24814 for bucket 132 bucket 143: 40% Sorting block of length 27748 for bucket 110 bucket 138: 40% (Using difference cover) bucket 140: 50% bucket 128: 10% bucket 127: 10% bucket 117: 40% bucket 109: 100% bucket 137: 60% bucket 118: 40% bucket 147: 20% bucket 120: 40% bucket 134: 100% bucket 119: 40% Sorting block of length 14355 for bucket 135 (Using difference cover) bucket 124: 30% Returning block of 12501 for bucket 133 bucket 144: 40% bucket 145: 40% bucket 126: 20% Sorting block time: 00:00:00 bucket 114: 90% bucket 122: 40% Sorting block time: 00:00:00 bucket 142: 50% bucket 139: 60% bucket 136: 80% bucket 121: 30% bucket 112: 100% Entering block accumulator loop for bucket 134: Entering block accumulator loop for bucket 135: bucket 115: 70% bucket 123: 30% bucket 132: 10% Sorting block of length 24643 for bucket 111 (Using difference cover) bucket 129: 10% bucket 131: 10% bucket 130: 10% bucket 125: 30% bucket 113: 90% bucket 116: 50% Entering block accumulator loop for bucket 154: Entering block accumulator loop for bucket 155: bucket 141: 50% bucket 146: 30% bucket 148: 20% bucket 149: 20% bucket 150: 20% Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 156: Sorting block time: 00:00:00 bucket 133: 10% bucket 152: 10% Sorting block of length 22712 for bucket 109 (Using difference cover) Returning block of 27749 for bucket 110 bucket 118: 50% bucket 117: 50% bucket 119: 50% bucket 128: 20% bucket 127: 20% Sorting block of length 21849 for bucket 112 (Using difference cover) bucket 151: 20% Reserving size (31083) for bucket 158 bucket 153: 10% Sorting block of length 19839 for bucket 134 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14356 for bucket 135 bucket 143: 50% bucket 140: 60% bucket 144: 50% bucket 145: 50% bucket 124: 40% bucket 120: 50% bucket 126: 30% bucket 137: 70% bucket 147: 30% bucket 138: 50% bucket 139: 70% bucket 136: 90% bucket 114: 100% bucket 122: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 115: 80% Returning block of 24644 for bucket 111 bucket 113: 100% bucket 116: 60% bucket 125: 40% bucket 132: 20% Entering block accumulator loop for bucket 157: bucket 142: 60% bucket 146: 40% bucket 141: 60% bucket 149: 30% bucket 148: 30% bucket 150: 30% Calculating Z arrays for bucket 158 Returning block of 19840 for bucket 134 Getting block 159 of 206 bucket 129: 20% bucket 131: 20% bucket 130: 20% bucket 123: 40% Getting block 160 of 206 bucket 152: 20% bucket 121: 40% bucket 119: 60% bucket 117: 60% bucket 128: 30% bucket 127: 30% bucket 134: 10% bucket 133: 20% Sorting block of length 4802 for bucket 114 (Using difference cover) Returning block of 22713 for bucket 109 bucket 153: 20% bucket 151: 30% bucket 143: 60% bucket 144: 60% bucket 145: 60% bucket 140: 70% bucket 136: 100% bucket 139: 80% Sorting block time: 00:00:00 Returning block of 21850 for bucket 112 bucket 118: 60% bucket 120: 60% bucket 137: 80% Sorting block of length 28591 for bucket 113 bucket 147: 40% (Using difference cover) Entering block accumulator loop for bucket 158: Reserving size (31083) for bucket 159 bucket 138: 60% bucket 154: 10% bucket 155: 10% bucket 156: 10% bucket 146: 50% Reserving size (31083) for bucket 160 Getting block 161 of 206 bucket 141: 70% bucket 150: 40% bucket 148: 40% bucket 149: 40% bucket 142: 70% Sorting block of length 30027 for bucket 136 (Using difference cover) bucket 152: 30% bucket 143: 70% bucket 144: 70% bucket 153: 30% bucket 151: 40% Calculating Z arrays for bucket 159 Getting block 162 of 206 Calculating Z arrays for bucket 160 Reserving size (31083) for bucket 161 bucket 139: 90% bucket 145: 70% bucket 140: 80% Sorting block time: 00:00:00 bucket 124: 50% bucket 126: 40% bucket 135: 10% bucket 122: 60% Getting block 136 of 208 bucket 115: 90% bucket 116: 70% bucket 125: 50% bucket 132: 30% bucket 123: 50% bucket 129: 30% bucket 131: 30% Sorting block time: 00:00:00 bucket 146: 60% bucket 130: 30% bucket 137: 90% bucket 138: 70% bucket 141: 80% bucket 154: 20% bucket 155: 20% bucket 156: 20% bucket 147: 50% bucket 148: 50% Returning block of 4803 for bucket 114 bucket 150: 50% Entering block accumulator loop for bucket 159: Reserving size (31083) for bucket 162 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 160: bucket 157: 10% Returning block of 30028 for bucket 136 bucket 158: 10% bucket 143: 80% bucket 144: 80% bucket 149: 50% bucket 119: 70% bucket 121: 50% bucket 139: 100% bucket 117: 70% bucket 145: 80% bucket 128: 40% bucket 140: 90% bucket 127: 40% bucket 153: 40% bucket 134: 20% bucket 152: 40% bucket 133: 30% bucket 151: 50% bucket 142: 80% bucket 146: 70% Returning block of 28592 for bucket 113 bucket 118: 70% bucket 120: 70% Getting block 137 of 208 Reserving size (31083) for bucket 136 bucket 126: 50% bucket 124: 60% bucket 135: 20% bucket 122: 70% Calculating Z arrays for bucket 162 bucket 115: 100% bucket 116: 80% Entering block accumulator loop for bucket 161: bucket 141: 90% bucket 138: 80% bucket 154: 30% bucket 155: 30% bucket 156: 30% bucket 137: 100% bucket 150: 60% bucket 148: 60% bucket 125: 60% bucket 123: 60% bucket 132: 40% bucket 129: 40% Sorting block of length 24882 for bucket 139 (Using difference cover) bucket 147: 60% bucket 157: 20% bucket 143: 90% bucket 144: 90% bucket 145: 90% bucket 140: 100% bucket 152: 50% bucket 153: 50% bucket 151: 60% Getting block 138 of 208 Sorting block time: 00:00:00 bucket 142: 90% bucket 149: 60% bucket 159: 10% bucket 131: 40% bucket 130: 40% bucket 119: 80% bucket 117: 80% bucket 128: 50% bucket 121: 60% bucket 127: 50% bucket 134: 30% Entering block accumulator loop for bucket 162: bucket 146: 80% Sorting block of length 29815 for bucket 137 (Using difference cover) bucket 158: 20% bucket 160: 10% bucket 138: 90% bucket 141: 100% bucket 154: 40% bucket 155: 40% bucket 150: 70% bucket 156: 40% bucket 148: 70% Getting block 139 of 208 bucket 133: 40% Reserving size (31083) for bucket 137 Calculating Z arrays for bucket 136 bucket 118: 80% Sorting block time: 00:00:00 Getting block 163 of 206 Sorting block of length 26009 for bucket 140 (Using difference cover) Returning block of 24883 for bucket 139 bucket 143: 100% bucket 145: 100% bucket 144: 100% bucket 147: 70% bucket 151: 70% bucket 153: 60% bucket 152: 60% bucket 157: 30% bucket 159: 20% Sorting block of length 26705 for bucket 115 (Using difference cover) bucket 120: 80% bucket 122: 80% bucket 126: 60% Sorting block time: 00:00:00 Sorting block of length 17911 for bucket 141 (Using difference cover) bucket 142: 100% bucket 124: 70% bucket 135: 30% bucket 116: 90% Sorting block time: 00:00:00 bucket 149: 70% Returning block of 29816 for bucket 137 bucket 158: 30% bucket 160: 20% bucket 161: 10% bucket 146: 90% bucket 138: 100% bucket 154: 50% Sorting block time: 00:00:00 Reserving size (31083) for bucket 138 bucket 123: 70% bucket 125: 70% bucket 132: 50% bucket 129: 50% Getting block 140 of 208 bucket 119: 90% Reserving size (31083) for bucket 163 bucket 150: 80% bucket 155: 50% bucket 121: 70% bucket 131: 50% bucket 156: 50% bucket 148: 80% Sorting block of length 15189 for bucket 143 (Using difference cover) Sorting block of length 15409 for bucket 145 (Using difference cover) Sorting block of length 19639 for bucket 144 (Using difference cover) bucket 127: 60% bucket 117: 90% bucket 128: 60% bucket 134: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 26010 for bucket 140 bucket 159: 30% bucket 147: 80% Reserving size (31083) for bucket 139 bucket 130: 50% Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 136: Getting block 141 of 208 bucket 118: 90% bucket 133: 50% Sorting block of length 26987 for bucket 142 (Using difference cover) bucket 151: 80% bucket 152: 70% bucket 153: 70% bucket 157: 40% Returning block of 17912 for bucket 141 Sorting block of length 23666 for bucket 138 (Using difference cover) Returning block of 26706 for bucket 115 bucket 120: 90% bucket 122: 90% bucket 126: 70% bucket 116: 100% Calculating Z arrays for bucket 138 bucket 124: 80% bucket 135: 40% Reserving size (31083) for bucket 140 bucket 123: 80% bucket 119: 100% bucket 125: 80% bucket 162: 10% bucket 132: 60% bucket 158: 40% bucket 129: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 160: 30% bucket 161: 20% bucket 146: 100% bucket 121: 80% bucket 149: 80% bucket 131: 60% bucket 154: 60% bucket 117: 100% bucket 127: 70% bucket 134: 50% bucket 128: 70% Calculating Z arrays for bucket 163 bucket 150: 90% bucket 155: 60% Returning block of 15410 for bucket 145 Returning block of 15190 for bucket 143 Returning block of 19640 for bucket 144 bucket 148: 90% Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 137: Getting block 164 of 206 bucket 156: 60% Reserving size (31083) for bucket 141 Sorting block of length 26525 for bucket 116 (Using difference cover) Sorting block time: 00:00:00 Entering block accumulator loop for bucket 138: Calculating Z arrays for bucket 140 Sorting block of length 30282 for bucket 119 (Using difference cover) bucket 118: 100% bucket 133: 60% bucket 130: 60% bucket 122: 100% bucket 120: 100% bucket 126: 80% bucket 125: 90% bucket 124: 90% bucket 123: 90% Sorting block of length 28385 for bucket 117 (Using difference cover) bucket 135: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 132: 70% bucket 121: 90% bucket 129: 70% bucket 127: 80% bucket 134: 60% Entering block accumulator loop for bucket 139: bucket 131: 70% bucket 128: 80% bucket 136: 10% Calculating Z arrays for bucket 141 Returning block of 26526 for bucket 116 Entering block accumulator loop for bucket 140: Sorting block of length 28080 for bucket 118 (Using difference cover) Sorting block time: 00:00:00 Getting block 142 of 208 Sorting block of length 8195 for bucket 122 (Using difference cover) Sorting block of length 11824 for bucket 120 (Using difference cover) Returning block of 30283 for bucket 119 Returning block of 28386 for bucket 117 bucket 125: 100% bucket 126: 90% bucket 124: 100% bucket 123: 100% bucket 133: 70% bucket 130: 70% bucket 135: 60% bucket 121: 100% bucket 127: 90% bucket 129: 80% bucket 159: 40% bucket 147: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 132: 80% bucket 134: 70% Getting block 165 of 206 Returning block of 23667 for bucket 138 Returning block of 26988 for bucket 142 bucket 152: 80% bucket 151: 90% bucket 153: 80% bucket 158: 50% bucket 162: 20% bucket 137: 10% bucket 128: 90% Sorting block of length 21978 for bucket 146 (Using difference cover) bucket 160: 40% bucket 161: 30% bucket 149: 90% bucket 154: 70% bucket 131: 80% bucket 136: 20% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 163: bucket 157: 50% Reserving size (31083) for bucket 164 bucket 150: 100% bucket 155: 70% bucket 156: 70% bucket 148: 100% Getting block 166 of 206 Getting block 167 of 206 Reserving size (31083) for bucket 165 bucket 159: 50% bucket 147: 100% bucket 158: 60% bucket 151: 100% bucket 152: 90% bucket 153: 90% Entering block accumulator loop for bucket 141: Returning block of 28081 for bucket 118 Reserving size (31083) for bucket 142 Sorting block of length 17073 for bucket 125 (Using difference cover) Sorting block time: 00:00:00 Sorting block of length 18379 for bucket 124 (Using difference cover) Sorting block of length 26808 for bucket 123 Sorting block of length 29267 for bucket 121 (Using difference cover) (Using difference cover) Returning block of 8196 for bucket 122 Returning block of 11825 for bucket 120 bucket 138: 10% Returning block of 21979 for bucket 146 bucket 160: 50% bucket 161: 40% bucket 154: 80% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 126: 100% bucket 129: 90% bucket 127: 100% bucket 135: 70% bucket 133: 80% bucket 130: 80% bucket 134: 80% bucket 132: 90% Calculating Z arrays for bucket 164 Getting block 168 of 206 Getting block 169 of 206 Getting block 170 of 206 Sorting block of length 21587 for bucket 150 (Using difference cover) Sorting block of length 27845 for bucket 148 (Using difference cover) Reserving size (31083) for bucket 166 Reserving size (31083) for bucket 167 Sorting block time: 00:00:00 bucket 128: 100% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Calculating Z arrays for bucket 165 Getting block 171 of 206 bucket 139: 10% bucket 149: 100% bucket 137: 20% bucket 162: 30% bucket 131: 90% Sorting block of length 30069 for bucket 147 (Using difference cover) Sorting block time: 00:00:00 Getting block 172 of 206 Sorting block of length 19067 for bucket 151 (Using difference cover) bucket 156: 80% bucket 155: 80% bucket 157: 60% bucket 158: 70% bucket 159: 60% bucket 152: 100% bucket 153: 100% bucket 160: 60% bucket 161: 50% bucket 136: 30% bucket 154: 90% Reserving size (31083) for bucket 168 Entering block accumulator loop for bucket 164: Reserving size (31083) for bucket 169 Reserving size (31083) for bucket 170 Calculating Z arrays for bucket 166 Calculating Z arrays for bucket 167 Sorting block time: 00:00:00 Returning block of 21588 for bucket 150 Returning block of 27846 for bucket 148 bucket 163: 10% Reserving size (31083) for bucket 171 Entering block accumulator loop for bucket 165: Sorting block of length 11187 for bucket 149 (Using difference cover) Returning block of 30070 for bucket 147 Reserving size (31083) for bucket 172 Sorting block time: 00:00:00 bucket 162: 40% Sorting block of length 23822 for bucket 152 (Using difference cover) Sorting block of length 29047 for bucket 153 (Using difference cover) Getting block 173 of 206 Calculating Z arrays for bucket 168 Calculating Z arrays for bucket 169 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 166: Entering block accumulator loop for bucket 167: Returning block of 19068 for bucket 151 Calculating Z arrays for bucket 171 Calculating Z arrays for bucket 142 Returning block of 17074 for bucket 125 bucket 140: 10% Returning block of 26809 for bucket 123 Returning block of 18380 for bucket 124 bucket 138: 20% Getting block 143 of 208 Getting block 144 of 208 Getting block 145 of 208 Sorting block of length 19670 for bucket 126 (Using difference cover) Sorting block of length 29067 for bucket 127 (Using difference cover) Returning block of 29268 for bucket 121 bucket 129: 100% bucket 135: 80% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Calculating Z arrays for bucket 172 bucket 158: 80% Returning block of 11188 for bucket 149 bucket 155: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 29783 for bucket 128 (Using difference cover) bucket 133: 90% bucket 134: 90% bucket 132: 100% bucket 130: 90% bucket 159: 70% Reserving size (31083) for bucket 173 Entering block accumulator loop for bucket 168: Entering block accumulator loop for bucket 169: Entering block accumulator loop for bucket 170: Getting block 174 of 206 Entering block accumulator loop for bucket 171: bucket 157: 70% bucket 160: 70% bucket 161: 60% bucket 163: 20% bucket 156: 90% Returning block of 23823 for bucket 152 Returning block of 29048 for bucket 153 bucket 164: 10% Sorting block time: 00:00:00 bucket 139: 20% bucket 131: 100% bucket 137: 30% Getting block 175 of 206 bucket 165: 10% Entering block accumulator loop for bucket 172: bucket 154: 100% bucket 162: 50% Getting block 176 of 206 Calculating Z arrays for bucket 173 Reserving size (31083) for bucket 174 Getting block 177 of 206 bucket 158: 90% bucket 155: 100% bucket 136: 40% Entering block accumulator loop for bucket 142: Getting block 146 of 208 Getting block 147 of 208 Getting block 148 of 208 Reserving size (31083) for bucket 143 Reserving size (31083) for bucket 144 Reserving size (31083) for bucket 145 Sorting block of length 10781 for bucket 129 (Using difference cover) Returning block of 19671 for bucket 126 bucket 166: 10% bucket 167: 10% bucket 163: 30% bucket 164: 20% Sorting block time: 00:00:00 bucket 141: 10% bucket 140: 20% Returning block of 29068 for bucket 127 bucket 135: 90% Sorting block of length 31046 for bucket 132 bucket 138: 30% (Using difference cover) Reserving size (31083) for bucket 175 Getting block 178 of 206 Sorting block of length 17164 for bucket 154 (Using difference cover) bucket 161: 70% bucket 156: 100% bucket 160: 80% Sorting block time: 00:00:00 bucket 157: 80% bucket 159: 80% Reserving size (31083) for bucket 176 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 173: Reserving size (31083) for bucket 177 Getting block 179 of 206 Getting block 180 of 206 Sorting block of length 26686 for bucket 155 (Using difference cover) bucket 165: 20% bucket 158: 100% bucket 170: 10% bucket 169: 10% Sorting block time: 00:00:00 Returning block of 29784 for bucket 128 bucket 134: 100% bucket 162: 60% bucket 168: 10% bucket 171: 10% bucket 133: 100% Sorting block of length 28426 for bucket 131 (Using difference cover) bucket 130: 100% Sorting block time: 00:00:00 bucket 167: 20% bucket 139: 30% bucket 137: 40% bucket 166: 20% bucket 163: 40% bucket 164: 30% Sorting block time: 00:00:00 Reserving size (31083) for bucket 146 Reserving size (31083) for bucket 147 Reserving size (31083) for bucket 148 Calculating Z arrays for bucket 143 Getting block 149 of 208 Getting block 150 of 208 Calculating Z arrays for bucket 144 Calculating Z arrays for bucket 145 Getting block 151 of 208 Getting block 152 of 208 Returning block of 10782 for bucket 129 bucket 136: 50% Returning block of 31047 for bucket 132 Calculating Z arrays for bucket 175 Reserving size (31083) for bucket 178 Sorting block of length 23900 for bucket 156 (Using difference cover) Returning block of 17165 for bucket 154 bucket 161: 80% bucket 172: 10% bucket 160: 90% bucket 141: 20% bucket 135: 100% bucket 140: 30% bucket 138: 40% Sorting block of length 25246 for bucket 134 (Using difference cover) Sorting block of length 16862 for bucket 133 (Using difference cover) Sorting block of length 29030 for bucket 130 (Using difference cover) Returning block of 28427 for bucket 131 bucket 139: 40% Sorting block time: 00:00:00 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 174: Calculating Z arrays for bucket 177 Reserving size (31083) for bucket 179 Reserving size (31083) for bucket 180 Sorting block of length 30906 for bucket 158 (Using difference cover) bucket 159: 90% Returning block of 26687 for bucket 155 bucket 170: 20% bucket 165: 30% bucket 169: 20% bucket 157: 90% bucket 137: 50% bucket 142: 10% Sorting block time: 00:00:00 bucket 162: 70% bucket 168: 20% bucket 171: 20% bucket 167: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Calculating Z arrays for bucket 146 Calculating Z arrays for bucket 147 Calculating Z arrays for bucket 148 Reserving size (31083) for bucket 149 Entering block accumulator loop for bucket 143: Reserving size (31083) for bucket 150 Entering block accumulator loop for bucket 144: Entering block accumulator loop for bucket 145: Reserving size (31083) for bucket 151 Reserving size (31083) for bucket 152 Getting block 153 of 208 Getting block 154 of 208 bucket 136: 60% Sorting block of length 16990 for bucket 135 (Using difference cover) bucket 166: 30% bucket 163: 50% bucket 164: 40% Calculating Z arrays for bucket 178 Sorting block time: 00:00:00 Getting block 155 of 208 bucket 138: 50% bucket 140: 40% bucket 139: 50% bucket 141: 30% Returning block of 16863 for bucket 133 Entering block accumulator loop for bucket 175: Returning block of 23901 for bucket 156 bucket 161: 90% bucket 160: 100% bucket 172: 20% Entering block accumulator loop for bucket 176: Returning block of 25247 for bucket 134 Returning block of 29031 for bucket 130 bucket 137: 60% bucket 142: 20% Entering block accumulator loop for bucket 146: Entering block accumulator loop for bucket 147: Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 148: Calculating Z arrays for bucket 150 Calculating Z arrays for bucket 151 Calculating Z arrays for bucket 152 Reserving size (31083) for bucket 153 Reserving size (31083) for bucket 154 Getting block 156 of 208 Getting block 157 of 208 Returning block of 16991 for bucket 135 Reserving size (31083) for bucket 155 Getting block 158 of 208 Entering block accumulator loop for bucket 177: Calculating Z arrays for bucket 179 Calculating Z arrays for bucket 180 Returning block of 30907 for bucket 158 bucket 173: 10% bucket 170: 30% bucket 169: 30% bucket 159: 100% bucket 157: 100% bucket 165: 40% bucket 136: 70% bucket 138: 60% bucket 139: 60% bucket 167: 40% bucket 140: 50% bucket 162: 80% bucket 141: 40% Entering block accumulator loop for bucket 149: Entering block accumulator loop for bucket 150: Entering block accumulator loop for bucket 151: Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 152: Calculating Z arrays for bucket 154 Reserving size (31083) for bucket 156 Reserving size (31083) for bucket 157 Calculating Z arrays for bucket 155 Reserving size (31083) for bucket 158 bucket 168: 30% bucket 171: 30% bucket 137: 70% bucket 143: 10% bucket 145: 10% bucket 144: 10% bucket 142: 30% Getting block 159 of 208 Entering block accumulator loop for bucket 178: bucket 166: 40% bucket 163: 60% bucket 164: 50% bucket 136: 80% Getting block 181 of 206 Entering block accumulator loop for bucket 153: Calculating Z arrays for bucket 156 Sorting block of length 9393 for bucket 160 Entering block accumulator loop for bucket 154: (Using difference cover) Calculating Z arrays for bucket 157 bucket 172: 30% Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 155: bucket 139: 70% Sorting block time: 00:00:01 bucket 161: 100% bucket 174: 10% Getting block 160 of 208 Getting block 161 of 208 Getting block 162 of 208 bucket 138: 70% bucket 140: 60% bucket 148: 10% bucket 141: 50% bucket 146: 10% Reserving size (31083) for bucket 159 bucket 147: 10% Entering block accumulator loop for bucket 179: Getting block 182 of 206 Entering block accumulator loop for bucket 180: Sorting block of length 29816 for bucket 159 (Using difference cover) Sorting block of length 25552 for bucket 157 (Using difference cover) bucket 173: 20% bucket 170: 40% bucket 165: 50% bucket 169: 40% bucket 143: 20% bucket 145: 20% bucket 137: 80% bucket 144: 20% bucket 142: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 167: 50% bucket 162: 90% bucket 168: 40% bucket 171: 40% bucket 136: 90% bucket 151: 10% bucket 150: 10% bucket 149: 10% Entering block accumulator loop for bucket 156: Entering block accumulator loop for bucket 157: Entering block accumulator loop for bucket 158: bucket 139: 80% bucket 166: 50% bucket 163: 70% bucket 164: 60% Reserving size (31083) for bucket 160 Reserving size (31083) for bucket 161 Reserving size (31083) for bucket 162 bucket 152: 10% Calculating Z arrays for bucket 159 bucket 148: 20% bucket 138: 80% bucket 140: 70% bucket 141: 60% bucket 146: 20% bucket 147: 20% Reserving size (31083) for bucket 181 Getting block 183 of 206 Returning block of 9394 for bucket 160 bucket 175: 10% bucket 172: 40% Sorting block of length 28923 for bucket 161 (Using difference cover) bucket 143: 30% bucket 145: 30% bucket 144: 30% Sorting block time: 00:00:00 bucket 176: 10% bucket 174: 20% Reserving size (31083) for bucket 182 Getting block 184 of 206 Returning block of 25553 for bucket 157 Returning block of 29817 for bucket 159 bucket 137: 90% bucket 177: 10% bucket 173: 30% bucket 165: 60% bucket 170: 50% bucket 169: 50% bucket 142: 50% bucket 178: 10% bucket 136: 100% bucket 139: 90% bucket 167: 60% bucket 168: 50% bucket 171: 50% Calculating Z arrays for bucket 160 Calculating Z arrays for bucket 161 bucket 153: 10% bucket 154: 10% bucket 149: 20% bucket 151: 20% bucket 150: 20% bucket 155: 10% bucket 162: 100% bucket 166: 60% bucket 163: 80% Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 159: bucket 148: 30% bucket 138: 90% bucket 152: 20% bucket 141: 70% bucket 140: 80% bucket 146: 30% bucket 147: 30% Calculating Z arrays for bucket 181 Reserving size (31083) for bucket 183 bucket 164: 70% Returning block of 28924 for bucket 161 bucket 143: 40% bucket 145: 40% bucket 144: 40% bucket 137: 100% Sorting block of length 28403 for bucket 136 (Using difference cover) bucket 156: 10% bucket 157: 10% bucket 158: 10% bucket 175: 20% bucket 172: 50% Calculating Z arrays for bucket 182 bucket 142: 60% bucket 139: 100% Entering block accumulator loop for bucket 160: Entering block accumulator loop for bucket 161: bucket 153: 20% bucket 154: 20% bucket 149: 30% bucket 150: 30% bucket 155: 20% bucket 151: 30% Reserving size (31083) for bucket 184 bucket 176: 20% bucket 174: 30% bucket 180: 10% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 162: bucket 148: 40% bucket 138: 100% bucket 152: 30% bucket 141: 80% bucket 177: 20% bucket 178: 20% bucket 170: 60% bucket 173: 40% bucket 169: 60% bucket 165: 70% bucket 179: 10% Sorting block of length 26764 for bucket 162 (Using difference cover) Sorting block of length 22392 for bucket 137 (Using difference cover) bucket 146: 40% Sorting block of length 19672 for bucket 139 (Using difference cover) bucket 140: 90% bucket 147: 40% Returning block of 28404 for bucket 136 bucket 143: 50% bucket 145: 50% bucket 158: 20% bucket 144: 50% bucket 156: 20% bucket 157: 20% bucket 167: 70% bucket 159: 10% bucket 142: 70% bucket 154: 30% bucket 153: 30% bucket 149: 40% bucket 150: 40% bucket 151: 40% bucket 155: 30% Sorting block time: 00:00:00 bucket 168: 60% bucket 171: 60% bucket 166: 70% bucket 163: 90% Calculating Z arrays for bucket 183 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 19953 for bucket 138 (Using difference cover) bucket 148: 50% bucket 152: 40% Sorting block time: 00:00:00 bucket 141: 90% Entering block accumulator loop for bucket 181: Getting block 185 of 206 bucket 164: 80% Entering block accumulator loop for bucket 182: bucket 160: 10% bucket 146: 50% bucket 140: 100% bucket 143: 60% bucket 145: 60% bucket 159: 20% bucket 158: 30% bucket 147: 50% bucket 144: 60% bucket 156: 30% bucket 157: 30% bucket 175: 30% bucket 172: 60% Returning block of 19673 for bucket 139 Returning block of 22393 for bucket 137 bucket 161: 10% bucket 154: 40% bucket 142: 80% bucket 153: 40% bucket 149: 50% bucket 150: 50% bucket 151: 50% bucket 155: 40% Returning block of 19954 for bucket 138 Calculating Z arrays for bucket 184 Getting block 186 of 206 Getting block 187 of 206 bucket 180: 20% bucket 176: 30% bucket 174: 40% bucket 177: 30% bucket 178: 30% bucket 170: 70% bucket 173: 50% bucket 169: 70% bucket 165: 80% Returning block of 26765 for bucket 162 bucket 162: 10% bucket 148: 60% bucket 152: 50% Getting block 163 of 208 Sorting block of length 31056 for bucket 140 (Using difference cover) bucket 160: 20% bucket 143: 70% bucket 158: 40% bucket 167: 80% bucket 159: 30% bucket 179: 20% bucket 168: 70% Entering block accumulator loop for bucket 183: bucket 171: 70% Sorting block time: 00:00:00 bucket 145: 70% bucket 146: 60% bucket 144: 70% bucket 147: 60% bucket 154: 50% bucket 149: 60% bucket 166: 80% bucket 163: 100% bucket 142: 90% bucket 153: 50% bucket 155: 50% bucket 150: 60% bucket 151: 60% bucket 157: 40% bucket 141: 100% Reserving size (31083) for bucket 163 bucket 156: 40% bucket 161: 20% Reserving size (31083) for bucket 185 Returning block of 31057 for bucket 140 Getting block 188 of 206 bucket 164: 90% bucket 162: 20% bucket 148: 70% bucket 158: 50% bucket 152: 60% bucket 160: 30% bucket 175: 40% Reserving size (31083) for bucket 186 Entering block accumulator loop for bucket 184: Reserving size (31083) for bucket 187 bucket 172: 70% Getting block 164 of 208 Getting block 165 of 208 bucket 143: 80% bucket 176: 40% bucket 180: 30% bucket 170: 80% bucket 178: 40% bucket 173: 60% bucket 169: 80% bucket 165: 90% bucket 177: 40% Getting block 166 of 208 bucket 174: 50% bucket 167: 90% bucket 179: 30% bucket 168: 80% Sorting block of length 26965 for bucket 163 (Using difference cover) bucket 171: 80% Calculating Z arrays for bucket 185 bucket 159: 40% bucket 145: 80% bucket 146: 70% bucket 144: 80% Sorting block of length 12289 for bucket 141 (Using difference cover) Sorting block time: 00:00:00 Calculating Z arrays for bucket 163 bucket 147: 70% bucket 154: 60% bucket 149: 70% Sorting block time: 00:00:00 bucket 181: 10% bucket 166: 90% Reserving size (31083) for bucket 188 bucket 182: 10% bucket 164: 100% Calculating Z arrays for bucket 186 Calculating Z arrays for bucket 187 Getting block 189 of 206 bucket 175: 50% bucket 172: 80% bucket 153: 60% bucket 142: 100% bucket 155: 60% bucket 150: 70% bucket 151: 70% bucket 156: 50% bucket 161: 30% bucket 157: 50% bucket 158: 60% bucket 176: 50% bucket 162: 30% bucket 160: 40% bucket 180: 40% bucket 178: 50% bucket 173: 70% bucket 170: 90% bucket 177: 50% bucket 183: 10% bucket 169: 90% bucket 165: 100% Entering block accumulator loop for bucket 185: Returning block of 26966 for bucket 163 Reserving size (31083) for bucket 164 Reserving size (31083) for bucket 165 bucket 148: 80% bucket 152: 70% bucket 143: 90% bucket 174: 60% bucket 167: 100% bucket 179: 40% bucket 168: 90% Calculating Z arrays for bucket 188 bucket 171: 90% Sorting block of length 11710 for bucket 164 (Using difference cover) Entering block accumulator loop for bucket 186: Reserving size (31083) for bucket 189 Entering block accumulator loop for bucket 187: bucket 181: 20% Reserving size (31083) for bucket 166 Returning block of 12290 for bucket 141 Entering block accumulator loop for bucket 163: bucket 159: 50% bucket 145: 90% bucket 146: 80% bucket 144: 90% bucket 154: 70% bucket 147: 80% bucket 149: 80% Getting block 167 of 208 Sorting block time: 00:00:00 bucket 166: 100% bucket 175: 60% Sorting block of length 30919 for bucket 142 (Using difference cover) bucket 153: 70% bucket 150: 80% bucket 151: 80% bucket 155: 70% bucket 158: 70% bucket 161: 40% bucket 182: 20% bucket 156: 60% bucket 160: 50% Sorting block time: 00:00:00 Calculating Z arrays for bucket 164 Calculating Z arrays for bucket 165 bucket 162: 40% bucket 157: 60% bucket 143: 100% Calculating Z arrays for bucket 166 bucket 148: 90% bucket 152: 80% bucket 184: 10% bucket 172: 90% bucket 176: 60% Sorting block of length 28217 for bucket 165 (Using difference cover) bucket 178: 60% bucket 177: 60% bucket 180: 50% bucket 173: 80% bucket 170: 100% bucket 183: 20% bucket 169: 100% Sorting block of length 26075 for bucket 167 (Using difference cover) Entering block accumulator loop for bucket 188: Reserving size (31083) for bucket 167 bucket 159: 60% bucket 145: 100% bucket 146: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Calculating Z arrays for bucket 189 Returning block of 11711 for bucket 164 bucket 174: 70% bucket 181: 30% bucket 168: 100% Sorting block of length 24996 for bucket 166 (Using difference cover) bucket 171: 100% bucket 179: 50% bucket 175: 70% bucket 144: 100% bucket 182: 30% bucket 184: 20% bucket 172: 100% Sorting block time: 00:00:00 Getting block 190 of 206 Sorting block of length 11616 for bucket 170 (Using difference cover) Sorting block of length 28834 for bucket 169 (Using difference cover) Returning block of 26076 for bucket 167 bucket 154: 80% bucket 147: 90% bucket 149: 90% Returning block of 30920 for bucket 142 bucket 158: 80% bucket 160: 60% Returning block of 28218 for bucket 165 Entering block accumulator loop for bucket 164: bucket 161: 50% Entering block accumulator loop for bucket 165: bucket 153: 80% bucket 151: 90% bucket 150: 90% bucket 155: 80% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 180: 60% bucket 185: 10% bucket 176: 70% bucket 177: 70% bucket 178: 70% bucket 186: 10% Entering block accumulator loop for bucket 189: Sorting block of length 28843 for bucket 168 (Using difference cover) bucket 173: 90% Sorting block of length 22707 for bucket 171 (Using difference cover) bucket 183: 30% Sorting block of length 25544 for bucket 172 Sorting block of length 9687 for bucket 143 (Using difference cover) (Using difference cover) Sorting block time: 00:00:00 Entering block accumulator loop for bucket 166: bucket 156: 70% bucket 162: 50% bucket 163: 10% Getting block 168 of 208 Calculating Z arrays for bucket 167 bucket 148: 100% bucket 152: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 24997 for bucket 166 bucket 157: 70% Sorting block of length 21414 for bucket 145 (Using difference cover) Sorting block of length 28433 for bucket 144 (Using difference cover) bucket 159: 70% bucket 146: 100% bucket 160: 70% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 154: 90% bucket 147: 100% bucket 158: 90% bucket 149: 100% bucket 161: 60% bucket 150: 100% bucket 153: 90% bucket 151: 100% Sorting block time: 00:00:00 bucket 187: 10% bucket 155: 90% bucket 181: 40% Returning block of 9688 for bucket 143 Reserving size (31083) for bucket 190 bucket 184: 30% bucket 174: 80% Reserving size (31083) for bucket 168 Sorting block of length 17710 for bucket 148 (Using difference cover) Entering block accumulator loop for bucket 167: Getting block 169 of 208 Sorting block of length 25167 for bucket 146 (Using difference cover) Returning block of 21415 for bucket 145 Returning block of 28434 for bucket 144 bucket 182: 40% bucket 175: 80% bucket 179: 60% Returning block of 28835 for bucket 169 bucket 188: 10% Returning block of 11617 for bucket 170 bucket 180: 70% bucket 185: 20% bucket 162: 60% bucket 176: 80% Getting block 191 of 206 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 156: 80% bucket 163: 20% bucket 152: 100% bucket 160: 80% bucket 159: 80% Sorting block of length 29174 for bucket 147 (Using difference cover) bucket 177: 80% Sorting block of length 22825 for bucket 149 (Using difference cover) Sorting block of length 27405 for bucket 150 (Using difference cover) bucket 157: 80% Sorting block of length 18893 for bucket 151 (Using difference cover) bucket 165: 10% bucket 178: 80% Returning block of 22708 for bucket 171 Returning block of 28844 for bucket 168 bucket 186: 20% bucket 173: 100% bucket 183: 40% Returning block of 25545 for bucket 172 bucket 187: 20% bucket 181: 50% Sorting block time: 00:00:00 Calculating Z arrays for bucket 168 Reserving size (31083) for bucket 169 bucket 164: 10% bucket 158: 100% bucket 154: 100% bucket 153: 100% bucket 155: 100% Returning block of 17711 for bucket 148 Returning block of 25168 for bucket 146 Calculating Z arrays for bucket 190 Getting block 192 of 206 Getting block 193 of 206 Reserving size (31083) for bucket 191 bucket 184: 40% bucket 174: 90% bucket 182: 50% bucket 188: 20% bucket 179: 70% bucket 185: 30% bucket 180: 80% Sorting block time: 00:00:00 Sorting block of length 24541 for bucket 152 (Using difference cover) Getting block 170 of 208 bucket 162: 70% bucket 189: 10% bucket 176: 90% bucket 175: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 161: 70% bucket 166: 10% bucket 177: 90% bucket 160: 90% Sorting block of length 17229 for bucket 173 bucket 159: 90% (Using difference cover) bucket 163: 30% Getting block 194 of 206 Returning block of 22826 for bucket 149 bucket 178: 90% bucket 165: 20% Entering block accumulator loop for bucket 168: Calculating Z arrays for bucket 169 Sorting block of length 27578 for bucket 158 (Using difference cover) Sorting block of length 9287 for bucket 154 (Using difference cover) Sorting block of length 28244 for bucket 153 (Using difference cover) Sorting block of length 27970 for bucket 155 (Using difference cover) Getting block 171 of 208 Sorting block time: 00:00:00 bucket 187: 30% Returning block of 27406 for bucket 150 bucket 181: 60% Getting block 172 of 208 Reserving size (31083) for bucket 170 Returning block of 29175 for bucket 147 Entering block accumulator loop for bucket 190: Reserving size (31083) for bucket 192 Reserving size (31083) for bucket 193 Calculating Z arrays for bucket 191 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 157: 90% bucket 167: 10% bucket 164: 20% Returning block of 18894 for bucket 151 Returning block of 24542 for bucket 152 bucket 156: 90% bucket 162: 80% Getting block 195 of 206 Getting block 196 of 206 bucket 183: 50% bucket 186: 30% bucket 188: 30% bucket 180: 90% bucket 182: 60% bucket 160: 100% bucket 159: 100% bucket 165: 30% bucket 184: 50% bucket 179: 80% bucket 174: 100% Reserving size (31083) for bucket 194 Returning block of 17230 for bucket 173 bucket 189: 20% bucket 176: 100% bucket 175: 100% bucket 177: 100% Getting block 197 of 206 Getting block 198 of 206 Getting block 199 of 206 bucket 178: 100% bucket 185: 40% bucket 181: 70% bucket 161: 80% Entering block accumulator loop for bucket 169: bucket 163: 40% Reserving size (31083) for bucket 171 Getting block 173 of 208 Getting block 174 of 208 Reserving size (31083) for bucket 172 Calculating Z arrays for bucket 170 bucket 166: 20% Returning block of 9288 for bucket 154 Returning block of 27579 for bucket 158 Returning block of 28245 for bucket 153 Returning block of 27971 for bucket 155 Getting block 175 of 208 Calculating Z arrays for bucket 192 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 191: bucket 187: 40% Reserving size (31083) for bucket 195 Reserving size (31083) for bucket 196 bucket 188: 40% bucket 180: 100% bucket 183: 60% bucket 182: 70% bucket 186: 40% Sorting block of length 25504 for bucket 174 (Using difference cover) Calculating Z arrays for bucket 194 Sorting block of length 23563 for bucket 176 (Using difference cover) Sorting block of length 30993 for bucket 175 (Using difference cover) bucket 167: 20% bucket 162: 90% bucket 164: 30% Sorting block of length 23613 for bucket 177 (Using difference cover) Reserving size (31083) for bucket 197 bucket 184: 60% bucket 179: 90% Reserving size (31083) for bucket 198 Reserving size (31083) for bucket 199 Sorting block of length 23330 for bucket 178 (Using difference cover) bucket 189: 30% Sorting block of length 20659 for bucket 160 (Using difference cover) Sorting block of length 11304 for bucket 159 (Using difference cover) bucket 156: 100% bucket 157: 100% bucket 165: 40% Calculating Z arrays for bucket 171 Reserving size (31083) for bucket 173 Reserving size (31083) for bucket 174 Calculating Z arrays for bucket 172 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 185: 50% bucket 181: 80% Entering block accumulator loop for bucket 192: Entering block accumulator loop for bucket 193: Calculating Z arrays for bucket 195 Calculating Z arrays for bucket 196 Sorting block of length 12306 for bucket 180 (Using difference cover) Entering block accumulator loop for bucket 194: Calculating Z arrays for bucket 197 Getting block 200 of 206 bucket 190: 10% bucket 188: 50% bucket 187: 50% Calculating Z arrays for bucket 198 Calculating Z arrays for bucket 199 bucket 183: 70% bucket 186: 50% Returning block of 23564 for bucket 176 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 170: Getting block 176 of 208 Getting block 177 of 208 Reserving size (31083) for bucket 175 Getting block 178 of 208 Getting block 179 of 208 Returning block of 25505 for bucket 174 bucket 161: 90% bucket 168: 10% bucket 166: 30% bucket 163: 50% bucket 164: 40% Sorting block of length 27848 for bucket 156 (Using difference cover) Sorting block of length 13019 for bucket 157 (Using difference cover) Calculating Z arrays for bucket 173 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 171: Entering block accumulator loop for bucket 172: bucket 162: 100% Returning block of 11305 for bucket 159 bucket 167: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 179: 100% bucket 182: 80% Entering block accumulator loop for bucket 195: Entering block accumulator loop for bucket 196: Returning block of 20660 for bucket 160 bucket 169: 10% bucket 165: 50% Reserving size (31083) for bucket 176 Reserving size (31083) for bucket 177 Calculating Z arrays for bucket 175 Reserving size (31083) for bucket 178 Reserving size (31083) for bucket 179 Entering block accumulator loop for bucket 197: Reserving size (31083) for bucket 200 bucket 189: 40% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 198: Entering block accumulator loop for bucket 199: bucket 184: 70% bucket 185: 60% bucket 191: 10% bucket 190: 20% bucket 188: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 180 of 208 Getting block 181 of 208 Entering block accumulator loop for bucket 173: Getting block 182 of 208 Entering block accumulator loop for bucket 174: Sorting block of length 18647 for bucket 162 (Using difference cover) bucket 186: 60% bucket 187: 60% Sorting block time: 00:00:00 Getting block 183 of 208 bucket 168: 20% bucket 161: 100% bucket 164: 50% bucket 163: 60% Calculating Z arrays for bucket 176 Calculating Z arrays for bucket 177 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 175: Calculating Z arrays for bucket 179 bucket 167: 40% Returning block of 13020 for bucket 157 bucket 183: 80% Returning block of 23614 for bucket 177 Returning block of 12307 for bucket 180 Returning block of 30994 for bucket 175 bucket 181: 90% Sorting block of length 29910 for bucket 179 (Using difference cover) Returning block of 27849 for bucket 156 Reserving size (31083) for bucket 180 Reserving size (31083) for bucket 181 Reserving size (31083) for bucket 182 Calculating Z arrays for bucket 200 Returning block of 23331 for bucket 178 Sorting block time: 00:00:00 Getting block 201 of 206 bucket 193: 10% bucket 192: 10% bucket 182: 90% bucket 194: 10% bucket 189: 50% bucket 184: 80% bucket 185: 70% bucket 190: 30% bucket 188: 70% bucket 191: 20% bucket 187: 70% bucket 166: 40% bucket 165: 60% bucket 170: 10% Returning block of 18648 for bucket 162 Reserving size (31083) for bucket 183 Getting block 184 of 208 Sorting block of length 21620 for bucket 161 (Using difference cover) Entering block accumulator loop for bucket 176: Entering block accumulator loop for bucket 177: Entering block accumulator loop for bucket 178: bucket 186: 70% Getting block 202 of 206 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 179: bucket 172: 10% Getting block 185 of 208 Calculating Z arrays for bucket 180 bucket 171: 10% Calculating Z arrays for bucket 181 Calculating Z arrays for bucket 182 bucket 169: 20% bucket 168: 30% bucket 167: 50% bucket 173: 10% bucket 164: 60% bucket 163: 70% Calculating Z arrays for bucket 183 Reserving size (31083) for bucket 184 Entering block accumulator loop for bucket 200: Returning block of 29911 for bucket 179 bucket 183: 90% bucket 181: 100% bucket 197: 10% bucket 199: 10% bucket 174: 10% Returning block of 21621 for bucket 161 bucket 165: 70% Reserving size (31083) for bucket 201 bucket 198: 10% bucket 166: 50% bucket 170: 20% bucket 196: 10% bucket 192: 20% bucket 193: 20% bucket 194: 20% bucket 182: 100% bucket 188: 80% bucket 185: 80% bucket 184: 90% bucket 190: 40% Reserving size (31083) for bucket 185 Entering block accumulator loop for bucket 180: Entering block accumulator loop for bucket 181: Getting block 186 of 208 Getting block 187 of 208 Entering block accumulator loop for bucket 182: Entering block accumulator loop for bucket 183: Getting block 188 of 208 Calculating Z arrays for bucket 184 bucket 195: 10% bucket 175: 10% bucket 191: 30% bucket 168: 40% bucket 172: 20% bucket 169: 30% bucket 173: 20% bucket 167: 60% bucket 164: 70% bucket 163: 80% bucket 171: 20% Reserving size (31083) for bucket 202 bucket 187: 80% Getting block 203 of 206 Getting block 204 of 206 Getting block 205 of 206 Sorting block of length 29758 for bucket 181 (Using difference cover) bucket 189: 60% bucket 186: 80% bucket 176: 10% bucket 177: 10% bucket 165: 80% bucket 197: 20% bucket 199: 20% Sorting block time: 00:00:00 Calculating Z arrays for bucket 201 bucket 183: 100% bucket 198: 20% bucket 178: 10% bucket 174: 20% bucket 166: 60% Calculating Z arrays for bucket 185 bucket 170: 30% Reserving size (31083) for bucket 186 Getting block 206 of 206 Reserving size (31083) for bucket 187 Sorting block of length 17639 for bucket 182 (Using difference cover) bucket 192: 30% bucket 193: 30% bucket 194: 30% bucket 196: 20% bucket 188: 90% bucket 190: 50% bucket 185: 90% bucket 184: 100% Reserving size (31083) for bucket 188 Entering block accumulator loop for bucket 184: bucket 179: 10% bucket 168: 50% bucket 172: 30% bucket 173: 30% Sorting block time: 00:00:00 bucket 195: 20% bucket 169: 40% bucket 191: 40% bucket 167: 70% bucket 175: 20% Getting block 189 of 208 bucket 164: 80% bucket 163: 90% bucket 171: 30% Calculating Z arrays for bucket 202 Reserving size (31083) for bucket 203 Reserving size (31083) for bucket 204 Reserving size (31083) for bucket 205 bucket 200: 10% Returning block of 29759 for bucket 181 bucket 187: 90% bucket 165: 90% bucket 176: 20% bucket 177: 20% Entering block accumulator loop for bucket 185: Calculating Z arrays for bucket 186 Calculating Z arrays for bucket 187 bucket 181: 10% bucket 174: 30% bucket 170: 40% bucket 197: 30% bucket 199: 30% Entering block accumulator loop for bucket 201: Sorting block of length 29977 for bucket 183 (Using difference cover) bucket 198: 30% bucket 178: 20% bucket 180: 10% bucket 182: 10% bucket 183: 10% Sorting block time: 00:00:00 Reserving size (31083) for bucket 206 bucket 186: 90% bucket 189: 70% Sorting block of length 25270 for bucket 184 (Using difference cover) Calculating Z arrays for bucket 188 Reserving size (31083) for bucket 189 bucket 168: 60% bucket 173: 40% bucket 167: 80% bucket 169: 50% bucket 175: 30% bucket 164: 90% Returning block of 17640 for bucket 182 bucket 192: 40% Sorting block time: 00:00:00 bucket 194: 40% Entering block accumulator loop for bucket 186: Entering block accumulator loop for bucket 187: bucket 163: 100% bucket 171: 40% bucket 166: 70% bucket 165: 100% bucket 170: 50% bucket 174: 40% bucket 176: 30% bucket 177: 30% bucket 181: 20% bucket 193: 40% bucket 196: 30% bucket 190: 60% bucket 188: 100% bucket 185: 100% bucket 195: 30% bucket 191: 50% Calculating Z arrays for bucket 203 bucket 179: 20% bucket 172: 40% bucket 182: 20% bucket 178: 30% bucket 183: 20% Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 202: Calculating Z arrays for bucket 204 Calculating Z arrays for bucket 205 bucket 200: 20% bucket 187: 100% bucket 197: 40% bucket 199: 40% Entering block accumulator loop for bucket 188: bucket 180: 20% bucket 168: 70% bucket 167: 90% bucket 173: 50% bucket 169: 60% bucket 164: 100% bucket 175: 40% Sorting block of length 27356 for bucket 163 (Using difference cover) Returning block of 29978 for bucket 183 Sorting block of length 13962 for bucket 165 (Using difference cover) bucket 184: 10% bucket 166: 80% bucket 198: 40% bucket 170: 60% bucket 181: 30% bucket 185: 10% bucket 174: 50% bucket 176: 40% bucket 171: 50% bucket 177: 40% Entering block accumulator loop for bucket 189: bucket 172: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 179: 30% bucket 182: 30% Calculating Z arrays for bucket 206 Returning block of 25271 for bucket 184 bucket 192: 50% Sorting block of length 19494 for bucket 188 (Using difference cover) Sorting block of length 12051 for bucket 185 (Using difference cover) bucket 189: 80% bucket 178: 40% bucket 183: 30% Sorting block time: 00:00:00 bucket 186: 100% bucket 194: 50% bucket 193: 50% bucket 196: 40% Entering block accumulator loop for bucket 203: bucket 190: 70% Sorting block time: 00:00:00 bucket 195: 40% bucket 191: 60% Sorting block of length 20873 for bucket 164 (Using difference cover) bucket 168: 80% bucket 186: 10% bucket 167: 100% bucket 173: 60% bucket 187: 10% bucket 169: 70% bucket 180: 30% bucket 175: 50% Sorting block time: 00:00:00 Returning block of 13963 for bucket 165 Returning block of 27357 for bucket 163 bucket 184: 20% bucket 170: 70% bucket 174: 60% bucket 185: 20% bucket 181: 40% bucket 172: 60% bucket 176: 50% bucket 171: 60% bucket 177: 50% bucket 182: 40% Entering block accumulator loop for bucket 204: Entering block accumulator loop for bucket 205: Sorting block of length 21811 for bucket 187 (Using difference cover) bucket 197: 50% bucket 200: 30% bucket 199: 50% bucket 178: 50% bucket 183: 40% Sorting block of length 28977 for bucket 167 (Using difference cover) bucket 179: 40% Sorting block time: 00:00:00 bucket 201: 10% bucket 198: 50% Entering block accumulator loop for bucket 206: Returning block of 12052 for bucket 185 Sorting block of length 20582 for bucket 186 (Using difference cover) Sorting block time: 00:00:00 bucket 166: 90% Returning block of 20874 for bucket 164 bucket 168: 90% bucket 188: 10% bucket 186: 20% bucket 189: 10% bucket 173: 70% bucket 169: 80% bucket 180: 40% bucket 175: 60% Returning block of 19495 for bucket 188 bucket 192: 60% bucket 194: 60% bucket 193: 60% bucket 196: 50% bucket 190: 80% bucket 189: 90% bucket 184: 30% bucket 172: 70% bucket 170: 80% bucket 174: 70% bucket 181: 50% bucket 176: 60% bucket 185: 30% bucket 171: 70% bucket 177: 60% bucket 182: 50% Returning block of 28978 for bucket 167 bucket 187: 20% bucket 195: 50% bucket 191: 70% Sorting block time: 00:00:00 bucket 202: 10% Returning block of 21812 for bucket 187 bucket 197: 60% bucket 199: 60% bucket 200: 40% bucket 178: 60% bucket 179: 50% bucket 183: 50% bucket 168: 100% Getting block 190 of 208 bucket 201: 20% bucket 198: 60% bucket 193: 70% bucket 194: 70% bucket 192: 70% bucket 203: 10% bucket 190: 90% bucket 196: 60% bucket 188: 20% bucket 189: 20% bucket 186: 30% bucket 166: 100% bucket 169: 90% bucket 173: 80% bucket 175: 70% Getting block 191 of 208 bucket 180: 50% bucket 189: 100% bucket 172: 80% bucket 184: 40% bucket 195: 60% Returning block of 20583 for bucket 186 bucket 191: 80% bucket 205: 10% bucket 204: 10% bucket 170: 90% bucket 181: 60% bucket 174: 80% bucket 176: 70% bucket 182: 60% bucket 177: 70% bucket 171: 80% bucket 185: 40% bucket 202: 20% bucket 197: 70% bucket 199: 70% bucket 200: 50% bucket 201: 30% bucket 206: 10% Getting block 192 of 208 Sorting block of length 6038 for bucket 168 (Using difference cover) Sorting block time: 00:00:00 Reserving size (31083) for bucket 190 bucket 178: 70% bucket 179: 60% bucket 183: 60% bucket 198: 70% bucket 203: 20% Sorting block of length 25153 for bucket 189 (Using difference cover) bucket 193: 80% bucket 192: 80% bucket 194: 80% bucket 196: 70% bucket 190: 100% Sorting block of length 24843 for bucket 166 (Using difference cover) Reserving size (31083) for bucket 191 bucket 187: 30% Getting block 193 of 208 bucket 188: 30% bucket 173: 90% bucket 169: 100% bucket 180: 60% bucket 175: 80% bucket 186: 40% bucket 189: 30% bucket 172: 90% bucket 184: 50% bucket 170: 100% bucket 181: 70% Sorting block time: 00:00:00 bucket 195: 70% bucket 205: 20% bucket 204: 20% bucket 197: 80% bucket 202: 30% bucket 199: 80% bucket 200: 60% Sorting block time: 00:00:00 bucket 174: 90% bucket 176: 80% bucket 182: 70% bucket 171: 90% bucket 177: 80% bucket 185: 50% bucket 191: 90% bucket 206: 20% Sorting block of length 26831 for bucket 190 (Using difference cover) bucket 201: 40% bucket 198: 80% bucket 193: 90% bucket 192: 90% bucket 194: 90% bucket 196: 80% Returning block of 25154 for bucket 189 bucket 203: 30% Reserving size (31083) for bucket 192 Returning block of 6039 for bucket 168 Calculating Z arrays for bucket 190 Calculating Z arrays for bucket 191 Reserving size (31083) for bucket 193 bucket 178: 80% bucket 183: 70% Sorting block time: 00:00:00 bucket 195: 80% bucket 205: 30% Sorting block of length 29392 for bucket 169 bucket 204: 30% (Using difference cover) bucket 197: 90% bucket 202: 40% bucket 199: 90% bucket 200: 70% bucket 206: 30% Returning block of 26832 for bucket 190 bucket 201: 50% bucket 191: 100% bucket 192: 100% Sorting block time: 00:00:00 Sorting block of length 29828 for bucket 170 bucket 193: 100% (Using difference cover) bucket 194: 100% Returning block of 24844 for bucket 166 bucket 196: 90% bucket 187: 40% bucket 198: 90% bucket 203: 40% bucket 188: 40% bucket 173: 100% bucket 186: 50% bucket 189: 40% bucket 172: 100% bucket 181: 80% bucket 180: 70% bucket 175: 90% bucket 184: 60% bucket 179: 70% bucket 174: 100% bucket 206: 40% bucket 197: 100% bucket 202: 50% Sorting block time: 00:00:00 bucket 176: 90% bucket 171: 100% bucket 185: 60% bucket 205: 40% bucket 200: 80% bucket 199: 100% bucket 195: 90% Sorting block of length 27162 for bucket 191 (Using difference cover) Sorting block of length 6998 for bucket 192 (Using difference cover) Sorting block of length 28362 for bucket 193 (Using difference cover) Sorting block of length 20202 for bucket 194 (Using difference cover) bucket 204: 40% bucket 201: 60% bucket 203: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 196: 100% bucket 198: 100% Sorting block of length 16980 for bucket 197 (Using difference cover) bucket 206: 50% bucket 202: 60% Sorting block of length 19923 for bucket 199 (Using difference cover) Returning block of 6999 for bucket 192 Calculating Z arrays for bucket 192 bucket 177: 90% Entering block accumulator loop for bucket 190: Entering block accumulator loop for bucket 191: Calculating Z arrays for bucket 193 bucket 182: 80% Returning block of 29393 for bucket 169 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 27163 for bucket 191 bucket 200: 90% bucket 204: 50% bucket 203: 60% bucket 201: 70% bucket 195: 100% Sorting block of length 24932 for bucket 196 (Using difference cover) Sorting block of length 27098 for bucket 198 (Using difference cover) Returning block of 28363 for bucket 193 bucket 206: 60% Returning block of 16981 for bucket 197 bucket 178: 90% bucket 183: 80% Sorting block of length 27891 for bucket 173 (Using difference cover) bucket 205: 50% Sorting block of length 7544 for bucket 172 (Using difference cover) Sorting block of length 23216 for bucket 174 (Using difference cover) Returning block of 29829 for bucket 170 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 202: 70% Sorting block time: 00:00:00 Sorting block of length 12314 for bucket 195 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 188: 50% bucket 189: 50% bucket 186: 60% bucket 180: 80% bucket 184: 70% bucket 175: 100% bucket 181: 90% Sorting block of length 27586 for bucket 171 (Using difference cover) bucket 187: 50% bucket 176: 100% bucket 185: 70% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 206: 70% Returning block of 19924 for bucket 199 Returning block of 20203 for bucket 194 bucket 200: 100% bucket 204: 60% bucket 201: 80% bucket 205: 60% bucket 203: 70% Returning block of 24933 for bucket 196 Returning block of 27099 for bucket 198 Returning block of 12315 for bucket 195 bucket 202: 80% Sorting block of length 29451 for bucket 200 (Using difference cover) bucket 206: 80% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 192: bucket 203: 80% bucket 205: 70% bucket 204: 70% bucket 201: 90% bucket 206: 90% Sorting block time: 00:00:00 Returning block of 29452 for bucket 200 bucket 202: 90% bucket 203: 90% bucket 205: 80% bucket 204: 80% bucket 201: 100% Sorting block of length 22504 for bucket 201 (Using difference cover) bucket 206: 100% Sorting block of length 14938 for bucket 206 (Using difference cover) Getting block 194 of 208 Entering block accumulator loop for bucket 193: Getting block 195 of 208 bucket 179: 80% bucket 182: 90% bucket 177: 100% Returning block of 7545 for bucket 172 Returning block of 27892 for bucket 173 bucket 178: 100% bucket 183: 90% Sorting block of length 29542 for bucket 175 (Using difference cover) bucket 202: 100% Sorting block of length 27027 for bucket 202 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14939 for bucket 206 Sorting block time: 00:00:00 Returning block of 22505 for bucket 201 bucket 203: 100% Sorting block of length 14743 for bucket 203 (Using difference cover) bucket 205: 90% bucket 204: 90% Sorting block time: 00:00:00 Sorting block of length 28344 for bucket 176 (Using difference cover) Returning block of 23217 for bucket 174 Returning block of 27587 for bucket 171 bucket 189: 60% bucket 186: 70% bucket 188: 60% bucket 187: 60% bucket 181: 100% bucket 180: 90% bucket 184: 80% bucket 185: 80% Sorting block time: 00:00:00 Returning block of 14744 for bucket 203 Sorting block time: 00:00:00 Returning block of 27028 for bucket 202 bucket 205: 100% Sorting block of length 30003 for bucket 205 (Using difference cover) bucket 204: 100% Sorting block of length 26555 for bucket 204 (Using difference cover) Sorting block time: 00:00:00 bucket 191: 10% bucket 190: 10% Sorting block time: 00:00:00 Returning block of 26556 for bucket 204 Sorting block time: 00:00:00 Returning block of 30004 for bucket 205 Reserving size (31083) for bucket 194 Reserving size (31083) for bucket 195 Getting block 196 of 208 Sorting block of length 19727 for bucket 177 (Using difference cover) Exited Ebwt loop fchr[A]: 0 fchr[C]: 2320179 fchr[G]: 3500270 fchr[T]: 3500270 fchr[$]: 4641652 Sorting block time: 00:00:00 Sorting block of length 14351 for bucket 178 (Using difference cover) Returning block of 29543 for bucket 175 Getting block 197 of 208 Sorting block of length 13251 for bucket 181 (Using difference cover) bucket 179: 90% bucket 182: 100% bucket 183: 100% Returning block of 28345 for bucket 176 bucket 187: 70% bucket 186: 80% bucket 189: 70% bucket 188: 70% bucket 180: 100% bucket 184: 90% bucket 185: 90% Calculating Z arrays for bucket 194 Calculating Z arrays for bucket 195 Reserving size (31083) for bucket 196 Returning block of 19728 for bucket 177 Getting block 198 of 208 Getting block 199 of 208 Reserving size (31083) for bucket 197 Getting block 200 of 208 Sorting block of length 29790 for bucket 182 (Using difference cover) Sorting block of length 15076 for bucket 183 (Using difference cover) Getting block 201 of 208 Sorting block of length 25447 for bucket 180 (Using difference cover) Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 194: Entering block accumulator loop for bucket 195: Reserving size (31083) for bucket 198 Reserving size (31083) for bucket 199 Calculating Z arrays for bucket 197 Reserving size (31083) for bucket 200 Reserving size (31083) for bucket 201 Entering block accumulator loop for bucket 196: Calculating Z arrays for bucket 198 Calculating Z arrays for bucket 199 Calculating Z arrays for bucket 200 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 197: Entering block accumulator loop for bucket 198: Entering block accumulator loop for bucket 199: Entering block accumulator loop for bucket 200: Entering block accumulator loop for bucket 201: bucket 191: 20% bucket 192: 10% bucket 190: 20% Getting block 202 of 208 Reserving size (31083) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 193: 10% Sorting block time: 00:00:00 Returning block of 14352 for bucket 178 Sorting block time: 00:00:00 Returning block of 13252 for bucket 181 Sorting block time: 00:00:00 Returning block of 15077 for bucket 183 Getting block 203 of 208 Reserving size (31083) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: Getting block 204 of 208 Reserving size (31083) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: Getting block 205 of 208 Reserving size (31083) for bucket 205 Calculating Z arrays for bucket 205 Entering block accumulator loop for bucket 205: Sorting block time: 00:00:00 Returning block of 29791 for bucket 182 Sorting block time: 00:00:00 Returning block of 25448 for bucket 180 bucket 186: 90% bucket 187: 80% bucket 189: 80% Getting block 206 of 208 bucket 179: 100% Reserving size (31083) for bucket 206 Sorting block of length 22042 for bucket 179 (Using difference cover) Calculating Z arrays for bucket 206 Entering block accumulator loop for bucket 206: bucket 184: 100% Sorting block of length 18785 for bucket 184 (Using difference cover) bucket 194: 10% bucket 191: 30% Getting block 207 of 208 bucket 188: 80% Reserving size (31083) for bucket 207 Calculating Z arrays for bucket 207 Entering block accumulator loop for bucket 207: bucket 198: 10% bucket 199: 10% bucket 185: 100% bucket 200: 10% Sorting block of length 22750 for bucket 185 (Using difference cover) bucket 195: 10% bucket 196: 10% bucket 197: 10% Getting block 208 of 208 Reserving size (31083) for bucket 208 Calculating Z arrays for bucket 208 Entering block accumulator loop for bucket 208: bucket 201: 10% bucket 192: 20% bucket 190: 30% bucket 202: 10% bucket 193: 20% Sorting block time: 00:00:00 Returning block of 18786 for bucket 184 bucket 203: 10% bucket 204: 10% Sorting block time: 00:00:00 Returning block of 22043 for bucket 179 bucket 205: 10% bucket 186: 100% Sorting block of length 24511 for bucket 186 (Using difference cover) bucket 189: 90% bucket 187: 90% bucket 191: 40% bucket 206: 10% bucket 194: 20% bucket 207: 10% bucket 199: 20% bucket 198: 20% bucket 200: 20% bucket 188: 90% Sorting block time: 00:00:00 Returning block of 22751 for bucket 185 bucket 196: 20% bucket 201: 20% bucket 195: 20% bucket 197: 20% bucket 192: 30% bucket 202: 20% bucket 190: 40% bucket 193: 30% Sorting block time: 00:00:00 Returning block of 24512 for bucket 186 bucket 203: 20% bucket 204: 20% bucket 208: 10% bucket 205: 20% bucket 189: 100% Sorting block of length 18515 for bucket 189 (Using difference cover) bucket 187: 100% Sorting block of length 25030 for bucket 187 (Using difference cover) bucket 191: 50% bucket 199: 30% bucket 207: 20% bucket 206: 20% bucket 194: 30% bucket 200: 30% bucket 198: 30% bucket 201: 30% bucket 196: 30% bucket 188: 100% Sorting block of length 17873 for bucket 188 (Using difference cover) bucket 197: 30% bucket 195: 30% bucket 202: 30% bucket 208: 20% bucket 193: 40% bucket 190: 50% Sorting block time: 00:00:00 Returning block of 18516 for bucket 189 bucket 192: 40% bucket 203: 30% Sorting block time: 00:00:00 Returning block of 17874 for bucket 188 Sorting block time: 00:00:00 Returning block of 25031 for bucket 187 bucket 204: 30% bucket 205: 30% bucket 191: 60% bucket 199: 40% bucket 207: 30% bucket 206: 30% bucket 194: 40% bucket 200: 40% bucket 198: 40% bucket 201: 40% bucket 196: 40% bucket 208: 30% bucket 197: 40% bucket 195: 40% bucket 202: 40% bucket 193: 50% bucket 190: 60% bucket 203: 40% bucket 192: 50% bucket 204: 40% bucket 205: 40% bucket 208: 40% bucket 191: 70% bucket 199: 50% bucket 207: 40% bucket 200: 50% bucket 194: 50% bucket 206: 40% bucket 198: 50% bucket 201: 50% bucket 196: 50% bucket 197: 50% bucket 195: 50% bucket 202: 50% bucket 193: 60% bucket 203: 50% bucket 208: 50% bucket 190: 70% bucket 204: 50% bucket 205: 50% bucket 192: 60% bucket 191: 80% bucket 199: 60% bucket 207: 50% bucket 200: 60% bucket 194: 60% bucket 206: 50% bucket 198: 60% bucket 201: 60% bucket 196: 60% bucket 208: 60% bucket 197: 60% bucket 195: 60% bucket 202: 60% bucket 193: 70% bucket 203: 60% bucket 204: 60% bucket 190: 80% bucket 205: 60% bucket 191: 90% bucket 199: 70% bucket 192: 70% bucket 207: 60% bucket 208: 70% bucket 200: 70% bucket 194: 70% bucket 206: 60% bucket 198: 70% bucket 201: 70% bucket 196: 70% bucket 195: 70% bucket 197: 70% bucket 202: 70% bucket 193: 80% bucket 203: 70% bucket 204: 70% bucket 208: 80% bucket 190: 90% bucket 205: 70% bucket 191: 100% Sorting block of length 6540 for bucket 191 (Using difference cover) bucket 199: 80% bucket 207: 70% bucket 200: 80% bucket 194: 80% bucket 206: 70% Sorting block time: 00:00:00 Returning block of 6541 for bucket 191 bucket 201: 80% bucket 198: 80% bucket 192: 80% bucket 196: 80% bucket 195: 80% bucket 193: 90% bucket 197: 80% bucket 202: 80% bucket 208: 90% bucket 203: 80% bucket 204: 80% bucket 205: 80% bucket 190: 100% Sorting block of length 26837 for bucket 190 (Using difference cover) bucket 199: 90% bucket 207: 80% bucket 200: 90% bucket 194: 90% bucket 206: 80% bucket 201: 90% bucket 198: 90% bucket 196: 90% bucket 208: 100% Sorting block of length 25920 for bucket 208 (Using difference cover) bucket 192: 90% bucket 193: 100% Sorting block of length 23117 for bucket 193 (Using difference cover) bucket 202: 90% bucket 195: 90% bucket 197: 90% bucket 203: 90% Sorting block time: 00:00:00 Returning block of 26838 for bucket 190 bucket 204: 90% bucket 205: 90% Sorting block time: 00:00:00 Returning block of 25921 for bucket 208 bucket 199: 100% Sorting block of length 11005 for bucket 199 (Using difference cover) bucket 207: 90% bucket 200: 100% Sorting block of length 22072 for bucket 200 (Using difference cover) bucket 194: 100% Sorting block of length 11541 for bucket 194 (Using difference cover) bucket 206: 90% Sorting block time: 00:00:00 Returning block of 23118 for bucket 193 bucket 201: 100% Sorting block of length 27380 for bucket 201 (Using difference cover) bucket 198: 100% Sorting block of length 21743 for bucket 198 (Using difference cover) bucket 196: 100% Sorting block of length 23176 for bucket 196 (Using difference cover) Sorting block time: 00:00:00 Returning block of 11006 for bucket 199 bucket 202: 100% Sorting block of length 22751 for bucket 202 (Using difference cover) bucket 195: 100% Sorting block of length 28533 for bucket 195 (Using difference cover) Sorting block time: 00:00:00 Returning block of 11542 for bucket 194 bucket 192: 100% Sorting block of length 27908 for bucket 192 (Using difference cover) bucket 197: 100% Sorting block of length 28060 for bucket 197 (Using difference cover) bucket 203: 100% Sorting block of length 24589 for bucket 203 (Using difference cover) bucket 204: 100% Sorting block of length 25302 for bucket 204 (Using difference cover) Sorting block time: 00:00:00 Returning block of 22073 for bucket 200 bucket 205: 100% Sorting block of length 24284 for bucket 205 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23177 for bucket 196 bucket 207: 100% Sorting block of length 9979 for bucket 207 (Using difference cover) Sorting block time: 00:00:00 Returning block of 21744 for bucket 198 Sorting block time: 00:00:00 Returning block of 27381 for bucket 201 bucket 206: 100% Sorting block of length 28106 for bucket 206 (Using difference cover) Sorting block time: 00:00:00 Returning block of 22752 for bucket 202 Sorting block time: 00:00:00 Returning block of 9980 for bucket 207 Sorting block time: 00:00:00 Returning block of 24590 for bucket 203 Sorting block time: 00:00:00 Returning block of 27909 for bucket 192 Sorting block time: 00:00:00 Returning block of 28061 for bucket 197 Sorting block time: 00:00:00 Returning block of 28534 for bucket 195 Sorting block time: 00:00:00 Returning block of 25303 for bucket 204 Sorting block time: 00:00:00 Returning block of 24285 for bucket 205 Sorting block time: 00:00:00 Returning block of 28107 for bucket 206 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 5741754 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 1160420 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 4641652 bwtLen: 4641653 sz: 1160413 bwtSz: 1160414 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 290104 offsSz: 1160416 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 24176 numLines: 24176 ebwtTotLen: 1547264 ebwtTotSz: 1547264 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:03 Reading reference sizes Exited Ebwt loop fchr[A]: 0 fchr[C]: 1142742 fchr[G]: 1142742 fchr[T]: 2320179 fchr[$]: 4641652 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: 41443 Using parameters --bmax 31083 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 31083 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 5741754 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 1160420 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 4641652 bwtLen: 4641653 sz: 1160413 bwtSz: 1160414 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 290104 offsSz: 1160416 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 24176 numLines: 24176 ebwtTotLen: 1547264 ebwtTotSz: 1547264 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:03 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 42, merged 129; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 19, merged 19; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 12, merged 12; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 6, merged 8; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 4; iterating... Avg bucket size: 22102.1 (target: 31082) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 210 Reserving size (31083) for bucket 1 Getting block 2 of 210 Getting block 3 of 210 Getting block 4 of 210 Getting block 5 of 210 Getting block 6 of 210 Getting block 7 of 210 Getting block 8 of 210 Getting block 9 of 210 Getting block 10 of 210 Getting block 11 of 210 Getting block 12 of 210 Getting block 13 of 210 Getting block 14 of 210 Getting block 15 of 210 Getting block 16 of 210 Getting block 17 of 210 Getting block 18 of 210 Getting block 19 of 210 Getting block 20 of 210 Getting block 21 of 210 Getting block 22 of 210 Getting block 23 of 210 Calculating Z arrays for bucket 1 Reserving size (31083) for bucket 2 Reserving size (31083) for bucket 3 Reserving size (31083) for bucket 4 Reserving size (31083) for bucket 5 Reserving size (31083) for bucket 6 Getting block 24 of 210 Reserving size (31083) for bucket 7 Reserving size (31083) for bucket 8 Reserving size (31083) for bucket 9 Reserving size (31083) for bucket 10 Reserving size (31083) for bucket 11 Reserving size (31083) for bucket 12 Reserving size (31083) for bucket 13 Reserving size (31083) for bucket 14 Reserving size (31083) for bucket 15 Reserving size (31083) for bucket 16 Reserving size (31083) for bucket 17 Reserving size (31083) for bucket 18 Reserving size (31083) for bucket 19 Reserving size (31083) for bucket 20 Reserving size (31083) for bucket 21 Reserving size (31083) for bucket 22 Reserving size (31083) for bucket 23 Getting block 25 of 210 Calculating Z arrays for bucket 2 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 6 Reserving size (31083) for bucket 24 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 13 Calculating Z arrays for bucket 12 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 Reserving size (31083) for bucket 25 Entering block accumulator loop for bucket 2: Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 4: Calculating Z arrays for bucket 24 Entering block accumulator loop for bucket 6: Getting block 26 of 210 Entering block accumulator loop for bucket 5: 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 13: Entering block accumulator loop for bucket 12: 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 14: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 18: 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: Reserving size (31083) for bucket 26 Entering block accumulator loop for bucket 25: Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 26: bucket 2: 10% bucket 4: 10% bucket 6: 10% bucket 11: 10% bucket 8: 10% bucket 10: 10% bucket 9: 10% bucket 12: 10% bucket 13: 10% bucket 15: 10% bucket 17: 10% bucket 19: 10% bucket 16: 10% bucket 20: 10% bucket 22: 10% bucket 21: 10% bucket 25: 10% bucket 26: 10% bucket 23: 10% bucket 24: 10% Getting block 27 of 210 Reserving size (31083) for bucket 27 Calculating Z arrays for bucket 27 bucket 7: 10% Entering block accumulator loop for bucket 27: bucket 2: 20% bucket 4: 20% bucket 11: 20% bucket 6: 20% bucket 10: 20% bucket 9: 20% bucket 12: 20% bucket 13: 20% bucket 15: 20% bucket 8: 20% bucket 17: 20% bucket 19: 20% bucket 16: 20% bucket 5: 10% bucket 20: 20% bucket 22: 20% bucket 21: 20% bucket 1: 10% bucket 25: 20% bucket 26: 20% bucket 14: 10% bucket 23: 20% bucket 24: 20% bucket 18: 10% bucket 3: 10% bucket 2: 30% bucket 4: 30% bucket 27: 10% bucket 11: 30% bucket 6: 30% bucket 10: 30% bucket 9: 30% bucket 12: 30% bucket 8: 30% bucket 13: 30% bucket 15: 30% bucket 17: 30% bucket 19: 30% bucket 16: 30% bucket 20: 30% bucket 22: 30% bucket 21: 30% bucket 25: 30% bucket 26: 30% bucket 24: 30% bucket 23: 30% bucket 7: 20% bucket 2: 40% bucket 4: 40% bucket 11: 40% bucket 6: 40% bucket 10: 40% bucket 5: 20% bucket 27: 20% bucket 8: 40% bucket 12: 40% bucket 9: 40% bucket 3: 20% bucket 13: 40% bucket 15: 40% bucket 1: 20% bucket 17: 40% bucket 19: 40% bucket 16: 40% bucket 20: 40% bucket 22: 40% bucket 21: 40% bucket 14: 20% bucket 25: 40% bucket 26: 40% bucket 18: 20% bucket 24: 40% bucket 23: 40% bucket 2: 50% bucket 11: 50% bucket 6: 50% bucket 4: 50% bucket 8: 50% bucket 12: 50% bucket 10: 50% bucket 9: 50% bucket 13: 50% bucket 7: 30% bucket 15: 50% bucket 27: 30% bucket 17: 50% bucket 19: 50% bucket 16: 50% bucket 20: 50% bucket 22: 50% bucket 21: 50% bucket 25: 50% bucket 26: 50% bucket 3: 30% bucket 2: 60% bucket 23: 50% bucket 5: 30% bucket 24: 50% bucket 11: 60% bucket 6: 60% bucket 4: 60% bucket 1: 30% bucket 8: 60% bucket 10: 60% bucket 12: 60% bucket 9: 60% bucket 13: 60% bucket 15: 60% bucket 17: 60% bucket 14: 30% bucket 19: 60% bucket 16: 60% bucket 27: 40% bucket 20: 60% bucket 22: 60% bucket 21: 60% bucket 18: 30% bucket 2: 70% bucket 7: 40% bucket 25: 60% bucket 26: 60% bucket 23: 60% bucket 11: 70% bucket 6: 70% bucket 4: 70% bucket 24: 60% bucket 8: 70% bucket 10: 70% bucket 12: 70% bucket 9: 70% bucket 3: 40% bucket 13: 70% bucket 15: 70% bucket 17: 70% bucket 19: 70% bucket 16: 70% bucket 27: 50% bucket 20: 70% bucket 22: 70% bucket 21: 70% bucket 5: 40% bucket 2: 80% bucket 25: 70% bucket 11: 80% bucket 6: 80% bucket 4: 80% bucket 23: 70% bucket 14: 40% bucket 8: 80% bucket 10: 80% bucket 24: 70% bucket 26: 70% bucket 12: 80% bucket 9: 80% bucket 1: 40% bucket 7: 50% bucket 13: 80% bucket 15: 80% bucket 17: 80% bucket 19: 80% bucket 16: 80% bucket 20: 80% bucket 18: 40% bucket 27: 60% bucket 21: 80% bucket 22: 80% bucket 3: 50% bucket 2: 90% bucket 11: 90% bucket 6: 90% bucket 4: 90% bucket 25: 80% bucket 8: 90% bucket 1: 50% bucket 10: 90% bucket 23: 80% bucket 12: 90% bucket 5: 50% bucket 9: 90% bucket 13: 90% bucket 26: 80% bucket 24: 80% bucket 15: 90% bucket 17: 90% bucket 19: 90% bucket 16: 90% bucket 20: 90% bucket 21: 90% bucket 7: 60% bucket 27: 70% bucket 2: 100% Sorting block of length 26627 for bucket 2 (Using difference cover) bucket 14: 50% bucket 22: 90% bucket 11: 100% Sorting block of length 10581 for bucket 11 (Using difference cover) bucket 4: 100% bucket 6: 100% Sorting block of length 23452 for bucket 4 Sorting block of length 28563 for bucket 6 (Using difference cover) (Using difference cover) bucket 1: 60% bucket 10: 100% Sorting block of length 25599 for bucket 10 (Using difference cover) bucket 3: 60% bucket 25: 90% bucket 8: 100% Sorting block of length 21035 for bucket 8 (Using difference cover) bucket 12: 100% Sorting block of length 24858 for bucket 12 (Using difference cover) bucket 9: 100% Sorting block of length 30463 for bucket 9 (Using difference cover) bucket 13: 100% Sorting block of length 26102 for bucket 13 (Using difference cover) bucket 23: 90% bucket 15: 100% Sorting block of length 25723 for bucket 15 (Using difference cover) bucket 18: 50% bucket 26: 90% bucket 17: 100% Sorting block of length 20211 for bucket 17 (Using difference cover) bucket 19: 100% Sorting block of length 25177 for bucket 19 (Using difference cover) bucket 24: 90% bucket 16: 100% Sorting block of length 15523 for bucket 16 (Using difference cover) bucket 20: 100% Sorting block of length 26779 for bucket 20 (Using difference cover) bucket 5: 60% bucket 21: 100% Sorting block of length 28690 for bucket 21 (Using difference cover) bucket 27: 80% Sorting block time: 00:00:00 Returning block of 10582 for bucket 11 bucket 1: 70% Getting block 28 of 210 Reserving size (31083) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 7: 70% bucket 3: 70% bucket 22: 100% Sorting block of length 29740 for bucket 22 (Using difference cover) bucket 25: 100% Sorting block of length 29238 for bucket 25 (Using difference cover) bucket 14: 60% bucket 23: 100% Sorting block of length 27716 for bucket 23 (Using difference cover) bucket 26: 100% Sorting block of length 21428 for bucket 26 (Using difference cover) bucket 24: 100% Sorting block of length 30726 for bucket 24 (Using difference cover) bucket 1: 80% Sorting block time: 00:00:00 Returning block of 23453 for bucket 4 bucket 27: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 21036 for bucket 8 Returning block of 26628 for bucket 2 bucket 3: 80% bucket 18: 60% bucket 28: 10% Sorting block time: 00:00:00 Returning block of 24859 for bucket 12 bucket 5: 70% Getting block 29 of 210 Reserving size (31083) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: Sorting block time: 00:00:00 Returning block of 28564 for bucket 6 Getting block 30 of 210 Reserving size (31083) for bucket 30 Calculating Z arrays for bucket 30 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 20212 for bucket 17 Returning block of 30464 for bucket 9 Entering block accumulator loop for bucket 30: Sorting block time: 00:00:00 Returning block of 15524 for bucket 16 bucket 7: 80% Getting block 31 of 210 Reserving size (31083) for bucket 31 Getting block 32 of 210 Calculating Z arrays for bucket 31 Reserving size (31083) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 31: Entering block accumulator loop for bucket 32: Getting block 33 of 210 Reserving size (31083) for bucket 33 Calculating Z arrays for bucket 33 Sorting block time: 00:00:00 Returning block of 25600 for bucket 10 Entering block accumulator loop for bucket 33: Sorting block time: 00:00:00 Returning block of 25724 for bucket 15 Getting block 34 of 210 Reserving size (31083) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: Getting block 35 of 210 Reserving size (31083) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: Sorting block time: 00:00:00 Returning block of 26103 for bucket 13 Sorting block time: 00:00:00 Returning block of 28691 for bucket 21 bucket 1: 90% Sorting block time: 00:00:00 Returning block of 26780 for bucket 20 Sorting block time: 00:00:00 Returning block of 25178 for bucket 19 bucket 14: 70% Sorting block time: 00:00:00 Returning block of 21429 for bucket 26 bucket 3: 90% bucket 27: 100% Sorting block of length 12139 for bucket 27 (Using difference cover) Sorting block time: 00:00:00 Returning block of 27717 for bucket 23 Sorting block time: 00:00:00 Returning block of 29239 for bucket 25 bucket 28: 20% Sorting block time: 00:00:00 Returning block of 29741 for bucket 22 Getting block 36 of 210 Reserving size (31083) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Getting block 37 of 210 Reserving size (31083) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: Getting block 38 of 210 Reserving size (31083) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: Getting block 39 of 210 Reserving size (31083) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Sorting block time: 00:00:00 Returning block of 30727 for bucket 24 Getting block 40 of 210 Reserving size (31083) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: Getting block 41 of 210 Reserving size (31083) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: bucket 29: 10% Getting block 42 of 210 Reserving size (31083) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: Getting block 43 of 210 Reserving size (31083) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: bucket 30: 10% Sorting block time: 00:00:00 Returning block of 12140 for bucket 27 bucket 31: 10% Getting block 44 of 210 Reserving size (31083) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: bucket 32: 10% Getting block 45 of 210 Reserving size (31083) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Getting block 46 of 210 bucket 5: 80% Reserving size (31083) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: bucket 33: 10% bucket 7: 90% bucket 18: 70% bucket 1: 100% Sorting block of length 15589 for bucket 1 (Using difference cover) bucket 34: 10% bucket 3: 100% Sorting block of length 18467 for bucket 3 (Using difference cover) bucket 35: 10% Sorting block time: 00:00:00 Returning block of 15590 for bucket 1 bucket 28: 30% bucket 36: 10% bucket 14: 80% bucket 38: 10% bucket 37: 10% bucket 40: 10% Sorting block time: 00:00:00 Returning block of 18468 for bucket 3 bucket 41: 10% bucket 29: 20% bucket 43: 10% bucket 42: 10% bucket 30: 20% bucket 31: 20% Getting block 47 of 210 Reserving size (31083) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 44: 10% Getting block 48 of 210 Reserving size (31083) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: bucket 32: 20% bucket 45: 10% Getting block 49 of 210 Reserving size (31083) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: bucket 33: 20% bucket 39: 10% bucket 46: 10% bucket 34: 20% bucket 7: 100% Sorting block of length 16819 for bucket 7 (Using difference cover) bucket 5: 90% bucket 35: 20% bucket 18: 80% bucket 28: 40% bucket 36: 20% bucket 38: 20% bucket 37: 20% bucket 40: 20% bucket 29: 30% bucket 41: 20% bucket 31: 30% bucket 42: 20% bucket 30: 30% Sorting block time: 00:00:00 Returning block of 16820 for bucket 7 bucket 43: 20% bucket 47: 10% bucket 44: 20% Getting block 50 of 210 Reserving size (31083) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 48: 10% bucket 14: 90% bucket 32: 30% bucket 45: 20% bucket 33: 30% bucket 49: 10% bucket 46: 20% bucket 34: 30% bucket 35: 30% bucket 39: 20% bucket 5: 100% Sorting block of length 13262 for bucket 5 (Using difference cover) bucket 28: 50% bucket 40: 30% bucket 36: 30% bucket 38: 30% bucket 37: 30% bucket 29: 40% bucket 31: 40% bucket 41: 30% bucket 18: 90% bucket 42: 30% bucket 30: 40% bucket 47: 20% bucket 44: 30% Sorting block time: 00:00:00 Returning block of 13263 for bucket 5 bucket 48: 20% bucket 45: 30% bucket 33: 40% bucket 32: 40% bucket 46: 30% bucket 43: 30% bucket 34: 40% bucket 49: 20% bucket 14: 100% bucket 50: 10% Sorting block of length 15840 for bucket 14 (Using difference cover) bucket 35: 40% Getting block 51 of 210 bucket 28: 60% Reserving size (31083) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 39: 30% bucket 40: 40% bucket 31: 50% bucket 36: 40% bucket 37: 40% bucket 29: 50% bucket 38: 40% bucket 41: 40% bucket 42: 40% bucket 44: 40% bucket 47: 30% Sorting block time: 00:00:00 Returning block of 15841 for bucket 14 bucket 30: 50% Getting block 52 of 210 bucket 48: 30% Reserving size (31083) for bucket 52 Calculating Z arrays for bucket 52 bucket 33: 50% bucket 45: 40% Entering block accumulator loop for bucket 52: bucket 32: 50% Getting block 53 of 210 Reserving size (31083) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 18: 100% Sorting block of length 22734 for bucket 18 (Using difference cover) bucket 46: 40% bucket 43: 40% bucket 34: 50% bucket 49: 30% bucket 35: 50% bucket 28: 70% bucket 50: 20% bucket 51: 10% bucket 40: 50% bucket 31: 60% bucket 29: 60% bucket 37: 50% bucket 36: 50% bucket 38: 50% bucket 42: 50% bucket 41: 50% bucket 39: 40% bucket 44: 50% bucket 47: 40% bucket 30: 60% bucket 33: 60% bucket 48: 40% bucket 45: 50% Sorting block time: 00:00:00 Returning block of 22735 for bucket 18 bucket 32: 60% bucket 43: 50% bucket 46: 50% bucket 34: 60% bucket 49: 40% bucket 28: 80% bucket 35: 60% bucket 53: 10% bucket 50: 30% bucket 31: 70% bucket 40: 60% bucket 51: 20% bucket 29: 70% bucket 37: 60% bucket 36: 60% bucket 42: 60% bucket 38: 60% bucket 41: 60% bucket 39: 50% bucket 44: 60% bucket 30: 70% bucket 52: 10% bucket 47: 50% bucket 33: 70% bucket 48: 50% bucket 45: 60% bucket 32: 70% bucket 43: 60% bucket 34: 70% bucket 46: 60% bucket 49: 50% bucket 28: 90% bucket 35: 70% bucket 50: 40% bucket 31: 80% bucket 40: 70% bucket 29: 80% bucket 37: 70% bucket 42: 70% bucket 51: 30% bucket 36: 70% bucket 38: 70% bucket 41: 70% bucket 39: 60% bucket 44: 70% bucket 53: 20% bucket 30: 80% bucket 47: 60% bucket 33: 80% bucket 48: 60% bucket 45: 70% bucket 32: 80% bucket 43: 70% bucket 34: 80% bucket 46: 70% bucket 52: 20% bucket 49: 60% bucket 28: 100% Sorting block of length 21325 for bucket 28 (Using difference cover) bucket 35: 80% bucket 50: 50% bucket 31: 90% bucket 40: 80% bucket 29: 90% Getting block 54 of 210 Reserving size (31083) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 37: 80% bucket 42: 80% bucket 36: 80% bucket 38: 80% bucket 41: 80% bucket 51: 40% bucket 39: 70% bucket 44: 80% bucket 30: 90% Sorting block time: 00:00:00 Returning block of 21326 for bucket 28 bucket 33: 90% bucket 48: 70% bucket 45: 80% Getting block 55 of 210 Reserving size (31083) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 32: 90% bucket 43: 80% bucket 34: 90% bucket 53: 30% bucket 46: 80% bucket 49: 70% bucket 35: 90% bucket 31: 100% Sorting block of length 2446 for bucket 31 (Using difference cover) bucket 52: 30% bucket 50: 60% bucket 40: 90% bucket 29: 100% Sorting block of length 13007 for bucket 29 (Using difference cover) bucket 42: 90% bucket 37: 90% Sorting block time: 00:00:00 Returning block of 2447 for bucket 31 bucket 36: 90% bucket 38: 90% bucket 54: 10% bucket 41: 90% bucket 39: 80% bucket 44: 90% bucket 51: 50% bucket 30: 100% Sorting block of length 29480 for bucket 30 (Using difference cover) bucket 47: 70% bucket 33: 100% Sorting block of length 18761 for bucket 33 (Using difference cover) bucket 48: 80% bucket 45: 90% Sorting block time: 00:00:00 Returning block of 13008 for bucket 29 bucket 43: 90% bucket 34: 100% Sorting block of length 29320 for bucket 34 (Using difference cover) bucket 32: 100% Sorting block of length 31020 for bucket 32 (Using difference cover) bucket 55: 10% Getting block 56 of 210 Reserving size (31083) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 46: 90% bucket 49: 80% bucket 53: 40% bucket 35: 100% Sorting block of length 22827 for bucket 35 (Using difference cover) Getting block 57 of 210 Reserving size (31083) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 50: 70% Sorting block time: 00:00:00 Returning block of 18762 for bucket 33 bucket 40: 100% Sorting block of length 10708 for bucket 40 (Using difference cover) bucket 42: 100% Sorting block of length 9448 for bucket 42 (Using difference cover) bucket 52: 40% bucket 37: 100% Sorting block of length 10403 for bucket 37 (Using difference cover) bucket 36: 100% Sorting block of length 29845 for bucket 36 (Using difference cover) bucket 38: 100% Sorting block of length 24605 for bucket 38 (Using difference cover) bucket 41: 100% Sorting block of length 26486 for bucket 41 (Using difference cover) Sorting block time: 00:00:00 Returning block of 29481 for bucket 30 bucket 54: 20% bucket 39: 90% bucket 44: 100% Sorting block of length 18003 for bucket 44 (Using difference cover) bucket 51: 60% bucket 47: 80% bucket 48: 90% Getting block 58 of 210 Reserving size (31083) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: bucket 45: 100% Sorting block of length 23930 for bucket 45 (Using difference cover) bucket 43: 100% Sorting block of length 29689 for bucket 43 (Using difference cover) Getting block 59 of 210 Reserving size (31083) for bucket 59 Calculating Z arrays for bucket 59 Sorting block time: 00:00:00 Returning block of 10709 for bucket 40 Entering block accumulator loop for bucket 59: Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 29321 for bucket 34 Returning block of 31021 for bucket 32 bucket 46: 100% Sorting block of length 29383 for bucket 46 (Using difference cover) bucket 55: 20% bucket 56: 10% Getting block 60 of 210 Reserving size (31083) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 49: 90% Getting block 61 of 210 Reserving size (31083) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: Getting block 62 of 210 Reserving size (31083) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: Sorting block time: 00:00:00 Returning block of 9449 for bucket 42 Sorting block time: 00:00:00 Returning block of 22828 for bucket 35 bucket 53: 50% Getting block 63 of 210 Reserving size (31083) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 50: 80% Getting block 64 of 210 Reserving size (31083) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: Sorting block time: 00:00:00 Returning block of 10404 for bucket 37 Getting block 65 of 210 Reserving size (31083) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: bucket 52: 50% bucket 57: 10% bucket 39: 100% Sorting block of length 27335 for bucket 39 (Using difference cover) bucket 54: 30% Sorting block time: 00:00:00 Returning block of 24606 for bucket 38 bucket 47: 90% bucket 48: 100% bucket 51: 70% Sorting block of length 29359 for bucket 48 (Using difference cover) bucket 58: 10% bucket 59: 10% bucket 56: 20% bucket 49: 100% Sorting block of length 24231 for bucket 49 (Using difference cover) Getting block 66 of 210 Reserving size (31083) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: bucket 55: 30% bucket 60: 10% bucket 61: 10% Sorting block time: 00:00:00 Returning block of 18004 for bucket 44 Sorting block time: 00:00:00 Returning block of 29846 for bucket 36 Sorting block time: 00:00:00 Returning block of 26487 for bucket 41 bucket 53: 60% bucket 50: 90% bucket 62: 10% bucket 63: 10% Getting block 67 of 210 Reserving size (31083) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: bucket 64: 10% Getting block 68 of 210 Reserving size (31083) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 52: 60% Sorting block time: 00:00:00 Returning block of 23931 for bucket 45 bucket 65: 10% bucket 57: 20% bucket 54: 40% Getting block 69 of 210 bucket 47: 100% Reserving size (31083) for bucket 69 Getting block 70 of 210 Sorting block of length 11232 for bucket 47 (Using difference cover) Calculating Z arrays for bucket 69 Reserving size (31083) for bucket 70 bucket 51: 80% Sorting block time: 00:00:00 Calculating Z arrays for bucket 70 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 Entering block accumulator loop for bucket 69: Returning block of 29690 for bucket 43 Entering block accumulator loop for bucket 70: Returning block of 24232 for bucket 49 bucket 58: 20% Returning block of 29384 for bucket 46 bucket 59: 20% bucket 56: 30% Returning block of 27336 for bucket 39 Returning block of 29360 for bucket 48 Returning block of 11233 for bucket 47 bucket 55: 40% bucket 60: 20% bucket 61: 20% bucket 66: 10% bucket 50: 100% Sorting block of length 9260 for bucket 50 (Using difference cover) bucket 53: 70% bucket 62: 20% bucket 63: 20% Getting block 71 of 210 Reserving size (31083) for bucket 71 Getting block 72 of 210 Calculating Z arrays for bucket 71 Reserving size (31083) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 71: Entering block accumulator loop for bucket 72: Getting block 73 of 210 Reserving size (31083) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: bucket 67: 10% bucket 64: 20% bucket 52: 70% bucket 68: 10% bucket 65: 20% Sorting block time: 00:00:00 Returning block of 9261 for bucket 50 bucket 54: 50% bucket 57: 30% Getting block 74 of 210 Reserving size (31083) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: Getting block 75 of 210 Reserving size (31083) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: Getting block 76 of 210 Reserving size (31083) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: Getting block 77 of 210 Reserving size (31083) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 51: 90% bucket 56: 40% bucket 58: 30% bucket 59: 30% bucket 55: 50% bucket 61: 30% bucket 60: 30% bucket 69: 10% bucket 70: 10% bucket 66: 20% bucket 53: 80% bucket 62: 30% bucket 63: 30% bucket 71: 10% bucket 72: 10% bucket 73: 10% bucket 52: 80% bucket 64: 30% bucket 67: 20% bucket 68: 20% bucket 65: 30% bucket 54: 60% bucket 57: 40% bucket 74: 10% bucket 75: 10% bucket 76: 10% bucket 77: 10% bucket 51: 100% Sorting block of length 27534 for bucket 51 (Using difference cover) bucket 56: 50% bucket 58: 40% bucket 55: 60% bucket 59: 40% bucket 61: 40% bucket 60: 40% bucket 53: 90% bucket 62: 40% bucket 66: 30% bucket 70: 20% bucket 69: 20% bucket 63: 40% bucket 52: 90% bucket 71: 20% bucket 72: 20% bucket 64: 40% bucket 73: 20% bucket 67: 30% bucket 68: 30% bucket 54: 70% bucket 65: 40% Sorting block time: 00:00:00 Returning block of 27535 for bucket 51 bucket 57: 50% bucket 74: 20% bucket 75: 20% bucket 76: 20% bucket 77: 20% Getting block 78 of 210 Reserving size (31083) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 56: 60% bucket 55: 70% bucket 58: 50% bucket 61: 50% bucket 59: 50% bucket 60: 50% bucket 53: 100% Sorting block of length 29485 for bucket 53 (Using difference cover) bucket 63: 50% bucket 66: 40% bucket 52: 100% Sorting block of length 18978 for bucket 52 (Using difference cover) bucket 70: 30% bucket 69: 30% bucket 71: 30% bucket 64: 50% bucket 72: 30% bucket 73: 30% bucket 67: 40% bucket 68: 40% bucket 54: 80% bucket 65: 50% bucket 57: 60% Sorting block time: 00:00:00 Returning block of 18979 for bucket 52 bucket 75: 30% bucket 74: 30% bucket 76: 30% bucket 77: 30% bucket 56: 70% Sorting block time: 00:00:00 Returning block of 29486 for bucket 53 bucket 55: 80% bucket 58: 60% bucket 60: 60% bucket 61: 60% bucket 59: 60% bucket 63: 60% bucket 62: 50% bucket 66: 50% bucket 70: 40% bucket 69: 40% bucket 64: 60% bucket 71: 40% bucket 72: 40% bucket 73: 40% bucket 54: 90% bucket 67: 50% bucket 68: 50% bucket 65: 60% bucket 57: 70% bucket 74: 40% bucket 75: 40% bucket 76: 40% bucket 56: 80% bucket 77: 40% bucket 60: 70% bucket 61: 70% bucket 58: 70% bucket 55: 90% bucket 59: 70% Getting block 79 of 210 Reserving size (31083) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 63: 70% bucket 78: 10% Getting block 80 of 210 Reserving size (31083) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 66: 60% bucket 64: 70% bucket 70: 50% bucket 69: 50% bucket 71: 50% bucket 62: 60% bucket 54: 100% Sorting block of length 23394 for bucket 54 (Using difference cover) bucket 72: 50% bucket 68: 60% bucket 67: 60% bucket 73: 50% bucket 65: 70% bucket 57: 80% bucket 56: 90% bucket 74: 50% bucket 75: 50% bucket 76: 50% bucket 77: 50% bucket 61: 80% bucket 60: 80% Sorting block time: 00:00:00 Returning block of 23395 for bucket 54 bucket 55: 100% Sorting block of length 30627 for bucket 55 (Using difference cover) bucket 58: 80% bucket 59: 80% bucket 63: 80% bucket 79: 10% bucket 78: 20% bucket 80: 10% bucket 64: 80% bucket 66: 70% bucket 62: 70% bucket 70: 60% bucket 69: 60% bucket 71: 60% bucket 68: 70% bucket 72: 60% bucket 67: 70% bucket 73: 60% bucket 65: 80% bucket 57: 90% bucket 56: 100% Sorting block of length 8597 for bucket 56 (Using difference cover) Sorting block time: 00:00:00 Returning block of 30628 for bucket 55 bucket 74: 60% bucket 75: 60% bucket 76: 60% bucket 77: 60% Getting block 81 of 210 Reserving size (31083) for bucket 81 bucket 61: 90% Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 60: 90% Sorting block time: 00:00:00 Returning block of 8598 for bucket 56 bucket 58: 90% bucket 59: 90% Getting block 82 of 210 Reserving size (31083) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 63: 90% bucket 64: 90% bucket 79: 20% bucket 78: 30% bucket 66: 80% bucket 62: 80% bucket 80: 20% Getting block 83 of 210 Reserving size (31083) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 70: 70% bucket 71: 70% bucket 69: 70% bucket 68: 80% bucket 72: 70% bucket 67: 80% bucket 73: 70% bucket 65: 90% bucket 57: 100% Sorting block of length 25267 for bucket 57 (Using difference cover) bucket 74: 70% bucket 61: 100% Sorting block of length 25622 for bucket 61 (Using difference cover) bucket 75: 70% bucket 76: 70% bucket 60: 100% Sorting block of length 24881 for bucket 60 (Using difference cover) bucket 77: 70% bucket 81: 10% bucket 58: 100% Sorting block of length 25701 for bucket 58 (Using difference cover) bucket 59: 100% Sorting block of length 21397 for bucket 59 (Using difference cover) bucket 82: 10% bucket 63: 100% Sorting block of length 28695 for bucket 63 (Using difference cover) bucket 64: 100% Sorting block of length 16476 for bucket 64 (Using difference cover) bucket 62: 90% bucket 66: 90% bucket 79: 30% bucket 78: 40% bucket 71: 80% bucket 80: 30% bucket 83: 10% bucket 70: 80% bucket 69: 80% bucket 68: 90% bucket 72: 80% bucket 67: 90% bucket 73: 80% bucket 65: 100% Sorting block of length 29963 for bucket 65 (Using difference cover) Sorting block time: 00:00:00 Returning block of 21398 for bucket 59 bucket 74: 80% Sorting block time: 00:00:00 Returning block of 24882 for bucket 60 Sorting block time: 00:00:00 Returning block of 25623 for bucket 61 bucket 81: 20% bucket 75: 80% bucket 76: 80% bucket 77: 80% Getting block 84 of 210 Reserving size (31083) for bucket 84 Calculating Z arrays for bucket 84 Getting block 85 of 210 Reserving size (31083) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 84: Entering block accumulator loop for bucket 85: bucket 82: 20% Sorting block time: 00:00:00 Returning block of 25702 for bucket 58 Sorting block time: 00:00:00 Returning block of 28696 for bucket 63 Sorting block time: 00:00:00 Returning block of 16477 for bucket 64 Sorting block time: 00:00:00 Returning block of 25268 for bucket 57 bucket 62: 100% Sorting block of length 19085 for bucket 62 (Using difference cover) Getting block 86 of 210 Reserving size (31083) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 66: 100% Sorting block of length 28353 for bucket 66 (Using difference cover) Getting block 87 of 210 Reserving size (31083) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 71: 90% Getting block 88 of 210 bucket 83: 20% Reserving size (31083) for bucket 88 bucket 78: 50% Calculating Z arrays for bucket 88 Sorting block time: 00:00:00 bucket 79: 40% Returning block of 29964 for bucket 65 Entering block accumulator loop for bucket 88: bucket 70: 90% bucket 80: 40% bucket 69: 90% bucket 68: 100% Sorting block of length 17308 for bucket 68 (Using difference cover) bucket 72: 90% bucket 73: 90% bucket 67: 100% Sorting block of length 18632 for bucket 67 (Using difference cover) Getting block 89 of 210 Reserving size (31083) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: Sorting block time: 00:00:00 Returning block of 19086 for bucket 62 bucket 74: 90% Getting block 90 of 210 Reserving size (31083) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 81: 30% Sorting block time: 00:00:00 Returning block of 17309 for bucket 68 bucket 76: 90% bucket 75: 90% bucket 77: 90% bucket 84: 10% bucket 82: 30% bucket 85: 10% Getting block 91 of 210 Reserving size (31083) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: Sorting block time: 00:00:00 Returning block of 18633 for bucket 67 Sorting block time: 00:00:00 Returning block of 28354 for bucket 66 Getting block 92 of 210 Reserving size (31083) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: bucket 86: 10% bucket 87: 10% bucket 71: 100% Sorting block of length 24377 for bucket 71 (Using difference cover) bucket 83: 30% bucket 70: 100% Sorting block of length 27758 for bucket 70 (Using difference cover) bucket 78: 60% bucket 69: 100% bucket 88: 10% Sorting block of length 26963 for bucket 69 (Using difference cover) bucket 80: 50% bucket 79: 50% bucket 72: 100% Sorting block of length 20349 for bucket 72 (Using difference cover) bucket 73: 100% Sorting block of length 29250 for bucket 73 (Using difference cover) bucket 89: 10% Getting block 93 of 210 Reserving size (31083) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: Getting block 94 of 210 Reserving size (31083) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: Getting block 95 of 210 Reserving size (31083) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 81: 40% bucket 90: 10% bucket 74: 100% Sorting block of length 14275 for bucket 74 (Using difference cover) bucket 84: 20% bucket 76: 100% Sorting block of length 13400 for bucket 76 (Using difference cover) Sorting block time: 00:00:00 Returning block of 24378 for bucket 71 bucket 75: 100% bucket 77: 100% Sorting block of length 30723 for bucket 75 (Using difference cover) Sorting block of length 26634 for bucket 77 (Using difference cover) bucket 82: 40% bucket 91: 10% bucket 85: 20% Sorting block time: 00:00:00 Returning block of 20350 for bucket 72 Sorting block time: 00:00:00 Returning block of 26964 for bucket 69 Sorting block time: 00:00:00 Returning block of 27759 for bucket 70 bucket 92: 10% Getting block 96 of 210 Reserving size (31083) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: Sorting block time: 00:00:00 Returning block of 29251 for bucket 73 bucket 86: 20% Getting block 97 of 210 Reserving size (31083) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: Getting block 98 of 210 Reserving size (31083) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 83: 40% bucket 87: 20% Getting block 99 of 210 Sorting block time: 00:00:00 Reserving size (31083) for bucket 99 Returning block of 13401 for bucket 76 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: Sorting block time: 00:00:00 Returning block of 14276 for bucket 74 bucket 80: 60% bucket 88: 20% bucket 78: 70% bucket 79: 60% Getting block 100 of 210 Reserving size (31083) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: Getting block 101 of 210 Reserving size (31083) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 93: 10% bucket 94: 10% Sorting block time: 00:00:00 Returning block of 26635 for bucket 77 Sorting block time: 00:00:00 Returning block of 30724 for bucket 75 bucket 95: 10% bucket 81: 50% bucket 90: 20% bucket 84: 30% bucket 82: 50% bucket 91: 20% Getting block 102 of 210 Reserving size (31083) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 85: 30% Getting block 103 of 210 Reserving size (31083) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: Getting block 104 of 210 Reserving size (31083) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: bucket 92: 20% bucket 96: 10% bucket 86: 30% bucket 83: 50% bucket 87: 30% bucket 97: 10% bucket 88: 30% bucket 99: 10% bucket 80: 70% bucket 98: 10% bucket 78: 80% bucket 79: 70% bucket 100: 10% bucket 94: 20% bucket 81: 60% bucket 95: 20% bucket 90: 30% bucket 84: 40% bucket 82: 60% bucket 91: 30% bucket 85: 40% bucket 102: 10% bucket 103: 10% bucket 92: 30% bucket 104: 10% bucket 96: 20% bucket 86: 40% bucket 83: 60% bucket 87: 40% bucket 88: 40% bucket 97: 20% bucket 89: 20% bucket 80: 80% bucket 99: 20% bucket 78: 90% bucket 79: 80% bucket 100: 20% bucket 98: 20% bucket 81: 70% bucket 94: 30% bucket 84: 50% bucket 90: 40% bucket 95: 30% bucket 82: 70% bucket 91: 40% bucket 85: 50% bucket 103: 20% bucket 92: 40% bucket 104: 20% bucket 96: 30% bucket 86: 50% bucket 83: 70% bucket 87: 50% bucket 88: 50% bucket 89: 30% bucket 80: 90% bucket 99: 30% bucket 97: 30% bucket 79: 90% bucket 93: 20% bucket 100: 30% bucket 78: 100% bucket 101: 10% bucket 98: 30% bucket 81: 80% bucket 84: 60% bucket 82: 80% bucket 90: 50% bucket 94: 40% bucket 95: 40% bucket 91: 50% bucket 85: 60% bucket 103: 30% bucket 102: 20% bucket 83: 80% bucket 86: 60% bucket 96: 40% bucket 87: 60% bucket 104: 30% bucket 92: 50% bucket 88: 60% bucket 89: 40% Sorting block of length 14611 for bucket 78 (Using difference cover) bucket 80: 100% bucket 79: 100% bucket 99: 40% bucket 97: 40% Sorting block of length 17643 for bucket 80 (Using difference cover) Sorting block of length 28975 for bucket 79 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14612 for bucket 78 Sorting block time: 00:00:00 Returning block of 17644 for bucket 80 bucket 82: 90% bucket 84: 70% bucket 91: 60% bucket 81: 90% bucket 90: 60% bucket 93: 30% bucket 95: 50% bucket 85: 70% bucket 94: 50% bucket 101: 20% bucket 103: 40% bucket 100: 40% bucket 98: 40% Getting block 105 of 210 Reserving size (31083) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: Getting block 106 of 210 Reserving size (31083) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 92: 60% bucket 88: 70% bucket 87: 70% bucket 83: 90% bucket 86: 70% bucket 96: 50% bucket 102: 30% bucket 104: 40% bucket 89: 50% bucket 99: 50% bucket 97: 50% Sorting block time: 00:00:00 Returning block of 28976 for bucket 79 bucket 91: 70% bucket 84: 80% bucket 82: 100% Sorting block of length 17521 for bucket 82 (Using difference cover) bucket 81: 100% Sorting block of length 29116 for bucket 81 (Using difference cover) bucket 90: 70% bucket 93: 40% bucket 95: 60% bucket 85: 80% bucket 94: 60% bucket 103: 50% bucket 101: 30% bucket 100: 50% bucket 98: 50% bucket 106: 10% bucket 92: 70% bucket 88: 80% bucket 105: 10% bucket 87: 80% bucket 83: 100% bucket 96: 60% bucket 86: 80% bucket 102: 40% bucket 104: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 29649 for bucket 83 (Using difference cover) Returning block of 17522 for bucket 82 bucket 89: 60% bucket 99: 60% bucket 97: 60% Returning block of 29117 for bucket 81 bucket 91: 80% bucket 84: 90% bucket 90: 80% bucket 93: 50% bucket 95: 70% bucket 85: 90% bucket 103: 60% bucket 94: 70% bucket 101: 40% bucket 100: 60% Getting block 107 of 210 bucket 98: 60% Reserving size (31083) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 106: 20% bucket 92: 80% Getting block 108 of 210 Reserving size (31083) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 88: 90% Getting block 109 of 210 Reserving size (31083) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 87: 90% bucket 96: 70% bucket 86: 90% bucket 102: 50% bucket 104: 60% bucket 105: 20% Sorting block time: 00:00:00 Returning block of 29650 for bucket 83 Getting block 110 of 210 Reserving size (31083) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 91: 90% bucket 84: 100% Sorting block of length 9855 for bucket 84 (Using difference cover) bucket 90: 90% bucket 106: 30% bucket 89: 70% bucket 93: 60% bucket 95: 80% bucket 85: 100% Sorting block of length 27388 for bucket 85 (Using difference cover) bucket 103: 70% bucket 99: 70% bucket 101: 50% bucket 94: 80% bucket 97: 70% bucket 92: 90% bucket 100: 70% bucket 108: 10% bucket 98: 70% bucket 88: 100% Sorting block of length 26375 for bucket 88 (Using difference cover) bucket 109: 10% Sorting block time: 00:00:00 Returning block of 9856 for bucket 84 bucket 87: 100% Sorting block of length 14384 for bucket 87 (Using difference cover) bucket 86: 100% Sorting block of length 23845 for bucket 86 (Using difference cover) bucket 96: 80% bucket 102: 60% Getting block 111 of 210 Reserving size (31083) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: bucket 104: 70% bucket 105: 30% bucket 107: 10% Sorting block time: 00:00:00 Returning block of 14385 for bucket 87 Sorting block time: 00:00:00 Returning block of 27389 for bucket 85 Sorting block time: 00:00:00 Returning block of 26376 for bucket 88 bucket 110: 10% Getting block 112 of 210 Reserving size (31083) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 91: 100% Sorting block of length 8488 for bucket 91 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23846 for bucket 86 bucket 106: 40% bucket 90: 100% Sorting block of length 26077 for bucket 90 (Using difference cover) Getting block 113 of 210 Reserving size (31083) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 95: 90% bucket 92: 100% Sorting block of length 24416 for bucket 92 (Using difference cover) bucket 93: 70% bucket 103: 80% bucket 101: 60% bucket 108: 20% bucket 94: 90% bucket 99: 80% Getting block 114 of 210 Reserving size (31083) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 97: 80% bucket 109: 20% bucket 100: 80% bucket 98: 80% Sorting block time: 00:00:00 Returning block of 8489 for bucket 91 Getting block 115 of 210 Reserving size (31083) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 96: 90% bucket 102: 70% bucket 89: 80% bucket 111: 10% bucket 104: 80% bucket 105: 40% bucket 107: 20% Sorting block time: 00:00:00 Returning block of 24417 for bucket 92 Sorting block time: 00:00:00 Returning block of 26078 for bucket 90 Getting block 116 of 210 Reserving size (31083) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: bucket 112: 10% bucket 110: 20% Getting block 117 of 210 Reserving size (31083) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: bucket 106: 50% bucket 113: 10% bucket 95: 100% Sorting block of length 19656 for bucket 95 (Using difference cover) bucket 114: 10% bucket 108: 30% bucket 93: 80% bucket 103: 90% bucket 109: 30% bucket 94: 100% Sorting block of length 17484 for bucket 94 (Using difference cover) bucket 99: 90% bucket 97: 90% bucket 101: 70% bucket 100: 90% bucket 98: 90% bucket 115: 10% bucket 96: 100% Sorting block of length 24098 for bucket 96 (Using difference cover) bucket 89: 90% bucket 111: 20% bucket 102: 80% Getting block 118 of 210 Reserving size (31083) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: bucket 104: 90% bucket 105: 50% bucket 107: 30% Sorting block time: 00:00:00 Returning block of 19657 for bucket 95 Sorting block time: 00:00:00 Returning block of 17485 for bucket 94 Getting block 119 of 210 Reserving size (31083) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: Getting block 120 of 210 Reserving size (31083) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 116: 10% bucket 112: 20% bucket 110: 30% bucket 117: 10% bucket 106: 60% bucket 113: 20% Sorting block time: 00:00:00 Returning block of 24099 for bucket 96 bucket 114: 20% bucket 108: 40% bucket 109: 40% Getting block 121 of 210 Reserving size (31083) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 93: 90% bucket 103: 100% Sorting block of length 13502 for bucket 103 (Using difference cover) bucket 99: 100% Sorting block of length 25836 for bucket 99 (Using difference cover) bucket 115: 20% bucket 97: 100% bucket 101: 80% Sorting block of length 26877 for bucket 97 (Using difference cover) bucket 100: 100% Sorting block of length 27598 for bucket 100 (Using difference cover) bucket 98: 100% Sorting block of length 25897 for bucket 98 (Using difference cover) bucket 111: 30% bucket 102: 90% bucket 118: 10% bucket 107: 40% bucket 104: 100% Sorting block of length 22085 for bucket 104 (Using difference cover) bucket 105: 60% bucket 89: 100% Sorting block of length 16736 for bucket 89 (Using difference cover) bucket 119: 10% bucket 120: 10% bucket 116: 20% bucket 112: 30% bucket 106: 70% bucket 110: 40% bucket 117: 20% Sorting block time: 00:00:00 Returning block of 13503 for bucket 103 bucket 113: 30% Getting block 122 of 210 Reserving size (31083) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 114: 30% bucket 121: 10% bucket 108: 50% bucket 109: 50% Sorting block time: 00:00:00 Returning block of 26878 for bucket 97 Sorting block time: 00:00:00 Returning block of 25898 for bucket 98 bucket 93: 100% Sorting block of length 19377 for bucket 93 (Using difference cover) bucket 115: 30% Getting block 123 of 210 Reserving size (31083) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 101: 90% Sorting block time: 00:00:00 Returning block of 25837 for bucket 99 bucket 111: 40% bucket 118: 20% bucket 102: 100% Sorting block of length 29897 for bucket 102 (Using difference cover) Getting block 124 of 210 Reserving size (31083) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 107: 50% Sorting block time: 00:00:00 Returning block of 16737 for bucket 89 Sorting block time: 00:00:00 Returning block of 22086 for bucket 104 bucket 105: 70% bucket 119: 20% Sorting block time: 00:00:00 Returning block of 19378 for bucket 93 bucket 120: 20% Getting block 125 of 210 Reserving size (31083) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: Getting block 126 of 210 Reserving size (31083) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: Sorting block time: 00:00:00 Returning block of 27599 for bucket 100 bucket 112: 40% bucket 106: 80% bucket 116: 30% bucket 110: 50% bucket 117: 30% bucket 113: 40% Getting block 127 of 210 Reserving size (31083) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 122: 10% Getting block 128 of 210 Reserving size (31083) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: bucket 114: 40% bucket 121: 20% bucket 108: 60% bucket 109: 60% bucket 115: 40% bucket 123: 10% Sorting block time: 00:00:00 Returning block of 29898 for bucket 102 Getting block 129 of 210 Reserving size (31083) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: bucket 111: 50% bucket 101: 100% Sorting block of length 8752 for bucket 101 (Using difference cover) bucket 124: 10% bucket 107: 60% bucket 118: 30% Sorting block time: 00:00:00 Returning block of 8753 for bucket 101 bucket 125: 10% bucket 119: 30% bucket 105: 80% bucket 126: 10% bucket 120: 30% bucket 112: 50% Getting block 130 of 210 Reserving size (31083) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: bucket 106: 90% bucket 113: 50% bucket 116: 40% bucket 110: 60% bucket 117: 40% bucket 122: 20% bucket 127: 10% bucket 128: 10% bucket 114: 50% bucket 121: 30% bucket 109: 70% bucket 108: 70% bucket 115: 50% bucket 123: 20% bucket 129: 10% bucket 111: 60% bucket 107: 70% bucket 124: 20% bucket 118: 40% bucket 125: 20% bucket 119: 40% bucket 126: 20% bucket 105: 90% bucket 112: 60% bucket 106: 100% Sorting block of length 25304 for bucket 106 (Using difference cover) bucket 130: 10% bucket 113: 60% bucket 122: 30% bucket 110: 70% bucket 117: 50% bucket 116: 50% bucket 114: 60% bucket 121: 40% bucket 127: 20% bucket 128: 20% Getting block 131 of 210 Reserving size (31083) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 109: 80% bucket 108: 80% bucket 115: 60% bucket 123: 30% bucket 129: 20% bucket 111: 70% bucket 107: 80% bucket 124: 30% Sorting block time: 00:00:00 Returning block of 25305 for bucket 106 bucket 118: 50% bucket 125: 30% bucket 119: 50% bucket 126: 30% bucket 112: 70% bucket 120: 40% bucket 113: 70% bucket 105: 100% Sorting block of length 20783 for bucket 105 (Using difference cover) bucket 122: 40% bucket 110: 80% bucket 117: 60% bucket 116: 60% bucket 114: 70% bucket 121: 50% bucket 109: 90% bucket 131: 10% bucket 108: 90% bucket 128: 30% bucket 127: 30% bucket 115: 70% bucket 123: 40% bucket 111: 80% bucket 107: 90% Sorting block time: 00:00:00 Returning block of 20784 for bucket 105 bucket 129: 30% bucket 124: 40% Getting block 132 of 210 Reserving size (31083) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 118: 60% bucket 125: 40% bucket 119: 60% bucket 126: 40% bucket 112: 80% bucket 120: 50% bucket 113: 80% bucket 122: 50% bucket 117: 70% bucket 110: 90% bucket 114: 80% bucket 121: 60% bucket 116: 70% bucket 109: 100% Sorting block of length 26523 for bucket 109 (Using difference cover) bucket 131: 20% bucket 108: 100% Sorting block of length 18106 for bucket 108 (Using difference cover) bucket 128: 40% bucket 127: 40% bucket 115: 80% bucket 123: 50% Getting block 133 of 210 Reserving size (31083) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 107: 100% Sorting block of length 17343 for bucket 107 (Using difference cover) bucket 111: 90% bucket 129: 40% bucket 124: 50% bucket 132: 10% Sorting block time: 00:00:00 Returning block of 18107 for bucket 108 bucket 125: 50% bucket 118: 70% bucket 119: 70% Getting block 134 of 210 Reserving size (31083) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 126: 50% bucket 112: 90% bucket 130: 20% Sorting block time: 00:00:00 Returning block of 26524 for bucket 109 bucket 120: 60% bucket 113: 90% bucket 122: 60% Sorting block time: 00:00:00 Returning block of 17344 for bucket 107 bucket 121: 70% bucket 114: 90% bucket 117: 80% bucket 110: 100% Sorting block of length 17298 for bucket 110 (Using difference cover) bucket 116: 80% bucket 131: 30% Getting block 135 of 210 Reserving size (31083) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 128: 50% bucket 127: 50% bucket 115: 90% bucket 123: 60% bucket 133: 10% bucket 111: 100% Sorting block of length 27264 for bucket 111 (Using difference cover) Sorting block time: 00:00:00 Returning block of 17299 for bucket 110 bucket 124: 60% bucket 129: 50% Getting block 136 of 210 Reserving size (31083) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 125: 60% bucket 132: 20% bucket 119: 80% bucket 118: 80% bucket 134: 10% bucket 120: 70% bucket 112: 100% bucket 126: 60% Sorting block of length 14372 for bucket 112 (Using difference cover) bucket 130: 30% bucket 122: 70% bucket 113: 100% Sorting block of length 21429 for bucket 113 (Using difference cover) bucket 121: 80% bucket 114: 100% Sorting block of length 26041 for bucket 114 (Using difference cover) bucket 117: 90% bucket 116: 90% bucket 135: 10% Sorting block time: 00:00:00 Returning block of 14373 for bucket 112 bucket 131: 40% Sorting block time: 00:00:00 Returning block of 27265 for bucket 111 bucket 128: 60% bucket 123: 70% Getting block 137 of 210 Reserving size (31083) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: Getting block 138 of 210 bucket 115: 100% Reserving size (31083) for bucket 138 Sorting block of length 27149 for bucket 115 (Using difference cover) Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 127: 60% Getting block 139 of 210 Reserving size (31083) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: Sorting block time: 00:00:00 Returning block of 21430 for bucket 113 bucket 133: 20% bucket 124: 70% bucket 129: 60% Getting block 140 of 210 Reserving size (31083) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: bucket 136: 10% bucket 125: 70% bucket 119: 90% bucket 120: 80% Sorting block time: 00:00:00 Returning block of 26042 for bucket 114 bucket 134: 20% bucket 132: 30% bucket 126: 70% bucket 118: 90% bucket 122: 80% Getting block 141 of 210 bucket 121: 90% Reserving size (31083) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 117: 100% Sorting block of length 16747 for bucket 117 (Using difference cover) Sorting block time: 00:00:00 Returning block of 27150 for bucket 115 bucket 135: 20% bucket 116: 100% Sorting block of length 21425 for bucket 116 (Using difference cover) Getting block 142 of 210 Reserving size (31083) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 131: 50% bucket 123: 80% bucket 128: 70% bucket 138: 10% bucket 139: 10% bucket 137: 10% bucket 127: 70% bucket 130: 40% bucket 124: 80% Sorting block time: 00:00:00 Returning block of 16748 for bucket 117 bucket 140: 10% bucket 136: 20% bucket 133: 30% bucket 129: 70% bucket 125: 80% bucket 120: 90% Sorting block time: 00:00:00 Returning block of 21426 for bucket 116 bucket 134: 30% bucket 126: 80% Getting block 143 of 210 bucket 122: 90% Reserving size (31083) for bucket 143 bucket 119: 100% Calculating Z arrays for bucket 143 Sorting block of length 17637 for bucket 119 (Using difference cover) bucket 141: 10% bucket 132: 40% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 143: bucket 118: 100% bucket 121: 100% bucket 135: 30% bucket 142: 10% bucket 139: 20% bucket 123: 90% bucket 138: 20% bucket 137: 20% bucket 131: 60% bucket 128: 80% Returning block of 17638 for bucket 119 Getting block 144 of 210 Sorting block of length 29096 for bucket 118 (Using difference cover) Sorting block of length 21088 for bucket 121 (Using difference cover) bucket 127: 80% bucket 130: 50% Reserving size (31083) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 140: 20% bucket 124: 90% bucket 136: 30% bucket 129: 80% bucket 133: 40% bucket 125: 90% bucket 120: 100% Sorting block of length 26941 for bucket 120 (Using difference cover) bucket 122: 100% bucket 126: 90% Sorting block of length 16315 for bucket 122 (Using difference cover) bucket 134: 40% bucket 141: 20% bucket 132: 50% Sorting block time: 00:00:00 Returning block of 21089 for bucket 121 Sorting block time: 00:00:00 Returning block of 16316 for bucket 122 Sorting block time: 00:00:00 Returning block of 29097 for bucket 118 bucket 139: 30% bucket 135: 40% bucket 142: 20% Getting block 145 of 210 Reserving size (31083) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 138: 30% bucket 137: 30% bucket 123: 100% Sorting block of length 26392 for bucket 123 (Using difference cover) Getting block 146 of 210 Reserving size (31083) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: bucket 131: 70% bucket 128: 90% bucket 144: 10% Sorting block time: 00:00:00 Returning block of 26942 for bucket 120 bucket 143: 10% bucket 140: 30% bucket 136: 40% bucket 124: 100% Sorting block of length 30049 for bucket 124 (Using difference cover) bucket 127: 90% bucket 130: 60% Getting block 147 of 210 Reserving size (31083) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 129: 90% bucket 125: 100% Sorting block of length 11684 for bucket 125 (Using difference cover) bucket 133: 50% bucket 141: 30% bucket 126: 100% Sorting block of length 30166 for bucket 126 (Using difference cover) Getting block 148 of 210 Reserving size (31083) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 134: 50% Sorting block time: 00:00:00 Returning block of 11685 for bucket 125 bucket 132: 60% Sorting block time: 00:00:00 Returning block of 26393 for bucket 123 Getting block 149 of 210 Reserving size (31083) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: Getting block 150 of 210 Reserving size (31083) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 139: 40% bucket 145: 10% bucket 135: 50% Sorting block time: 00:00:00 Returning block of 30050 for bucket 124 bucket 142: 30% bucket 146: 10% bucket 137: 40% bucket 138: 40% Getting block 151 of 210 Reserving size (31083) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 144: 20% bucket 131: 80% Getting block 152 of 210 Reserving size (31083) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: bucket 128: 100% Sorting block of length 30644 for bucket 128 (Using difference cover) bucket 140: 40% bucket 136: 50% bucket 147: 10% Sorting block time: 00:00:00 Returning block of 30167 for bucket 126 bucket 127: 100% Sorting block of length 26658 for bucket 127 (Using difference cover) bucket 130: 70% bucket 129: 100% Sorting block of length 10728 for bucket 129 (Using difference cover) bucket 141: 40% bucket 133: 60% bucket 148: 10% bucket 143: 20% bucket 134: 60% Sorting block time: 00:00:00 Returning block of 10729 for bucket 129 bucket 132: 70% bucket 149: 10% bucket 150: 10% bucket 139: 50% bucket 145: 20% bucket 135: 60% bucket 142: 40% bucket 146: 20% Sorting block time: 00:00:00 Returning block of 30645 for bucket 128 bucket 137: 50% Sorting block time: 00:00:00 Returning block of 26659 for bucket 127 bucket 138: 50% bucket 144: 30% Getting block 153 of 210 Reserving size (31083) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 151: 10% bucket 152: 10% bucket 140: 50% bucket 131: 90% bucket 136: 60% bucket 147: 20% Getting block 154 of 210 Reserving size (31083) for bucket 154 Getting block 155 of 210 Calculating Z arrays for bucket 154 Reserving size (31083) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 154: Entering block accumulator loop for bucket 155: bucket 130: 80% bucket 141: 50% bucket 143: 30% bucket 133: 70% bucket 148: 20% bucket 134: 70% bucket 149: 20% bucket 132: 80% bucket 139: 60% bucket 135: 70% bucket 145: 30% bucket 150: 20% bucket 142: 50% bucket 146: 30% bucket 144: 40% bucket 137: 60% bucket 138: 60% bucket 140: 60% bucket 153: 10% bucket 147: 30% bucket 151: 20% bucket 136: 70% bucket 152: 20% bucket 131: 100% Sorting block of length 17917 for bucket 131 (Using difference cover) bucket 155: 10% bucket 154: 10% bucket 141: 60% bucket 130: 90% bucket 134: 80% bucket 143: 40% bucket 148: 30% bucket 133: 80% Sorting block time: 00:00:00 Returning block of 17918 for bucket 131 bucket 149: 30% bucket 139: 70% bucket 135: 80% bucket 145: 40% bucket 132: 90% Getting block 156 of 210 Reserving size (31083) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 144: 50% bucket 150: 30% bucket 138: 70% bucket 137: 70% bucket 142: 60% bucket 146: 40% Getting block 157 of 210 Reserving size (31083) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 140: 70% bucket 147: 40% bucket 136: 80% bucket 153: 20% bucket 152: 30% bucket 151: 30% bucket 155: 20% bucket 141: 70% bucket 154: 20% bucket 130: 100% Sorting block of length 21555 for bucket 130 (Using difference cover) bucket 134: 90% bucket 143: 50% bucket 148: 40% bucket 133: 90% bucket 139: 80% bucket 135: 90% bucket 149: 40% bucket 145: 50% bucket 144: 60% bucket 156: 10% bucket 138: 80% bucket 137: 80% bucket 132: 100% Sorting block of length 16060 for bucket 132 (Using difference cover) bucket 142: 70% bucket 146: 50% bucket 150: 40% Sorting block time: 00:00:00 Returning block of 21556 for bucket 130 bucket 140: 80% bucket 147: 50% bucket 136: 90% bucket 157: 10% Getting block 158 of 210 Reserving size (31083) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: bucket 141: 80% bucket 152: 40% bucket 153: 30% bucket 155: 30% bucket 151: 40% bucket 154: 30% Sorting block time: 00:00:00 Returning block of 16061 for bucket 132 Getting block 159 of 210 Reserving size (31083) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 134: 100% Sorting block of length 29708 for bucket 134 (Using difference cover) bucket 139: 90% bucket 143: 60% bucket 148: 50% bucket 135: 100% Sorting block of length 17317 for bucket 135 (Using difference cover) bucket 133: 100% Sorting block of length 16696 for bucket 133 (Using difference cover) bucket 144: 70% bucket 145: 60% bucket 149: 50% bucket 138: 90% bucket 137: 90% bucket 156: 20% bucket 142: 80% bucket 146: 60% bucket 150: 50% bucket 140: 90% bucket 147: 60% bucket 136: 100% Sorting block of length 28629 for bucket 136 (Using difference cover) bucket 157: 20% bucket 141: 90% Sorting block time: 00:00:00 Returning block of 17318 for bucket 135 Sorting block time: 00:00:00 Returning block of 16697 for bucket 133 bucket 158: 10% bucket 152: 50% bucket 155: 40% Getting block 160 of 210 Reserving size (31083) for bucket 160 bucket 153: 40% Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: Getting block 161 of 210 Reserving size (31083) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 151: 50% bucket 154: 40% Sorting block time: 00:00:00 Returning block of 29709 for bucket 134 Getting block 162 of 210 Reserving size (31083) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 159: 10% bucket 139: 100% Sorting block of length 7963 for bucket 139 (Using difference cover) bucket 143: 70% bucket 144: 80% bucket 148: 60% bucket 145: 70% bucket 149: 60% bucket 138: 100% Sorting block of length 23530 for bucket 138 (Using difference cover) bucket 137: 100% Sorting block of length 24794 for bucket 137 (Using difference cover) Sorting block time: 00:00:00 Returning block of 7964 for bucket 139 Sorting block time: 00:00:00 Returning block of 28630 for bucket 136 bucket 146: 70% bucket 142: 90% bucket 156: 30% Getting block 163 of 210 Reserving size (31083) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: bucket 147: 70% bucket 140: 100% Sorting block of length 25136 for bucket 140 (Using difference cover) Getting block 164 of 210 Reserving size (31083) for bucket 164 bucket 150: 60% Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 141: 100% Sorting block of length 7359 for bucket 141 (Using difference cover) bucket 157: 30% bucket 161: 10% bucket 155: 50% bucket 152: 60% Sorting block time: 00:00:00 Returning block of 7360 for bucket 141 bucket 158: 20% bucket 153: 50% bucket 151: 60% Getting block 165 of 210 Reserving size (31083) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 160: 10% bucket 154: 50% bucket 162: 10% Sorting block time: 00:00:00 Returning block of 24795 for bucket 137 Sorting block time: 00:00:00 Returning block of 23531 for bucket 138 bucket 159: 20% bucket 144: 90% Sorting block time: 00:00:00 Returning block of 25137 for bucket 140 Getting block 166 of 210 Reserving size (31083) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 143: 80% bucket 145: 80% bucket 148: 70% bucket 149: 70% bucket 146: 80% bucket 142: 100% Sorting block of length 29623 for bucket 142 (Using difference cover) bucket 147: 80% Getting block 167 of 210 Reserving size (31083) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: bucket 156: 40% bucket 163: 10% Getting block 168 of 210 Reserving size (31083) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 164: 10% bucket 150: 70% bucket 161: 20% bucket 157: 40% bucket 155: 60% bucket 152: 70% bucket 158: 30% bucket 153: 60% bucket 162: 20% bucket 165: 10% bucket 151: 70% bucket 154: 60% bucket 160: 20% bucket 144: 100% Sorting block of length 7536 for bucket 144 (Using difference cover) bucket 166: 10% bucket 145: 90% bucket 159: 30% Sorting block time: 00:00:00 Returning block of 29624 for bucket 142 bucket 143: 90% bucket 148: 80% Sorting block time: 00:00:00 Returning block of 7537 for bucket 144 bucket 149: 80% bucket 146: 90% Getting block 169 of 210 Reserving size (31083) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 147: 90% Getting block 170 of 210 Reserving size (31083) for bucket 170 bucket 167: 10% Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 164: 20% bucket 163: 20% bucket 168: 10% bucket 156: 50% bucket 161: 30% bucket 150: 80% bucket 157: 50% bucket 155: 70% bucket 162: 30% bucket 152: 80% bucket 165: 20% bucket 158: 40% bucket 153: 70% bucket 151: 80% bucket 154: 70% bucket 166: 20% bucket 145: 100% Sorting block of length 35977 for bucket 145 (Using difference cover) bucket 160: 30% bucket 159: 40% bucket 143: 100% Sorting block of length 2070 for bucket 143 (Using difference cover) bucket 169: 10% bucket 148: 90% bucket 146: 100% Sorting block of length 12421 for bucket 146 (Using difference cover) bucket 147: 100% Sorting block of length 27878 for bucket 147 (Using difference cover) bucket 149: 90% bucket 164: 30% bucket 170: 10% bucket 167: 20% Sorting block time: 00:00:00 Returning block of 2071 for bucket 143 bucket 163: 30% bucket 168: 20% bucket 161: 40% Getting block 171 of 210 bucket 156: 60% Reserving size (31083) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 150: 90% Sorting block time: 00:00:00 Returning block of 12422 for bucket 146 bucket 162: 40% bucket 155: 80% bucket 157: 60% bucket 165: 30% bucket 152: 90% bucket 158: 50% Getting block 172 of 210 Reserving size (31083) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: bucket 154: 80% bucket 153: 80% bucket 151: 90% bucket 166: 30% Sorting block time: 00:00:00 Returning block of 35978 for bucket 145 Sorting block time: 00:00:00 Returning block of 27879 for bucket 147 bucket 169: 20% bucket 159: 50% bucket 170: 20% bucket 164: 40% bucket 167: 30% bucket 160: 40% bucket 163: 40% bucket 149: 100% Sorting block of length 6319 for bucket 149 (Using difference cover) bucket 148: 100% Sorting block of length 27107 for bucket 148 (Using difference cover) bucket 161: 50% bucket 168: 30% Getting block 173 of 210 Reserving size (31083) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: Getting block 174 of 210 Reserving size (31083) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 171: 10% Sorting block time: 00:00:00 Returning block of 6320 for bucket 149 bucket 156: 70% bucket 162: 50% bucket 150: 100% Sorting block of length 28173 for bucket 150 (Using difference cover) bucket 155: 90% bucket 165: 40% bucket 157: 70% bucket 152: 100% Sorting block of length 22579 for bucket 152 (Using difference cover) bucket 172: 10% bucket 158: 60% bucket 166: 40% bucket 154: 90% bucket 151: 100% Sorting block of length 28455 for bucket 151 (Using difference cover) bucket 153: 90% Sorting block time: 00:00:00 Returning block of 27108 for bucket 148 bucket 169: 30% bucket 170: 30% bucket 164: 50% bucket 167: 40% bucket 161: 60% bucket 159: 60% bucket 163: 50% Sorting block time: 00:00:00 Returning block of 28174 for bucket 150 bucket 168: 40% bucket 173: 10% bucket 160: 50% bucket 174: 10% bucket 171: 20% Sorting block time: 00:00:00 Returning block of 22580 for bucket 152 bucket 162: 60% Getting block 175 of 210 Reserving size (31083) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 156: 80% Getting block 176 of 210 Reserving size (31083) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: Getting block 177 of 210 Reserving size (31083) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 155: 100% Sorting block of length 27960 for bucket 155 (Using difference cover) bucket 165: 50% bucket 172: 20% bucket 157: 80% Sorting block time: 00:00:00 Returning block of 28456 for bucket 151 bucket 158: 70% bucket 166: 50% Getting block 178 of 210 Reserving size (31083) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: bucket 154: 100% Sorting block of length 28110 for bucket 154 (Using difference cover) bucket 153: 100% Sorting block of length 27186 for bucket 153 (Using difference cover) bucket 170: 40% bucket 164: 60% bucket 169: 40% bucket 167: 50% bucket 161: 70% bucket 163: 60% bucket 159: 70% bucket 168: 50% bucket 173: 20% bucket 171: 30% bucket 174: 20% bucket 162: 70% Sorting block time: 00:00:00 Returning block of 27961 for bucket 155 Getting block 179 of 210 Reserving size (31083) for bucket 179 Calculating Z arrays for bucket 179 bucket 175: 10% Entering block accumulator loop for bucket 179: bucket 176: 10% bucket 160: 60% bucket 177: 10% bucket 156: 90% bucket 165: 60% bucket 172: 30% Sorting block time: 00:00:00 Returning block of 27187 for bucket 153 Sorting block time: 00:00:00 Returning block of 28111 for bucket 154 bucket 157: 90% bucket 158: 80% Getting block 180 of 210 Reserving size (31083) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 166: 60% Getting block 181 of 210 Reserving size (31083) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: bucket 178: 10% bucket 170: 50% bucket 169: 50% bucket 161: 80% bucket 167: 60% bucket 164: 70% bucket 163: 70% bucket 171: 40% bucket 168: 60% bucket 173: 30% bucket 159: 80% bucket 174: 30% bucket 162: 80% bucket 179: 10% bucket 176: 20% bucket 175: 20% bucket 177: 20% bucket 156: 100% Sorting block of length 16514 for bucket 156 (Using difference cover) bucket 165: 70% bucket 172: 40% bucket 160: 70% Getting block 182 of 210 Reserving size (31083) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 181: 10% bucket 180: 10% bucket 166: 70% bucket 158: 90% bucket 157: 100% Sorting block of length 24784 for bucket 157 (Using difference cover) bucket 178: 20% bucket 170: 60% bucket 169: 60% bucket 161: 90% Sorting block time: 00:00:00 Returning block of 16515 for bucket 156 bucket 164: 80% bucket 167: 70% bucket 163: 80% Getting block 183 of 210 bucket 171: 50% Reserving size (31083) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: bucket 173: 40% bucket 168: 70% bucket 174: 40% bucket 162: 90% bucket 159: 90% bucket 179: 20% bucket 176: 30% bucket 177: 30% bucket 175: 30% Sorting block time: 00:00:00 Returning block of 24785 for bucket 157 bucket 172: 50% bucket 165: 80% bucket 182: 10% Getting block 184 of 210 Reserving size (31083) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 181: 20% bucket 180: 20% bucket 160: 80% bucket 166: 80% bucket 178: 30% bucket 158: 100% Sorting block of length 4677 for bucket 158 (Using difference cover) bucket 170: 70% bucket 161: 100% Sorting block of length 23963 for bucket 161 (Using difference cover) bucket 169: 70% bucket 164: 90% Sorting block time: 00:00:00 Returning block of 4678 for bucket 158 bucket 167: 80% bucket 171: 60% Getting block 185 of 210 Reserving size (31083) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 163: 90% bucket 183: 10% bucket 173: 50% bucket 162: 100% Sorting block of length 29045 for bucket 162 (Using difference cover) bucket 168: 80% bucket 174: 50% bucket 179: 30% bucket 176: 40% bucket 177: 40% bucket 159: 100% Sorting block of length 27283 for bucket 159 (Using difference cover) bucket 175: 40% bucket 182: 20% bucket 172: 60% bucket 184: 10% bucket 165: 90% bucket 181: 30% Sorting block time: 00:00:00 Returning block of 23964 for bucket 161 bucket 180: 30% bucket 166: 90% Getting block 186 of 210 Reserving size (31083) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: bucket 178: 40% bucket 170: 80% bucket 160: 90% bucket 169: 80% bucket 164: 100% Sorting block of length 15400 for bucket 164 (Using difference cover) bucket 167: 90% Sorting block time: 00:00:00 Returning block of 29046 for bucket 162 bucket 185: 10% bucket 171: 70% bucket 183: 20% bucket 163: 100% Sorting block of length 29113 for bucket 163 (Using difference cover) bucket 173: 60% Sorting block time: 00:00:00 Returning block of 27284 for bucket 159 bucket 179: 40% bucket 174: 60% bucket 168: 90% Getting block 187 of 210 Reserving size (31083) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: Getting block 188 of 210 Reserving size (31083) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 176: 50% bucket 177: 50% bucket 175: 50% bucket 182: 30% bucket 184: 20% Sorting block time: 00:00:00 Returning block of 15401 for bucket 164 bucket 181: 40% bucket 172: 70% bucket 165: 100% Sorting block of length 23219 for bucket 165 (Using difference cover) bucket 180: 40% bucket 186: 10% bucket 166: 100% Sorting block of length 25917 for bucket 166 (Using difference cover) bucket 178: 50% bucket 170: 90% Getting block 189 of 210 Reserving size (31083) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: Sorting block time: 00:00:00 Returning block of 29114 for bucket 163 bucket 169: 90% bucket 185: 20% bucket 183: 30% bucket 167: 100% Sorting block of length 22907 for bucket 167 (Using difference cover) bucket 171: 80% Getting block 190 of 210 Reserving size (31083) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 160: 100% Sorting block of length 24220 for bucket 160 (Using difference cover) bucket 173: 70% bucket 179: 50% bucket 187: 10% bucket 188: 10% bucket 174: 70% bucket 168: 100% Sorting block of length 28997 for bucket 168 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23220 for bucket 165 bucket 176: 60% bucket 177: 60% bucket 182: 40% bucket 184: 30% bucket 175: 60% Getting block 191 of 210 Reserving size (31083) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: bucket 181: 50% Sorting block time: 00:00:00 Returning block of 25918 for bucket 166 bucket 172: 80% bucket 180: 50% Getting block 192 of 210 Reserving size (31083) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: Sorting block time: 00:00:00 Returning block of 22908 for bucket 167 bucket 186: 20% Getting block 193 of 210 Reserving size (31083) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: bucket 178: 60% Sorting block time: 00:00:00 Returning block of 24221 for bucket 160 bucket 189: 10% bucket 170: 100% Sorting block of length 30846 for bucket 170 (Using difference cover) bucket 183: 40% bucket 185: 30% bucket 169: 100% Sorting block of length 19109 for bucket 169 (Using difference cover) Getting block 194 of 210 Reserving size (31083) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 171: 90% bucket 190: 10% Sorting block time: 00:00:00 Returning block of 28998 for bucket 168 bucket 179: 60% bucket 173: 80% bucket 187: 20% bucket 188: 20% Getting block 195 of 210 Reserving size (31083) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 174: 80% bucket 182: 50% bucket 184: 40% bucket 191: 10% bucket 176: 70% bucket 177: 70% bucket 181: 60% bucket 175: 70% Sorting block time: 00:00:00 Returning block of 19110 for bucket 169 bucket 180: 60% bucket 172: 90% bucket 192: 10% bucket 186: 30% Getting block 196 of 210 Reserving size (31083) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 193: 10% Sorting block time: 00:00:00 Returning block of 30847 for bucket 170 bucket 189: 20% bucket 178: 70% bucket 183: 50% Getting block 197 of 210 Reserving size (31083) for bucket 197 Calculating Z arrays for bucket 197 bucket 185: 40% Entering block accumulator loop for bucket 197: bucket 194: 10% bucket 171: 100% Sorting block of length 25918 for bucket 171 (Using difference cover) bucket 190: 20% bucket 187: 30% bucket 179: 70% bucket 188: 30% bucket 173: 90% bucket 195: 10% bucket 182: 60% bucket 184: 50% bucket 174: 90% bucket 191: 20% bucket 181: 70% bucket 176: 80% bucket 177: 80% bucket 175: 80% bucket 180: 70% bucket 196: 10% bucket 192: 20% bucket 172: 100% Sorting block of length 18038 for bucket 172 (Using difference cover) bucket 186: 40% bucket 193: 20% bucket 189: 30% Sorting block time: 00:00:00 Returning block of 25919 for bucket 171 bucket 197: 10% bucket 194: 20% bucket 183: 60% bucket 185: 50% bucket 178: 80% bucket 190: 30% bucket 187: 40% bucket 179: 80% Getting block 198 of 210 bucket 188: 40% Reserving size (31083) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: Sorting block time: 00:00:00 Returning block of 18039 for bucket 172 bucket 173: 100% Sorting block of length 23328 for bucket 173 (Using difference cover) bucket 195: 20% bucket 182: 70% bucket 184: 60% bucket 191: 30% bucket 174: 100% Sorting block of length 28444 for bucket 174 (Using difference cover) bucket 181: 80% bucket 177: 90% bucket 176: 90% bucket 196: 20% bucket 192: 30% bucket 180: 80% bucket 175: 90% bucket 186: 50% bucket 193: 30% Getting block 199 of 210 Reserving size (31083) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: bucket 197: 20% bucket 189: 40% bucket 194: 30% bucket 183: 70% bucket 185: 60% Sorting block time: 00:00:00 Returning block of 23329 for bucket 173 bucket 190: 40% bucket 178: 90% bucket 187: 50% bucket 188: 50% bucket 179: 90% Sorting block time: 00:00:00 Returning block of 28445 for bucket 174 bucket 182: 80% bucket 184: 70% bucket 195: 30% bucket 191: 40% bucket 198: 10% Getting block 200 of 210 Reserving size (31083) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 196: 30% bucket 181: 90% bucket 177: 100% Sorting block of length 20770 for bucket 177 (Using difference cover) Getting block 201 of 210 Reserving size (31083) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: bucket 176: 100% Sorting block of length 30176 for bucket 176 (Using difference cover) bucket 192: 40% bucket 186: 60% bucket 180: 90% bucket 193: 40% bucket 199: 10% bucket 175: 100% Sorting block of length 26548 for bucket 175 (Using difference cover) bucket 197: 30% bucket 189: 50% bucket 194: 40% bucket 183: 80% bucket 185: 70% bucket 190: 50% bucket 187: 60% bucket 178: 100% Sorting block of length 19876 for bucket 178 (Using difference cover) bucket 188: 60% bucket 179: 100% Sorting block of length 29586 for bucket 179 (Using difference cover) Sorting block time: 00:00:00 Returning block of 20771 for bucket 177 bucket 182: 90% bucket 184: 80% bucket 195: 40% bucket 191: 50% bucket 198: 20% bucket 200: 10% bucket 196: 40% bucket 181: 100% Sorting block of length 25860 for bucket 181 (Using difference cover) bucket 201: 10% Getting block 202 of 210 Reserving size (31083) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: Sorting block time: 00:00:00 Returning block of 26549 for bucket 175 Sorting block time: 00:00:00 Returning block of 30177 for bucket 176 bucket 192: 50% bucket 199: 20% bucket 186: 70% bucket 193: 50% bucket 180: 100% Sorting block of length 16356 for bucket 180 (Using difference cover) bucket 197: 40% Sorting block time: 00:00:00 Returning block of 19877 for bucket 178 bucket 189: 60% bucket 194: 50% bucket 183: 90% bucket 185: 80% bucket 187: 70% bucket 190: 60% Getting block 203 of 210 Reserving size (31083) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: bucket 188: 70% Getting block 204 of 210 Reserving size (31083) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: Sorting block time: 00:00:00 Returning block of 29587 for bucket 179 Getting block 205 of 210 Reserving size (31083) for bucket 205 Calculating Z arrays for bucket 205 Sorting block time: 00:00:00 Returning block of 16357 for bucket 180 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 205: bucket 182: 100% bucket 184: 90% Returning block of 25861 for bucket 181 bucket 198: 30% bucket 191: 60% bucket 195: 50% bucket 196: 50% bucket 200: 20% bucket 201: 20% bucket 202: 10% bucket 199: 30% bucket 197: 50% bucket 193: 60% bucket 192: 60% bucket 186: 80% bucket 189: 70% bucket 183: 100% bucket 194: 60% bucket 185: 90% bucket 187: 80% bucket 203: 10% bucket 190: 70% Sorting block of length 7102 for bucket 182 (Using difference cover) Getting block 206 of 210 Getting block 207 of 210 Sorting block of length 24731 for bucket 183 (Using difference cover) bucket 188: 80% Reserving size (31083) for bucket 206 Reserving size (31083) for bucket 207 Calculating Z arrays for bucket 206 Calculating Z arrays for bucket 207 Entering block accumulator loop for bucket 206: Entering block accumulator loop for bucket 207: Getting block 208 of 210 Reserving size (31083) for bucket 208 Calculating Z arrays for bucket 208 Entering block accumulator loop for bucket 208: bucket 204: 10% Sorting block time: 00:00:00 Returning block of 7103 for bucket 182 Sorting block time: 00:00:00 Returning block of 24732 for bucket 183 bucket 201: 30% bucket 196: 60% bucket 198: 40% bucket 200: 30% bucket 203: 20% bucket 199: 40% bucket 197: 60% bucket 202: 20% bucket 205: 10% bucket 191: 70% bucket 206: 10% Getting block 209 of 210 bucket 193: 70% Reserving size (31083) for bucket 209 bucket 186: 90% bucket 207: 10% Calculating Z arrays for bucket 209 bucket 194: 70% bucket 187: 90% Entering block accumulator loop for bucket 209: bucket 184: 100% bucket 195: 60% bucket 189: 80% bucket 192: 70% Sorting block of length 7761 for bucket 184 (Using difference cover) bucket 188: 90% bucket 185: 100% bucket 190: 80% Sorting block of length 30633 for bucket 185 (Using difference cover) bucket 208: 10% Getting block 210 of 210 Reserving size (31083) for bucket 210 Calculating Z arrays for bucket 210 Entering block accumulator loop for bucket 210: bucket 204: 20% Sorting block time: 00:00:00 Returning block of 7762 for bucket 184 bucket 210: 10% bucket 203: 30% bucket 196: 70% bucket 198: 50% bucket 200: 40% bucket 201: 40% bucket 199: 50% bucket 205: 20% bucket 206: 20% bucket 202: 30% bucket 197: 70% bucket 207: 20% bucket 209: 10% bucket 191: 80% bucket 193: 80% bucket 194: 80% bucket 208: 20% bucket 187: 100% bucket 186: 100% Sorting block of length 14590 for bucket 187 (Using difference cover) Sorting block of length 26724 for bucket 186 (Using difference cover) bucket 189: 90% Sorting block time: 00:00:00 Returning block of 30634 for bucket 185 bucket 192: 80% bucket 188: 100% Sorting block of length 27602 for bucket 188 bucket 190: 90% (Using difference cover) bucket 195: 70% bucket 204: 30% bucket 210: 20% Sorting block time: 00:00:00 Returning block of 14591 for bucket 187 bucket 203: 40% bucket 196: 80% bucket 205: 30% bucket 200: 50% bucket 206: 30% bucket 209: 20% bucket 199: 60% bucket 198: 60% bucket 202: 40% bucket 207: 30% bucket 197: 80% bucket 201: 50% Sorting block time: 00:00:00 Returning block of 26725 for bucket 186 Sorting block time: 00:00:00 Returning block of 27603 for bucket 188 bucket 208: 30% bucket 191: 90% bucket 193: 90% bucket 194: 90% bucket 210: 30% bucket 204: 40% bucket 192: 90% bucket 189: 100% Sorting block of length 14058 for bucket 189 (Using difference cover) bucket 190: 100% Sorting block of length 22532 for bucket 190 (Using difference cover) bucket 195: 80% Sorting block time: 00:00:00 Returning block of 14059 for bucket 189 bucket 210: 40% bucket 203: 50% bucket 196: 90% bucket 205: 40% bucket 209: 30% bucket 206: 40% bucket 200: 60% Sorting block time: 00:00:00 Returning block of 22533 for bucket 190 bucket 207: 40% bucket 199: 70% bucket 202: 50% bucket 197: 90% bucket 198: 70% bucket 201: 60% bucket 208: 40% bucket 204: 50% bucket 191: 100% Sorting block of length 23010 for bucket 191 (Using difference cover) bucket 194: 100% Sorting block of length 16315 for bucket 194 (Using difference cover) bucket 193: 100% Sorting block of length 19870 for bucket 193 (Using difference cover) bucket 192: 100% Sorting block of length 29961 for bucket 192 (Using difference cover) bucket 195: 90% bucket 210: 50% Sorting block time: 00:00:00 Returning block of 16316 for bucket 194 bucket 203: 60% Sorting block time: 00:00:00 Returning block of 19871 for bucket 193 bucket 209: 40% bucket 205: 50% bucket 196: 100% Sorting block of length 19534 for bucket 196 (Using difference cover) bucket 206: 50% bucket 207: 50% Sorting block time: 00:00:00 Returning block of 23011 for bucket 191 bucket 200: 70% bucket 199: 80% bucket 197: 100% Sorting block of length 28448 for bucket 197 (Using difference cover) bucket 202: 60% bucket 208: 50% bucket 198: 80% bucket 210: 60% bucket 204: 60% bucket 201: 70% Sorting block time: 00:00:00 Returning block of 29962 for bucket 192 bucket 195: 100% Sorting block of length 22157 for bucket 195 (Using difference cover) Sorting block time: 00:00:00 Returning block of 19535 for bucket 196 bucket 210: 70% bucket 203: 70% bucket 209: 50% bucket 205: 60% bucket 206: 60% Sorting block time: 00:00:00 Returning block of 28449 for bucket 197 bucket 207: 60% bucket 200: 80% bucket 199: 90% bucket 208: 60% bucket 202: 70% bucket 198: 90% bucket 204: 70% Sorting block time: 00:00:00 Returning block of 22158 for bucket 195 bucket 201: 80% bucket 210: 80% bucket 209: 60% bucket 203: 80% bucket 205: 70% bucket 206: 70% bucket 207: 70% bucket 199: 100% Sorting block of length 23147 for bucket 199 (Using difference cover) bucket 200: 90% bucket 208: 70% bucket 210: 90% bucket 202: 80% bucket 204: 80% bucket 198: 100% Sorting block of length 29033 for bucket 198 (Using difference cover) bucket 201: 90% bucket 210: 100% Sorting block of length 6549 for bucket 210 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23148 for bucket 199 bucket 203: 90% bucket 209: 70% bucket 205: 80% bucket 206: 80% Sorting block time: 00:00:00 Returning block of 6550 for bucket 210 Sorting block time: 00:00:00 Returning block of 29034 for bucket 198 bucket 207: 80% bucket 200: 100% Sorting block of length 23885 for bucket 200 (Using difference cover) bucket 208: 80% bucket 204: 90% bucket 202: 90% bucket 201: 100% Sorting block of length 21043 for bucket 201 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23886 for bucket 200 bucket 209: 80% bucket 203: 100% Sorting block of length 18025 for bucket 203 (Using difference cover) bucket 205: 90% Sorting block time: 00:00:00 Returning block of 21044 for bucket 201 bucket 206: 90% bucket 204: 100% Sorting block of length 17174 for bucket 204 (Using difference cover) bucket 207: 90% bucket 208: 90% bucket 202: 100% Sorting block of length 24897 for bucket 202 (Using difference cover) Sorting block time: 00:00:00 Returning block of 18026 for bucket 203 Sorting block time: 00:00:00 Returning block of 17175 for bucket 204 bucket 209: 90% bucket 205: 100% Sorting block of length 16612 for bucket 205 (Using difference cover) Sorting block time: 00:00:00 Returning block of 24898 for bucket 202 bucket 206: 100% Sorting block of length 19488 for bucket 206 (Using difference cover) bucket 208: 100% Sorting block of length 29255 for bucket 208 (Using difference cover) bucket 207: 100% Sorting block of length 26574 for bucket 207 (Using difference cover) Sorting block time: 00:00:00 Returning block of 16613 for bucket 205 Sorting block time: 00:00:00 Returning block of 19489 for bucket 206 bucket 209: 100% Sorting block of length 29553 for bucket 209 (Using difference cover) Sorting block time: 00:00:00 Returning block of 26575 for bucket 207 Sorting block time: 00:00:00 Returning block of 29256 for bucket 208 Sorting block time: 00:00:00 Returning block of 29554 for bucket 209 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2320179 fchr[G]: 3500270 fchr[T]: 3500270 fchr[$]: 4641652 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 5741754 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 1160420 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 4641652 bwtLen: 4641653 sz: 1160413 bwtSz: 1160414 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 290104 offsSz: 1160416 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 24176 numLines: 24176 ebwtTotLen: 1547264 ebwtTotSz: 1547264 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/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_R2_001_val_2.fq.gz 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 Created output directory lambda_tg/! Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth10_R1_001_val_1.fq.gz to Meth10_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth10_R1_001_val_1.fq.gz to Meth10_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth10_R1_001_val_1.fq.gz (83382907 sequences in total) Writing a C -> T converted version of the input file Meth10_R2_001_val_2.fq.gz to Meth10_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth10_R2_001_val_2.fq.gz to Meth10_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth10_R2_001_val_2.fq.gz (83382907 sequences in total) Input files are Meth10_R1_001_val_1.fq.gz_C_to_T.fastq and Meth10_R1_001_val_1.fq.gz_G_to_A.fastq and Meth10_R2_001_val_2.fq.gz_C_to_T.fastq and Meth10_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth10_R1_001_val_1.fq.gz_C_to_T.fastq and Meth10_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:23204:1000_1:N:0:AACCTGAA+NTGGTGAG/1 77 * 0 0 * * 0 0 ATGTGGAGTTTGTTTTTATTTTGTGGGGTGTTTTTGTTTGTATTTTTTTTAAAAATAAAGATATTGATAAATTGAAATTATTTTTGTTAATA FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23204:1000_2:N:0:AACCTGAA+NTGGTGAG/2 141 * 0 0 * * 0 0 TATTAACAAAAATAATTTCAATTTATCAATATCTTTATTTTTAAAAAAAATACAAACAAAAACACCCCACAAAATAAAAACAAACTCCACAT FFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF:FFFFF,FFF:FF:FFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth10_R1_001_val_1.fq.gz_G_to_A.fastq and Meth10_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:23204:1000_1:N:0:AACCTGAA+NTGGTGAG/1 77 * 0 0 * * 0 0 ATATAAAATTTATTTTTATTTTATAAAATATTTTTATTTATATTTTTTTTAAAAATAAAAATATTAATAAATTAAAATTATTTTTATTAATA FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23204:1000_2:N:0:AACCTGAA+NTGGTGAG/2 141 * 0 0 * * 0 0 TATTAATAAAAATAATTTTAATTTATTAATATTTTTATTTTTAAAAAAAATATAAATAAAAATATTTTATAAAATAAAAATAAATTTTATAT FFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF:FFFFF,FFF:FF:FFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth10_R1_001_val_1.fq.gz_G_to_A.fastq and Meth10_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:23204:1000_1:N:0:AACCTGAA+NTGGTGAG/1 77 * 0 0 * * 0 0 ATATAAAATTTATTTTTATTTTATAAAATATTTTTATTTATATTTTTTTTAAAAATAAAAATATTAATAAATTAAAATTATTTTTATTAATA FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23204:1000_2:N:0:AACCTGAA+NTGGTGAG/2 141 * 0 0 * * 0 0 TATTAATAAAAATAATTTTAATTTATTAATATTTTTATTTTTAAAAAAAATATAAATAAAAATATTTTATAAAATAAAAATAAATTTTATAT FFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF:FFFFF,FFF:FF:FFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth10_R1_001_val_1.fq.gz_C_to_T.fastq and Meth10_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:23204:1000_1:N:0:AACCTGAA+NTGGTGAG/1 77 * 0 0 * * 0 0 ATGTGGAGTTTGTTTTTATTTTGTGGGGTGTTTTTGTTTGTATTTTTTTTAAAAATAAAGATATTGATAAATTGAAATTATTTTTGTTAATA FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23204:1000_2:N:0:AACCTGAA+NTGGTGAG/2 141 * 0 0 * * 0 0 TATTAACAAAAATAATTTCAATTTATCAATATCTTTATTTTTAAAAAAAATACAAACAAAAACACCCCACAAAATAAAAACAAACTCCACAT FFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF:FFFFF,FFF:FF:FFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth10_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1351:32416:32863_1:N:0:GACCTGAA+TTGGTGAG NC_000913.3 4641525 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2601:14362:25708_1:N:0:GACCTGAA+TTGGTGAG NC_000913.3 4641525 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2601:14597:25739_1:N:0:GACCTGAA+TTGGTGAG NC_000913.3 4641525 Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far 83382907 reads; of these: 83382907 (100.00%) were paired; of these: 82848447 (99.36%) aligned concordantly 0 times 504974 (0.61%) aligned concordantly exactly 1 time 29486 (0.04%) aligned concordantly >1 times 0.64% overall alignment rate 83382907 reads; of these: 83382907 (100.00%) were paired; of these: 82716800 (99.20%) aligned concordantly 0 times 628727 (0.75%) aligned concordantly exactly 1 time 37380 (0.04%) aligned concordantly >1 times 0.80% overall alignment rate 83382907 reads; of these: 83382907 (100.00%) were paired; of these: 82845354 (99.36%) aligned concordantly 0 times 507712 (0.61%) aligned concordantly exactly 1 time 29841 (0.04%) aligned concordantly >1 times 0.64% overall alignment rate 83382907 reads; of these: 83382907 (100.00%) were paired; of these: 82720629 (99.21%) aligned concordantly 0 times 625109 (0.75%) aligned concordantly exactly 1 time 37169 (0.04%) aligned concordantly >1 times 0.79% overall alignment rate Processed 83382907 sequences in total Successfully deleted the temporary files Meth10_R1_001_val_1.fq.gz_C_to_T.fastq, Meth10_R1_001_val_1.fq.gz_G_to_A.fastq, Meth10_R2_001_val_2.fq.gz_C_to_T.fastq and Meth10_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 83382907 Number of paired-end alignments with a unique best hit: 2253304 Mapping efficiency: 2.7% Sequence pairs with no alignments under any condition: 81055905 Sequence pairs did not map uniquely: 73698 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 504410 ((converted) top strand) GA/CT/CT: 621911 (complementary to (converted) top strand) GA/CT/GA: 625521 (complementary to (converted) bottom strand) CT/GA/GA: 501459 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 122396335 Total methylated C's in CpG context: 463276 Total methylated C's in CHG context: 398915 Total methylated C's in CHH context: 718042 Total methylated C's in Unknown context: 55270 Total unmethylated C's in CpG context: 36486651 Total unmethylated C's in CHG context: 30449880 Total unmethylated C's in CHH context: 53879571 Total unmethylated C's in Unknown context: 310023 C methylated in CpG context: 1.3% C methylated in CHG context: 1.3% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 15.1% Bismark completed in 0d 1h 32m 59s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth11_R1_001_val_1.fq.gz to Meth11_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth11_R1_001_val_1.fq.gz to Meth11_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth11_R1_001_val_1.fq.gz (56845589 sequences in total) Writing a C -> T converted version of the input file Meth11_R2_001_val_2.fq.gz to Meth11_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth11_R2_001_val_2.fq.gz to Meth11_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth11_R2_001_val_2.fq.gz (56845589 sequences in total) Input files are Meth11_R1_001_val_1.fq.gz_C_to_T.fastq and Meth11_R1_001_val_1.fq.gz_G_to_A.fastq and Meth11_R2_001_val_2.fq.gz_C_to_T.fastq and Meth11_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth11_R1_001_val_1.fq.gz_C_to_T.fastq and Meth11_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:23095:1000_1:N:0:TCTCTACT+NGCGGTTC/1 77 * 0 0 * * 0 0 GGTAAAGTAAGTTGTTAGTTGTGAATATTTTGTGAAA FFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23095:1000_2:N:0:TCTCTACT+NGCGGTTC/2 141 * 0 0 * * 0 0 TTTCACAAAATATTCACAACTAACAACTTACTTTACC :FFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth11_R1_001_val_1.fq.gz_G_to_A.fastq and Meth11_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:23095:1000_1:N:0:TCTCTACT+NGCGGTTC/1 77 * 0 0 * * 0 0 AATAAAATAAATCATTAATCACAAATATTTTACAAAA FFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23095:1000_2:N:0:TCTCTACT+NGCGGTTC/2 141 * 0 0 * * 0 0 TTTTGTAAAATATTTGTGATTAATGATTTATTTTATT :FFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth11_R1_001_val_1.fq.gz_G_to_A.fastq and Meth11_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:23095:1000_1:N:0:TCTCTACT+NGCGGTTC/1 77 * 0 0 * * 0 0 AATAAAATAAATCATTAATCACAAATATTTTACAAAA FFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23095:1000_2:N:0:TCTCTACT+NGCGGTTC/2 141 * 0 0 * * 0 0 TTTTGTAAAATATTTGTGATTAATGATTTATTTTATT :FFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth11_R1_001_val_1.fq.gz_C_to_T.fastq and Meth11_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:23095:1000_1:N:0:TCTCTACT+NGCGGTTC/1 77 * 0 0 * * 0 0 GGTAAAGTAAGTTGTTAGTTGTGAATATTTTGTGAAA FFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23095:1000_2:N:0:TCTCTACT+NGCGGTTC/2 141 * 0 0 * * 0 0 TTTCACAAAATATTCACAACTAACAACTTACTTTACC :FFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth11_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far 56845589 reads; of these: 56845589 (100.00%) were paired; of these: 56683235 (99.71%) aligned concordantly 0 times 151671 (0.27%) aligned concordantly exactly 1 time 10683 (0.02%) aligned concordantly >1 times 0.29% overall alignment rate 56845589 reads; of these: 56845589 (100.00%) were paired; of these: 56641185 (99.64%) aligned concordantly 0 times 190889 (0.34%) aligned concordantly exactly 1 time 13515 (0.02%) aligned concordantly >1 times 0.36% overall alignment rate 56845589 reads; of these: 56845589 (100.00%) were paired; of these: 56681855 (99.71%) aligned concordantly 0 times 152355 (0.27%) aligned concordantly exactly 1 time 11379 (0.02%) aligned concordantly >1 times 0.2956845589% reads; of these: overall alignment rate 56845589 (100.00%) were paired; of these: 56640419 (99.64%) aligned concordantly 0 times 190981 (0.34%) aligned concordantly exactly 1 time 14189 (0.02%) aligned concordantly >1 times 0.36% overall alignment rate Processed 56845589 sequences in total Successfully deleted the temporary files Meth11_R1_001_val_1.fq.gz_C_to_T.fastq, Meth11_R1_001_val_1.fq.gz_G_to_A.fastq, Meth11_R2_001_val_2.fq.gz_C_to_T.fastq and Meth11_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 56845589 Number of paired-end alignments with a unique best hit: 676715 Mapping efficiency: 1.2% Sequence pairs with no alignments under any condition: 56139484 Sequence pairs did not map uniquely: 29390 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 150149 ((converted) top strand) GA/CT/CT: 188915 (complementary to (converted) top strand) GA/CT/GA: 188444 (complementary to (converted) bottom strand) CT/GA/GA: 149207 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 36266037 Total methylated C's in CpG context: 127853 Total methylated C's in CHG context: 109755 Total methylated C's in CHH context: 238440 Total methylated C's in Unknown context: 13844 Total unmethylated C's in CpG context: 10823684 Total unmethylated C's in CHG context: 9040624 Total unmethylated C's in CHH context: 15925681 Total unmethylated C's in Unknown context: 85814 C methylated in CpG context: 1.2% C methylated in CHG context: 1.2% C methylated in CHH context: 1.5% C methylated in unknown context (CN or CHN): 13.9% Bismark completed in 0d 0h 56m 28s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth12_R1_001_val_1.fq.gz to Meth12_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth12_R1_001_val_1.fq.gz to Meth12_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth12_R1_001_val_1.fq.gz (94422705 sequences in total) Writing a C -> T converted version of the input file Meth12_R2_001_val_2.fq.gz to Meth12_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth12_R2_001_val_2.fq.gz to Meth12_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth12_R2_001_val_2.fq.gz (94422705 sequences in total) Input files are Meth12_R1_001_val_1.fq.gz_C_to_T.fastq and Meth12_R1_001_val_1.fq.gz_G_to_A.fastq and Meth12_R2_001_val_2.fq.gz_C_to_T.fastq and Meth12_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth12_R1_001_val_1.fq.gz_C_to_T.fastq and Meth12_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:22318:1000_1:N:0:CTCTCGTC+NATAACCT/1 77 * 0 0 * * 0 0 GATGAAGTATTATTATAAGTGTGATTTTTTGAATTATTAAATGATTTTGAAAAAATATTGTGTTGAGTTAATATAGGAATTTTGTTATTTTGGTAAATTTTTATGTTATTTATTTTTTAAGGTGATATGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:22318:1000_2:N:0:CTCTCGTC+NATAACCT/2 141 * 0 0 * * 0 0 AAATTCAATTTAATAACAAAAAAAATAAAAACATTTCCATATCACCTTAAAAAATAAATAACATAAAAATTTACCAAAATAACAAAATTCCTATATTAACTCAACACAATATTTTTTCAAAATCATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth12_R1_001_val_1.fq.gz_G_to_A.fastq and Meth12_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:22318:1000_1:N:0:CTCTCGTC+NATAACCT/1 77 * 0 0 * * 0 0 AATAAAATATTATTATAAATATAATTTTTTAAATTATTAAATAATTTTAAAAAAATATTATATTAAATTAATATAAAAATTTTATTATTTTAATAAATTTTTATATTATTTATTTTTTAAAATAATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:22318:1000_2:N:0:CTCTCGTC+NATAACCT/2 141 * 0 0 * * 0 0 AAATTTAATTTAATAATAAAAAAAATAAAAATATTTTTATATTATTTTAAAAAATAAATAATATAAAAATTTATTAAAATAATAAAATTTTTATATTAATTTAATATAATATTTTTTTAAAATTATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth12_R1_001_val_1.fq.gz_G_to_A.fastq and Meth12_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:22318:1000_1:N:0:CTCTCGTC+NATAACCT/1 77 * 0 0 * * 0 0 AATAAAATATTATTATAAATATAATTTTTTAAATTATTAAATAATTTTAAAAAAATATTATATTAAATTAATATAAAAATTTTATTATTTTAATAAATTTTTATATTATTTATTTTTTAAAATAATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:22318:1000_2:N:0:CTCTCGTC+NATAACCT/2 141 * 0 0 * * 0 0 AAATTTAATTTAATAATAAAAAAAATAAAAATATTTTTATATTATTTTAAAAAATAAATAATATAAAAATTTATTAAAATAATAAAATTTTTATATTAATTTAATATAATATTTTTTTAAAATTATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth12_R1_001_val_1.fq.gz_C_to_T.fastq and Meth12_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:22318:1000_1:N:0:CTCTCGTC+NATAACCT/1 77 * 0 0 * * 0 0 GATGAAGTATTATTATAAGTGTGATTTTTTGAATTATTAAATGATTTTGAAAAAATATTGTGTTGAGTTAATATAGGAATTTTGTTATTTTGGTAAATTTTTATGTTATTTATTTTTTAAGGTGATATGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:22318:1000_2:N:0:CTCTCGTC+NATAACCT/2 141 * 0 0 * * 0 0 AAATTCAATTTAATAACAAAAAAAATAAAAACATTTCCATATCACCTTAAAAAATAAATAACATAAAAATTTACCAAAATAACAAAATTCCTATATTAACTCAACACAATATTTTTTCAAAATCATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth12_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1378:18484:18286_1:N:0:CTCTCGTC+TATAACCT NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1378:18973:19539_1:N:0:CTCTCGTC+TATAACCT NC_000913.3 1 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2376:16911:32002_1:N:0:CTCTCGTC+TATAACCT NC_000913.3 1 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far 94422705 reads; of these: 94422705 (100.00%) were paired; of these: 93835939 (99.38%) aligned concordantly 0 times 556148 (0.59%) aligned concordantly exactly 1 time 30618 (0.03%) aligned concordantly >1 times 0.62% overall alignment rate 94422705 reads; of these: 94422705 (100.00%) were paired; of these: 93943876 (99.49%) aligned concordantly 0 times 453621 (0.48%) aligned concordantly exactly 1 time 25208 (0.03%) aligned concordantly >1 times 0.51% overall alignment rate 94422705 reads; of these: 94422705 (100.00%) were paired; of these: 93838428 (99.38%) aligned concordantly 0 times 553529 (0.59%) aligned concordantly exactly 1 time 30748 (0.03%) aligned concordantly >1 times 0.62%94422705 overall alignment rate reads; of these: 94422705 (100.00%) were paired; of these: 93941982 (99.49%) aligned concordantly 0 times 455464 (0.48%) aligned concordantly exactly 1 time 25259 (0.03%) aligned concordantly >1 times 0.51% overall alignment rate Processed 94422705 sequences in total Successfully deleted the temporary files Meth12_R1_001_val_1.fq.gz_C_to_T.fastq, Meth12_R1_001_val_1.fq.gz_G_to_A.fastq, Meth12_R2_001_val_2.fq.gz_C_to_T.fastq and Meth12_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 94422705 Number of paired-end alignments with a unique best hit: 2013006 Mapping efficiency: 2.1% Sequence pairs with no alignments under any condition: 92350928 Sequence pairs did not map uniquely: 58771 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 453705 ((converted) top strand) GA/CT/CT: 554805 (complementary to (converted) top strand) GA/CT/GA: 552365 (complementary to (converted) bottom strand) CT/GA/GA: 452128 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 113300450 Total methylated C's in CpG context: 419417 Total methylated C's in CHG context: 362660 Total methylated C's in CHH context: 611397 Total methylated C's in Unknown context: 65250 Total unmethylated C's in CpG context: 33442289 Total unmethylated C's in CHG context: 28097754 Total unmethylated C's in CHH context: 50366933 Total unmethylated C's in Unknown context: 301861 C methylated in CpG context: 1.2% C methylated in CHG context: 1.3% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 17.8% Bismark completed in 0d 1h 42m 14s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth13_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth13_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth13_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth13_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth13_R1_001_val_1.fq.gz to Meth13_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth13_R1_001_val_1.fq.gz to Meth13_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth13_R1_001_val_1.fq.gz (100607927 sequences in total) Writing a C -> T converted version of the input file Meth13_R2_001_val_2.fq.gz to Meth13_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth13_R2_001_val_2.fq.gz to Meth13_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth13_R2_001_val_2.fq.gz (100607927 sequences in total) Input files are Meth13_R1_001_val_1.fq.gz_C_to_T.fastq and Meth13_R1_001_val_1.fq.gz_G_to_A.fastq and Meth13_R2_001_val_2.fq.gz_C_to_T.fastq and Meth13_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth13_R1_001_val_1.fq.gz_C_to_T.fastq and Meth13_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21974:1000_1:N:0:CCAAGTCT+NAGGATGA/1 77 * 0 0 * * 0 0 TNGTTGTGTTGAAGTATGGTATGTGTTGTAAAATATTTTGGTTGGTTT ,#,:FFFFF,:FFF:FF:,FFFFF:FFFFFFFFFF,,F::FFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21974:1000_2:N:0:CCAAGTCT+NAGGATGA/2 141 * 0 0 * * 0 0 AAACCAACCAAAATATTTTACAACACATACCATACTTCAACACAACCA FFF,,FF::FFFFFFFFFFF:FF:FFFFFFFFFFFFF,FFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth13_R1_001_val_1.fq.gz_G_to_A.fastq and Meth13_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21974:1000_1:N:0:CCAAGTCT+NAGGATGA/1 77 * 0 0 * * 0 0 TNATTATATTAAAATATAATATATATTATAAAATATTTTAATTAATTT ,#,:FFFFF,:FFF:FF:,FFFFF:FFFFFFFFFF,,F::FFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21974:1000_2:N:0:CCAAGTCT+NAGGATGA/2 141 * 0 0 * * 0 0 AAATTAATTAAAATATTTTATAATATATATTATATTTTAATATAATTA FFF,,FF::FFFFFFFFFFF:FF:FFFFFFFFFFFFF,FFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth13_R1_001_val_1.fq.gz_G_to_A.fastq and Meth13_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21974:1000_1:N:0:CCAAGTCT+NAGGATGA/1 77 * 0 0 * * 0 0 TNATTATATTAAAATATAATATATATTATAAAATATTTTAATTAATTT ,#,:FFFFF,:FFF:FF:,FFFFF:FFFFFFFFFF,,F::FFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21974:1000_2:N:0:CCAAGTCT+NAGGATGA/2 141 * 0 0 * * 0 0 AAATTAATTAAAATATTTTATAATATATATTATATTTTAATATAATTA FFF,,FF::FFFFFFFFFFF:FF:FFFFFFFFFFFFF,FFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth13_R1_001_val_1.fq.gz_C_to_T.fastq and Meth13_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21974:1000_1:N:0:CCAAGTCT+NAGGATGA/1 77 * 0 0 * * 0 0 TNGTTGTGTTGAAGTATGGTATGTGTTGTAAAATATTTTGGTTGGTTT ,#,:FFFFF,:FFF:FF:,FFFFF:FFFFFFFFFF,,F::FFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21974:1000_2:N:0:CCAAGTCT+NAGGATGA/2 141 * 0 0 * * 0 0 AAACCAACCAAAATATTTTACAACACATACCATACTTCAACACAACCA FFF,,FF::FFFFFFFFFFF:FF:FFFFFFFFFFFFF,FFFFFFF:FF YT:Z:UP >>> Writing bisulfite mapping results to Meth13_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth13_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth13_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far 100607927 reads; of these: 100607927 (100.00%) were paired; of these: 98914507 (98.32%) aligned concordantly 0 times 1556984 (1.55%) aligned concordantly exactly 1 time 136436 (0.14%) aligned concordantly >1 times 1.68% overall alignment rate 100607927 reads; of these: 100607927 (100607927100.00 reads; of these:%) were paired; of these: 98908702100607927 ( (98.31%) aligned concordantly 0 times 1561222 (1.55%) aligned concordantly exactly 1 time 138003100.00 (%0.14) were paired; of these:% ) aligned concordantly >1 times 988396941.69 (%98.24 overall alignment rate% ) aligned concordantly 0 times 1628108 (1.62%) aligned concordantly exactly 1 time 140125 (0.14%) aligned concordantly >1 times 1.76% overall alignment rate 100607927 reads; of these: 100607927 (100.00%) were paired; of these: 98829215 (98.23%) aligned concordantly 0 times 1634023 (1.62%) aligned concordantly exactly 1 time 144689 (0.14%) aligned concordantly >1 times 1.77% overall alignment rate Processed 100607927 sequences in total Successfully deleted the temporary files Meth13_R1_001_val_1.fq.gz_C_to_T.fastq, Meth13_R1_001_val_1.fq.gz_G_to_A.fastq, Meth13_R2_001_val_2.fq.gz_C_to_T.fastq and Meth13_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100607927 Number of paired-end alignments with a unique best hit: 6361993 Mapping efficiency: 6.3% Sequence pairs with no alignments under any condition: 93942886 Sequence pairs did not map uniquely: 303048 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1557822 ((converted) top strand) GA/CT/CT: 1627505 (complementary to (converted) top strand) GA/CT/GA: 1623625 (complementary to (converted) bottom strand) CT/GA/GA: 1553041 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 330622014 Total methylated C's in CpG context: 3076960 Total methylated C's in CHG context: 513693 Total methylated C's in CHH context: 1152918 Total methylated C's in Unknown context: 6198 Total unmethylated C's in CpG context: 102490675 Total unmethylated C's in CHG context: 84959815 Total unmethylated C's in CHH context: 138427953 Total unmethylated C's in Unknown context: 35868 C methylated in CpG context: 2.9% C methylated in CHG context: 0.6% C methylated in CHH context: 0.8% C methylated in unknown context (CN or CHN): 14.7% Bismark completed in 0d 2h 19m 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/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth14_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth14_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth14_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth14_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth14_R1_001_val_1.fq.gz to Meth14_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth14_R1_001_val_1.fq.gz to Meth14_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth14_R1_001_val_1.fq.gz (69159859 sequences in total) Writing a C -> T converted version of the input file Meth14_R2_001_val_2.fq.gz to Meth14_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth14_R2_001_val_2.fq.gz to Meth14_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth14_R2_001_val_2.fq.gz (69159859 sequences in total) Input files are Meth14_R1_001_val_1.fq.gz_C_to_T.fastq and Meth14_R1_001_val_1.fq.gz_G_to_A.fastq and Meth14_R2_001_val_2.fq.gz_C_to_T.fastq and Meth14_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth14_R1_001_val_1.fq.gz_C_to_T.fastq and Meth14_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21468:1000_1:N:0:TTAGACTC+NGAAGCAG/1 77 * 0 0 * * 0 0 TNATATATAAAAATAATTTTTGAATTTTAAATTTTAATATTGTAATTGTTTATTATTGATTTTTATATAAAAATAAATAAAAAATTGAATTAAAT F#FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21468:1000_2:N:0:TTAGACTC+NGAAGCAG/2 141 * 0 0 * * 0 0 CAATTTAATTCAATTTTTTATTTATTTTTATATAAAAATCAATAATAAACAATTACAATATTAAAATTTAAAATTCAAAAATTATTTTTATATATCA FFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF::FFFFF:FFF,FFFFFFFFFFFFFFF:FFFFF::FF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth14_R1_001_val_1.fq.gz_G_to_A.fastq and Meth14_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21468:1000_1:N:0:TTAGACTC+NGAAGCAG/1 77 * 0 0 * * 0 0 CNATATATAAAAATAATTTTCAAACTCTAAACCTTAATACCATAACCACTTATTATCAATCTTCACATAAAAATAAACAAAAAACCAAATCAAAC F#FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21468:1000_2:N:0:TTAGACTC+NGAAGCAG/2 141 * 0 0 * * 0 0 TGGTTTGATTTGGTTTTTTGTTTATTTTTATGTGAAGATTGATAATAAGTGGTTATGGTATTAAGGTTTAGAGTTTGAAAATTATTTTTATATATTG FFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF::FFFFF:FFF,FFFFFFFFFFFFFFF:FFFFF::FF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth14_R1_001_val_1.fq.gz_G_to_A.fastq and Meth14_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21468:1000_1:N:0:TTAGACTC+NGAAGCAG/1 77 * 0 0 * * 0 0 CNATATATAAAAATAATTTTCAAACTCTAAACCTTAATACCATAACCACTTATTATCAATCTTCACATAAAAATAAACAAAAAACCAAATCAAAC F#FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21468:1000_2:N:0:TTAGACTC+NGAAGCAG/2 141 * 0 0 * * 0 0 TGGTTTGATTTGGTTTTTTGTTTATTTTTATGTGAAGATTGATAATAAGTGGTTATGGTATTAAGGTTTAGAGTTTGAAAATTATTTTTATATATTG FFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF::FFFFF:FFF,FFFFFFFFFFFFFFF:FFFFF::FF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth14_R1_001_val_1.fq.gz_C_to_T.fastq and Meth14_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21468:1000_1:N:0:TTAGACTC+NGAAGCAG/1 77 * 0 0 * * 0 0 TNATATATAAAAATAATTTTTGAATTTTAAATTTTAATATTGTAATTGTTTATTATTGATTTTTATATAAAAATAAATAAAAAATTGAATTAAAT F#FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21468:1000_2:N:0:TTAGACTC+NGAAGCAG/2 141 * 0 0 * * 0 0 CAATTTAATTCAATTTTTTATTTATTTTTATATAAAAATCAATAATAAACAATTACAATATTAAAATTTAAAATTCAAAAATTATTTTTATATATCA FFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF::FFFFF:FFF,FFFFFFFFFFFFFFF:FFFFF::FF:FFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth14_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth14_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth14_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far 69159859 reads; of these: 69159859 (100.00%) were paired; of these: 67811853 (98.05%) aligned concordantly 0 times 1232831 (1.78%) aligned concordantly exactly 1 time 115175 (0.17%) aligned concordantly >1 times 1.95% overall alignment rate 69159859 reads; of these: 69159859 (100.00%) were paired; of these: 68087037 (98.45%) aligned concordantly 0 times 983884 (1.42%) aligned concordantly exactly 1 time 88938 (0.13%) aligned concordantly >1 times 1.55% overall alignment rate 69159859 reads; of these: 69159859 (100.00%) were paired; of these: 68077081 (98.43%) aligned concordantly 0 times 991472 (1.43%) aligned concordantly exactly 1 time 91306 (0.13%) aligned concordantly >1 times 1.57% overall alignment rate 69159859 reads; of these: 69159859 (100.00%) were paired; of these: 67810371 (98.05%) aligned concordantly 0 times 1233233 (1.78%) aligned concordantly exactly 1 time 116255 (0.17%) aligned concordantly >1 times 1.95% overall alignment rate Processed 69159859 sequences in total Successfully deleted the temporary files Meth14_R1_001_val_1.fq.gz_C_to_T.fastq, Meth14_R1_001_val_1.fq.gz_G_to_A.fastq, Meth14_R2_001_val_2.fq.gz_C_to_T.fastq and Meth14_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 69159859 Number of paired-end alignments with a unique best hit: 4416160 Mapping efficiency: 6.4% Sequence pairs with no alignments under any condition: 64514744 Sequence pairs did not map uniquely: 228955 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1229089 ((converted) top strand) GA/CT/CT: 982013 (complementary to (converted) top strand) GA/CT/GA: 975794 (complementary to (converted) bottom strand) CT/GA/GA: 1229264 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 222783977 Total methylated C's in CpG context: 1949119 Total methylated C's in CHG context: 318775 Total methylated C's in CHH context: 822127 Total methylated C's in Unknown context: 4145 Total unmethylated C's in CpG context: 69646106 Total unmethylated C's in CHG context: 57661846 Total unmethylated C's in CHH context: 92386004 Total unmethylated C's in Unknown context: 22921 C methylated in CpG context: 2.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 15.3% Bismark completed in 0d 1h 34m 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/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth15_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth15_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth15_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth15_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth15_R1_001_val_1.fq.gz to Meth15_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth15_R1_001_val_1.fq.gz to Meth15_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth15_R1_001_val_1.fq.gz (108911247 sequences in total) Writing a C -> T converted version of the input file Meth15_R2_001_val_2.fq.gz to Meth15_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth15_R2_001_val_2.fq.gz to Meth15_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth15_R2_001_val_2.fq.gz (108911247 sequences in total) Input files are Meth15_R1_001_val_1.fq.gz_C_to_T.fastq and Meth15_R1_001_val_1.fq.gz_G_to_A.fastq and Meth15_R2_001_val_2.fq.gz_C_to_T.fastq and Meth15_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth15_R1_001_val_1.fq.gz_C_to_T.fastq and Meth15_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21793:1000_1:N:0:GGCTTAAG+NCGTGACC/1 77 * 0 0 * * 0 0 TNGGATTTGGTGTTATATGTGGGTTGAGTTTGTTGGTTTATTATTTTGTATTGAGAGGTTTTTTTTATGTATTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21793:1000_2:N:0:GGCTTAAG+NCGTGACC/2 141 * 0 0 * * 0 0 AAATACATAAAAAAAACCTCTCAATACAAAATAATAAACCAACAAACTCAACCCACATATAACACCAAATCCCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth15_R1_001_val_1.fq.gz_G_to_A.fastq and Meth15_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21793:1000_1:N:0:GGCTTAAG+NCGTGACC/1 77 * 0 0 * * 0 0 TNAAATTTAATATTATATATAAATTAAATTTATTAATTTATTATTTTATATTAAAAAATTTTTTTTATATATTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21793:1000_2:N:0:GGCTTAAG+NCGTGACC/2 141 * 0 0 * * 0 0 AAATATATAAAAAAAATTTTTTAATATAAAATAATAAATTAATAAATTTAATTTATATATAATATTAAATTTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth15_R1_001_val_1.fq.gz_G_to_A.fastq and Meth15_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21793:1000_1:N:0:GGCTTAAG+NCGTGACC/1 77 * 0 0 * * 0 0 TNAAATTTAATATTATATATAAATTAAATTTATTAATTTATTATTTTATATTAAAAAATTTTTTTTATATATTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21793:1000_2:N:0:GGCTTAAG+NCGTGACC/2 141 * 0 0 * * 0 0 AAATATATAAAAAAAATTTTTTAATATAAAATAATAAATTAATAAATTTAATTTATATATAATATTAAATTTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth15_R1_001_val_1.fq.gz_C_to_T.fastq and Meth15_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21793:1000_1:N:0:GGCTTAAG+NCGTGACC/1 77 * 0 0 * * 0 0 TNGGATTTGGTGTTATATGTGGGTTGAGTTTGTTGGTTTATTATTTTGTATTGAGAGGTTTTTTTTATGTATTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21793:1000_2:N:0:GGCTTAAG+NCGTGACC/2 141 * 0 0 * * 0 0 AAATACATAAAAAAAACCTCTCAATACAAAATAATAAACCAACAAACTCAACCCACATATAACACCAAATCCCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth15_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth15_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth15_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Processed 107000000 sequence pairs so far Processed 108000000 sequence pairs so far 108911247 reads; of these: 108911247 (100.00%) were paired; of these: 106331595 (97.63%) aligned concordantly 0 times 2368764 (2.17%) aligned concordantly exactly 1 time 210888 (0.19%) aligned concordantly >1 times 2.37% overall alignment rate 108911247108911247 reads; of these: reads; of these: 108911247 (108911247 (100.00%) were paired; of these: 106491431 (97.78100.00%%) aligned concordantly 0 times) were paired; of these: 2210788106327968 ( (2.03%97.63) aligned concordantly exactly 1 time% ) aligned concordantly 0 times 209028 (23674160.19 (%2.17) aligned concordantly >1 times% ) aligned concordantly exactly 1 time2.22 % overall alignment rate215863 (0.20%) aligned concordantly >1 times 2.37% overall alignment rate 108911247 reads; of these: 108911247 (100.00%) were paired; of these: 106492475 (97.78%) aligned concordantly 0 times 2212585 (2.03%) aligned concordantly exactly 1 time 206187 (0.19%) aligned concordantly >1 times 2.22% overall alignment rate Processed 108911247 sequences in total Successfully deleted the temporary files Meth15_R1_001_val_1.fq.gz_C_to_T.fastq, Meth15_R1_001_val_1.fq.gz_G_to_A.fastq, Meth15_R2_001_val_2.fq.gz_C_to_T.fastq and Meth15_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 108911247 Number of paired-end alignments with a unique best hit: 9108570 Mapping efficiency: 8.4% Sequence pairs with no alignments under any condition: 99342731 Sequence pairs did not map uniquely: 459946 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2199593 ((converted) top strand) GA/CT/CT: 2351436 (complementary to (converted) top strand) GA/CT/GA: 2355183 (complementary to (converted) bottom strand) CT/GA/GA: 2202358 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 466793413 Total methylated C's in CpG context: 4433012 Total methylated C's in CHG context: 713048 Total methylated C's in CHH context: 1663938 Total methylated C's in Unknown context: 8878 Total unmethylated C's in CpG context: 144957150 Total unmethylated C's in CHG context: 120042295 Total unmethylated C's in CHH context: 194983970 Total unmethylated C's in Unknown context: 48293 C methylated in CpG context: 3.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.8% C methylated in unknown context (CN or CHN): 15.5% Bismark completed in 0d 2h 43m 48s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth16_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth16_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth16_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth16_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth16_R1_001_val_1.fq.gz to Meth16_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth16_R1_001_val_1.fq.gz to Meth16_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth16_R1_001_val_1.fq.gz (73273057 sequences in total) Writing a C -> T converted version of the input file Meth16_R2_001_val_2.fq.gz to Meth16_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth16_R2_001_val_2.fq.gz to Meth16_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth16_R2_001_val_2.fq.gz (73273057 sequences in total) Input files are Meth16_R1_001_val_1.fq.gz_C_to_T.fastq and Meth16_R1_001_val_1.fq.gz_G_to_A.fastq and Meth16_R2_001_val_2.fq.gz_C_to_T.fastq and Meth16_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth16_R1_001_val_1.fq.gz_C_to_T.fastq and Meth16_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21414:1000_1:N:0:AATCCGGA+NTACAGTT/1 77 * 0 0 * * 0 0 TTGATTTTAATAATAATTATTATTATAATTATTATATTTAAAATTAATTAAATAAAAAATTTAAAATTTTAAATATAA FFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21414:1000_2:N:0:AATCCGGA+NTACAGTT/2 141 * 0 0 * * 0 0 TTATATTTAAAATTTTAAATTTTTTATTTAATTAATTTTAAATATAATAATTATAATAATA FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth16_R1_001_val_1.fq.gz_G_to_A.fastq and Meth16_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21414:1000_1:N:0:AATCCGGA+NTACAGTT/1 77 * 0 0 * * 0 0 CCAATCTCAACAACAATCATCATTACAACCATCACACTTAAAATTAACTAAATAAAAAATTCAAAATCTTAAATACAA FFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21414:1000_2:N:0:AATCCGGA+NTACAGTT/2 141 * 0 0 * * 0 0 TTGTATTTAAGATTTTGAATTTTTTATTTAGTTAATTTTAAGTGTGATGGTTGTAATGATG FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth16_R1_001_val_1.fq.gz_G_to_A.fastq and Meth16_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21414:1000_1:N:0:AATCCGGA+NTACAGTT/1 77 * 0 0 * * 0 0 CCAATCTCAACAACAATCATCATTACAACCATCACACTTAAAATTAACTAAATAAAAAATTCAAAATCTTAAATACAA FFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21414:1000_2:N:0:AATCCGGA+NTACAGTT/2 141 * 0 0 * * 0 0 TTGTATTTAAGATTTTGAATTTTTTATTTAGTTAATTTTAAGTGTGATGGTTGTAATGATG FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth16_R1_001_val_1.fq.gz_C_to_T.fastq and Meth16_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21414:1000_1:N:0:AATCCGGA+NTACAGTT/1 77 * 0 0 * * 0 0 TTGATTTTAATAATAATTATTATTATAATTATTATATTTAAAATTAATTAAATAAAAAATTTAAAATTTTAAATATAA FFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21414:1000_2:N:0:AATCCGGA+NTACAGTT/2 141 * 0 0 * * 0 0 TTATATTTAAAATTTTAAATTTTTTATTTAATTAATTTTAAATATAATAATTATAATAATA FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth16_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth16_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth16_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1564:31620:3928_1:N:0:AATCCGGA+CTACAGTT NC_000913.3 1 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1625:20672:15468_1:N:0:AATCCGGA+CTACAGTT NC_000913.3 1 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2102:29713:26584_1:N:0:AATCCGGA+CTACAGTT NC_000913.3 4641547 Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2252:27724:15405_1:N:0:AATCCGGA+CTACAGTT NC_000913.3 4641547 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far 73273057 reads; of these: 73273057 (100.00%) were paired; of these: 69327911 (94.62%) aligned concordantly 0 times 3762260 (5.13%) aligned concordantly exactly 1 time 182886 (0.25%) aligned concordantly >1 times 5.38% overall alignment rate 73273057 reads; of these: 73273057 (100.00%) were paired; of these: 69994001 (95.52%) aligned concordantly 0 times 3123748 (4.26%) aligned concordantly exactly 1 time 155308 (0.21%) aligned concordantly >1 times 4.48% overall alignment rate 73273057 reads; of these: 73273057 (73273057100.00 reads; of these:% ) were paired; of these: 73273057 (69353375 (94.65%) aligned concordantly 0 times 100.003733794% () were paired; of these:5.10 % ) aligned concordantly exactly 1 time69966410 ( 95.49185888% () aligned concordantly 0 times0.25 % ) aligned concordantly >1 times3150965 (5.354.30%% overall alignment rate) aligned concordantly exactly 1 time 155682 (0.21%) aligned concordantly >1 times 4.51% overall alignment rate Processed 73273057 sequences in total Successfully deleted the temporary files Meth16_R1_001_val_1.fq.gz_C_to_T.fastq, Meth16_R1_001_val_1.fq.gz_G_to_A.fastq, Meth16_R2_001_val_2.fq.gz_C_to_T.fastq and Meth16_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 73273057 Number of paired-end alignments with a unique best hit: 13777977 Mapping efficiency: 18.8% Sequence pairs with no alignments under any condition: 59159400 Sequence pairs did not map uniquely: 335680 Sequence pairs which were discarded because genomic sequence could not be extracted: 4 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3151304 ((converted) top strand) GA/CT/CT: 3763289 (complementary to (converted) top strand) GA/CT/GA: 3738622 (complementary to (converted) bottom strand) CT/GA/GA: 3124758 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 796084119 Total methylated C's in CpG context: 3069507 Total methylated C's in CHG context: 2629289 Total methylated C's in CHH context: 3997006 Total methylated C's in Unknown context: 498343 Total unmethylated C's in CpG context: 234859593 Total unmethylated C's in CHG context: 197034366 Total unmethylated C's in CHH context: 354494358 Total unmethylated C's in Unknown context: 2188269 C methylated in CpG context: 1.3% C methylated in CHG context: 1.3% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 18.5% Bismark completed in 0d 3h 1m 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/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth17_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth17_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth17_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth17_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth17_R1_001_val_1.fq.gz to Meth17_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth17_R1_001_val_1.fq.gz to Meth17_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth17_R1_001_val_1.fq.gz (81609496 sequences in total) Writing a C -> T converted version of the input file Meth17_R2_001_val_2.fq.gz to Meth17_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth17_R2_001_val_2.fq.gz to Meth17_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth17_R2_001_val_2.fq.gz (81609496 sequences in total) Input files are Meth17_R1_001_val_1.fq.gz_C_to_T.fastq and Meth17_R1_001_val_1.fq.gz_G_to_A.fastq and Meth17_R2_001_val_2.fq.gz_C_to_T.fastq and Meth17_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth17_R1_001_val_1.fq.gz_C_to_T.fastq and Meth17_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21323:1000_1:N:0:TAATACAG+NTATTCAC/1 77 * 0 0 * * 0 0 GTTTGGTTATGAATAGAGGTTAGATTAAGTGGTATTATAGTAAATTGGGTGTTTGTTTTTTTTTGTAGAAATAGTATTTTGTAGTTGTTTGGAATGGATATTAGGTTATGTAGGTTTTGTTTTGTTTTTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21323:1000_2:N:0:TAATACAG+NTATTCAC/2 141 * 0 0 * * 0 0 CCAATCTCTTTTTACCACAAACAATACTTAAAAAAACCCAACAAAAACTAATTAATTTTCATAACTCCAATTTATCCTTAATAAAAATAAACCATCACTCCAACAAAATAATCACAATAACCACAAAAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth17_R1_001_val_1.fq.gz_G_to_A.fastq and Meth17_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21323:1000_1:N:0:TAATACAG+NTATTCAC/1 77 * 0 0 * * 0 0 ACCTAACCATAAATAAAAACCAAATTAAACAACACCATAACAAACTAAATACTTACTCCCCCTTACAAAAACAATACCTTATAATTATCCAAAACAAACATCAAATCACACAAATCCCACTCCACTTTCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21323:1000_2:N:0:TAATACAG+NTATTCAC/2 141 * 0 0 * * 0 0 TTGATTTTTTTTTGTTGTAAGTGGTGTTTGAAAGAGTTTAGTAAGAATTGGTTGATTTTTGTGGTTTTGGTTTGTTTTTAATGGAGATGAGTTATTGTTTTGATGAGGTGGTTGTAATGGTTATGAAAGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth17_R1_001_val_1.fq.gz_G_to_A.fastq and Meth17_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21323:1000_1:N:0:TAATACAG+NTATTCAC/1 77 * 0 0 * * 0 0 ACCTAACCATAAATAAAAACCAAATTAAACAACACCATAACAAACTAAATACTTACTCCCCCTTACAAAAACAATACCTTATAATTATCCAAAACAAACATCAAATCACACAAATCCCACTCCACTTTCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21323:1000_2:N:0:TAATACAG+NTATTCAC/2 141 * 0 0 * * 0 0 TTGATTTTTTTTTGTTGTAAGTGGTGTTTGAAAGAGTTTAGTAAGAATTGGTTGATTTTTGTGGTTTTGGTTTGTTTTTAATGGAGATGAGTTATTGTTTTGATGAGGTGGTTGTAATGGTTATGAAAGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth17_R1_001_val_1.fq.gz_C_to_T.fastq and Meth17_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21323:1000_1:N:0:TAATACAG+NTATTCAC/1 77 * 0 0 * * 0 0 GTTTGGTTATGAATAGAGGTTAGATTAAGTGGTATTATAGTAAATTGGGTGTTTGTTTTTTTTTGTAGAAATAGTATTTTGTAGTTGTTTGGAATGGATATTAGGTTATGTAGGTTTTGTTTTGTTTTTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21323:1000_2:N:0:TAATACAG+NTATTCAC/2 141 * 0 0 * * 0 0 CCAATCTCTTTTTACCACAAACAATACTTAAAAAAACCCAACAAAAACTAATTAATTTTCATAACTCCAATTTATCCTTAATAAAAATAAACCATCACTCCAACAAAATAATCACAATAACCACAAAAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP >>> Writing bisulfite mapping results to Meth17_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth17_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth17_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1212:9679:6230_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641525 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1212:9516:6417_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641525 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1212:12518:8015_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641525 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1225:6307:31986_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1318:21703:35884_1:N:0:TAATACAG+ATATTAAC NC_000913.3 4641525 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1347:32913:21981_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1366:2600:2049_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1367:25247:35665_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1367:25238:35837_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1367:24975:36072_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1414:5791:4946_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1415:4725:10614_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1423:23674:10645_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1471:14642:33082_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1625:7997:14278_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1632:27453:5822_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1632:27606:5963_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1663:28438:19304_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1663:26820:19476_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1663:26711:20478_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1677:3812:8093_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1677:5032:8609_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2211:3694:20353_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2211:3712:33379_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2226:10628:36902_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2226:10592:36965_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2305:23836:31219_1:N:0:TAATACAG+ATATTTAC NC_000913.3 4641533 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2312:24912:19429_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2320:22064:4820_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641525 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2320:20437:6605_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641525 Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2423:8214:29528_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2423:9661:29528_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2438:32633:22905_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2460:27371:21559_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2460:26621:21762_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2554:18096:15452_1:N:0:TAATACAG+ATATTCAC NC_000913.3 4641533 Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2650:4707:4726_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2650:4408:30358_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2650:3920:32174_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2652:5231:5228_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2663:25708:25128_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2666:20952:3709_1:N:0:TAATACAG+ATATTCAC NC_000913.3 1 Processed 81000000 sequence pairs so far 81609496 reads; of these: 81609496 (100.00%) were paired; of these: 78599374 (8160949696.31 reads; of these:%) aligned concordantly 0 times 816094962863001 ( (3.51%) aligned concordantly exactly 1 time 147121100.00 (%0.18) were paired; of these:% ) aligned concordantly >1 times 785823893.69 (%96.29 overall alignment rate% ) aligned concordantly 0 times 2878736 (3.53%) aligned concordantly exactly 1 time 148371 (0.18%) aligned concordantly >1 times 3.71% overall alignment rate 81609496 reads; of these: 81609496 (100.00%) were paired; of these: 77832732 (95.37%) aligned concordantly 0 times 3589488 (4.40%) aligned concordantly exactly 1 time 187276 (0.23%) aligned concordantly >1 times 4.63% overall alignment rate 81609496 reads; of these: 81609496 (100.00%) were paired; of these: 77818025 (95.35%) aligned concordantly 0 times 3605254 (4.42%) aligned concordantly exactly 1 time 186217 (0.23%) aligned concordantly >1 times 4.65% overall alignment rate Processed 81609496 sequences in total Successfully deleted the temporary files Meth17_R1_001_val_1.fq.gz_C_to_T.fastq, Meth17_R1_001_val_1.fq.gz_G_to_A.fastq, Meth17_R2_001_val_2.fq.gz_C_to_T.fastq and Meth17_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 81609496 Number of paired-end alignments with a unique best hit: 12928099 Mapping efficiency: 15.8% Sequence pairs with no alignments under any condition: 68349409 Sequence pairs did not map uniquely: 331988 Sequence pairs which were discarded because genomic sequence could not be extracted: 42 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2875566 ((converted) top strand) GA/CT/CT: 3602713 (complementary to (converted) top strand) GA/CT/GA: 3589290 (complementary to (converted) bottom strand) CT/GA/GA: 2860488 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 742657378 Total methylated C's in CpG context: 2672963 Total methylated C's in CHG context: 2279554 Total methylated C's in CHH context: 3606823 Total methylated C's in Unknown context: 393995 Total unmethylated C's in CpG context: 219441981 Total unmethylated C's in CHG context: 184177164 Total unmethylated C's in CHH context: 330478893 Total unmethylated C's in Unknown context: 1978042 C methylated in CpG context: 1.2% C methylated in CHG context: 1.2% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 16.6% Bismark completed in 0d 3h 1m 53s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth18_R1_001_val_1.fq.gz to Meth18_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth18_R1_001_val_1.fq.gz to Meth18_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth18_R1_001_val_1.fq.gz (61585400 sequences in total) Writing a C -> T converted version of the input file Meth18_R2_001_val_2.fq.gz to Meth18_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth18_R2_001_val_2.fq.gz to Meth18_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth18_R2_001_val_2.fq.gz (61585400 sequences in total) Input files are Meth18_R1_001_val_1.fq.gz_C_to_T.fastq and Meth18_R1_001_val_1.fq.gz_G_to_A.fastq and Meth18_R2_001_val_2.fq.gz_C_to_T.fastq and Meth18_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth18_R1_001_val_1.fq.gz_C_to_T.fastq and Meth18_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21395:1000_1:N:0:CGGCGTGA+NCGCCTGT/1 77 * 0 0 * * 0 0 TTTATAATAATATTTTTTTTTAATTAAATATATTAAATAATTAATAAATTTAATATATTATTTATATATATATAATAATTATTTTTTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21395:1000_2:N:0:CGGCGTGA+NCGCCTGT/2 141 * 0 0 * * 0 0 TATTAAAAAATAATTATTATATATATATAAATAATATATTAAATTTATTAATTATTTAATATATTTAATTAAAAAAAAATATTATTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth18_R1_001_val_1.fq.gz_G_to_A.fastq and Meth18_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21395:1000_1:N:0:CGGCGTGA+NCGCCTGT/1 77 * 0 0 * * 0 0 TTTACAACAACACCTCTTCCCAACCAAACACACCAAATAATTAATAAACTTAACATATCATTTACACATACATAATAATTACTTTTCAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21395:1000_2:N:0:CGGCGTGA+NCGCCTGT/2 141 * 0 0 * * 0 0 TGTTGAAAAGTAATTATTATGTATGTGTAAATGATATGTTAAGTTTATTAATTATTTGGTGTGTTTGGTTGGGAAGAGGTGTTGTTGTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth18_R1_001_val_1.fq.gz_G_to_A.fastq and Meth18_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21395:1000_1:N:0:CGGCGTGA+NCGCCTGT/1 77 * 0 0 * * 0 0 TTTACAACAACACCTCTTCCCAACCAAACACACCAAATAATTAATAAACTTAACATATCATTTACACATACATAATAATTACTTTTCAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21395:1000_2:N:0:CGGCGTGA+NCGCCTGT/2 141 * 0 0 * * 0 0 TGTTGAAAAGTAATTATTATGTATGTGTAAATGATATGTTAAGTTTATTAATTATTTGGTGTGTTTGGTTGGGAAGAGGTGTTGTTGTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth18_R1_001_val_1.fq.gz_C_to_T.fastq and Meth18_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21395:1000_1:N:0:CGGCGTGA+NCGCCTGT/1 77 * 0 0 * * 0 0 TTTATAATAATATTTTTTTTTAATTAAATATATTAAATAATTAATAAATTTAATATATTATTTATATATATATAATAATTATTTTTTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21395:1000_2:N:0:CGGCGTGA+NCGCCTGT/2 141 * 0 0 * * 0 0 TATTAAAAAATAATTATTATATATATATAAATAATATATTAAATTTATTAATTATTTAATATATTTAATTAAAAAAAAATATTATTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth18_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1213:10212:17362_1:N:0:CGGCGTGA+GCGCCTGT NC_000913.3 4641524 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2174:16568:16814_1:N:0:CGGCGTGA+GCGCCTGT NC_000913.3 4641524 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2606:8205:11694_1:N:0:CGGCGTGA+GCGCCTGT NC_000913.3 4641524 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far 61585400 reads; of these: 61585400 (100.00%) were paired; of these: 58248182 (94.58%) aligned concordantly 0 times 3181060 (5.17%) aligned concordantly exactly 1 time 156158 (0.25%) aligned concordantly >1 times 5.42% overall alignment rate 61585400 reads; of these: 61585400 (100.00%) were paired; of these: 58235812 (94.56%) aligned concordantly 0 times 3193064 (5.18%) aligned concordantly exactly 1 time 156524 (0.25%) aligned concordantly >1 times 5.44% overall alignment rate 61585400 reads; of these: 61585400 (100.00%) were paired; of these: 57317916 (93.07%) aligned concordantly 0 times 4071526 (6.61%) aligned concordantly exactly 1 time 195958 (0.32%) aligned concordantly >1 times 6.93% overall alignment rate 61585400 reads; of these: 61585400 (100.00%) were paired; of these: 57356148 (93.13%) aligned concordantly 0 times 4028718 (6.54%) aligned concordantly exactly 1 time 200534 (0.33%) aligned concordantly >1 times 6.87% overall alignment rate Processed 61585400 sequences in total Successfully deleted the temporary files Meth18_R1_001_val_1.fq.gz_C_to_T.fastq, Meth18_R1_001_val_1.fq.gz_G_to_A.fastq, Meth18_R2_001_val_2.fq.gz_C_to_T.fastq and Meth18_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 61585400 Number of paired-end alignments with a unique best hit: 14475532 Mapping efficiency: 23.5% Sequence pairs with no alignments under any condition: 46762677 Sequence pairs did not map uniquely: 347191 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3190745 ((converted) top strand) GA/CT/CT: 4071292 (complementary to (converted) top strand) GA/CT/GA: 4033406 (complementary to (converted) bottom strand) CT/GA/GA: 3180086 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 843168405 Total methylated C's in CpG context: 3139919 Total methylated C's in CHG context: 2705359 Total methylated C's in CHH context: 4288243 Total methylated C's in Unknown context: 452743 Total unmethylated C's in CpG context: 247647481 Total unmethylated C's in CHG context: 208262441 Total unmethylated C's in CHH context: 377124962 Total unmethylated C's in Unknown context: 2235542 C methylated in CpG context: 1.3% C methylated in CHG context: 1.3% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 16.8% Bismark completed in 0d 2h 56m 51s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth1_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth1_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth1_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth1_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth1_R1_001_val_1.fq.gz to Meth1_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth1_R1_001_val_1.fq.gz to Meth1_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth1_R1_001_val_1.fq.gz (74424695 sequences in total) Writing a C -> T converted version of the input file Meth1_R2_001_val_2.fq.gz to Meth1_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth1_R2_001_val_2.fq.gz to Meth1_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth1_R2_001_val_2.fq.gz (74424695 sequences in total) Input files are Meth1_R1_001_val_1.fq.gz_C_to_T.fastq and Meth1_R1_001_val_1.fq.gz_G_to_A.fastq and Meth1_R2_001_val_2.fq.gz_C_to_T.fastq and Meth1_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth1_R1_001_val_1.fq.gz_C_to_T.fastq and Meth1_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:22444:1000_1:N:0:CCGCGGTT+NGCGCTAG/1 77 * 0 0 * * 0 0 TTAATTTGTTTTGATATATTTTTTTATAAGTTGTTATAAAAGTTTGGTGATGGAATTTGTAAGAAGTAATTATTGAAA FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP A00387:192:GW191111360th:4:1101:22444:1000_2:N:0:CCGCGGTT+NGCGCTAG/2 141 * 0 0 * * 0 0 TTTCAATAATTACTTCTTACAAATTCCATCACCAAACTTTTATAACAACTTATAAAAAAATATATCAAAACAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth1_R1_001_val_1.fq.gz_G_to_A.fastq and Meth1_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:22444:1000_1:N:0:CCGCGGTT+NGCGCTAG/1 77 * 0 0 * * 0 0 TTAATTTATTTTAATATATTTTTTTATAAATTATTATAAAAATTTAATAATAAAATTTATAAAAAATAATTATTAAAA FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP A00387:192:GW191111360th:4:1101:22444:1000_2:N:0:CCGCGGTT+NGCGCTAG/2 141 * 0 0 * * 0 0 TTTTAATAATTATTTTTTATAAATTTTATTATTAAATTTTTATAATAATTTATAAAAAAATATATTAAAATAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth1_R1_001_val_1.fq.gz_G_to_A.fastq and Meth1_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:22444:1000_1:N:0:CCGCGGTT+NGCGCTAG/1 77 * 0 0 * * 0 0 TTAATTTATTTTAATATATTTTTTTATAAATTATTATAAAAATTTAATAATAAAATTTATAAAAAATAATTATTAAAA FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP A00387:192:GW191111360th:4:1101:22444:1000_2:N:0:CCGCGGTT+NGCGCTAG/2 141 * 0 0 * * 0 0 TTTTAATAATTATTTTTTATAAATTTTATTATTAAATTTTTATAATAATTTATAAAAAAATATATTAAAATAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth1_R1_001_val_1.fq.gz_C_to_T.fastq and Meth1_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:22444:1000_1:N:0:CCGCGGTT+NGCGCTAG/1 77 * 0 0 * * 0 0 TTAATTTGTTTTGATATATTTTTTTATAAGTTGTTATAAAAGTTTGGTGATGGAATTTGTAAGAAGTAATTATTGAAA FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP A00387:192:GW191111360th:4:1101:22444:1000_2:N:0:CCGCGGTT+NGCGCTAG/2 141 * 0 0 * * 0 0 TTTCAATAATTACTTCTTACAAATTCCATCACCAAACTTTTATAACAACTTATAAAAAAATATATCAAAACAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth1_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth1_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth1_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far 74424695 reads; of these: 74424695 (100.00%) were paired; of these: 73811788 (99.18%) aligned concordantly 0 times 580347 (0.78%) aligned concordantly exactly 1 time 32560 (0.04%) aligned concordantly >1 times 0.82% overall alignment rate 74424695 reads; of these: 74424695 (100.00%) were paired; of these: 73810526 (99.17%) aligned concordantly 0 times 581246 (0.78%) aligned concordantly exactly 1 time 32923 (0.04%) aligned concordantly >1 times 0.83% overall alignment rate 74424695 reads; of these: 74424695 (100.00%) were paired; of these: 73943267 (99.35%) aligned concordantly 0 times 455420 (0.61%) aligned concordantly exactly 1 time 26008 (0.03%) aligned concordantly >1 times 0.65% overall alignment rate 74424695 reads; of these: 74424695 (100.00%) were paired; of these: 73939888 (99.35%) aligned concordantly 0 times 458751 (0.62%) aligned concordantly exactly 1 time 26056 (0.04%) aligned concordantly >1 times 0.65% overall alignment rate Processed 74424695 sequences in total Successfully deleted the temporary files Meth1_R1_001_val_1.fq.gz_C_to_T.fastq, Meth1_R1_001_val_1.fq.gz_G_to_A.fastq, Meth1_R2_001_val_2.fq.gz_C_to_T.fastq and Meth1_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 74424695 Number of paired-end alignments with a unique best hit: 2067232 Mapping efficiency: 2.8% Sequence pairs with no alignments under any condition: 72294019 Sequence pairs did not map uniquely: 63444 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 456442 ((converted) top strand) GA/CT/CT: 579301 (complementary to (converted) top strand) GA/CT/GA: 578151 (complementary to (converted) bottom strand) CT/GA/GA: 453338 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 113082930 Total methylated C's in CpG context: 384537 Total methylated C's in CHG context: 331054 Total methylated C's in CHH context: 587823 Total methylated C's in Unknown context: 49069 Total unmethylated C's in CpG context: 33674518 Total unmethylated C's in CHG context: 28140062 Total unmethylated C's in CHH context: 49964936 Total unmethylated C's in Unknown context: 273288 C methylated in CpG context: 1.1% C methylated in CHG context: 1.2% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 15.2% Bismark completed in 0d 1h 23m 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/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth2_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth2_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth2_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth2_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth2_R1_001_val_1.fq.gz to Meth2_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth2_R1_001_val_1.fq.gz to Meth2_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth2_R1_001_val_1.fq.gz (84959218 sequences in total) Writing a C -> T converted version of the input file Meth2_R2_001_val_2.fq.gz to Meth2_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth2_R2_001_val_2.fq.gz to Meth2_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth2_R2_001_val_2.fq.gz (84959218 sequences in total) Input files are Meth2_R1_001_val_1.fq.gz_C_to_T.fastq and Meth2_R1_001_val_1.fq.gz_G_to_A.fastq and Meth2_R2_001_val_2.fq.gz_C_to_T.fastq and Meth2_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth2_R1_001_val_1.fq.gz_C_to_T.fastq and Meth2_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21540:1000_1:N:0:TTATAACC+NATATCGA/1 77 * 0 0 * * 0 0 TTTTGTTTTAGTAAAGTAATTGGTTAGATAATAAGTAGTGTATTGTGGAAGTAAGGTGAAGTATTTTTATTGAGAATTTGATTGTATTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21540:1000_2:N:0:TTATAACC+NATATCGA/2 141 * 0 0 * * 0 0 AAAAAATACAATCAAATTCTCAATAAAAATACTTCACCTTACTTCCACAATACACTACTTATTATCTAACCAATTACTTTACTAAAACAAAA FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth2_R1_001_val_1.fq.gz_G_to_A.fastq and Meth2_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21540:1000_1:N:0:TTATAACC+NATATCGA/1 77 * 0 0 * * 0 0 TTTTATTTTAATAAAATAATTAATTAAATAATAAATAATATATTATAAAAATAAAATAAAATATTTTTATTAAAAATTTAATTATATTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21540:1000_2:N:0:TTATAACC+NATATCGA/2 141 * 0 0 * * 0 0 AAAAAATATAATTAAATTTTTAATAAAAATATTTTATTTTATTTTTATAATATATTATTTATTATTTAATTAATTATTTTATTAAAATAAAA FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth2_R1_001_val_1.fq.gz_G_to_A.fastq and Meth2_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21540:1000_1:N:0:TTATAACC+NATATCGA/1 77 * 0 0 * * 0 0 TTTTATTTTAATAAAATAATTAATTAAATAATAAATAATATATTATAAAAATAAAATAAAATATTTTTATTAAAAATTTAATTATATTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21540:1000_2:N:0:TTATAACC+NATATCGA/2 141 * 0 0 * * 0 0 AAAAAATATAATTAAATTTTTAATAAAAATATTTTATTTTATTTTTATAATATATTATTTATTATTTAATTAATTATTTTATTAAAATAAAA FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth2_R1_001_val_1.fq.gz_C_to_T.fastq and Meth2_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21540:1000_1:N:0:TTATAACC+NATATCGA/1 77 * 0 0 * * 0 0 TTTTGTTTTAGTAAAGTAATTGGTTAGATAATAAGTAGTGTATTGTGGAAGTAAGGTGAAGTATTTTTATTGAGAATTTGATTGTATTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21540:1000_2:N:0:TTATAACC+NATATCGA/2 141 * 0 0 * * 0 0 AAAAAATACAATCAAATTCTCAATAAAAATACTTCACCTTACTTCCACAATACACTACTTATTATCTAACCAATTACTTTACTAAAACAAAA FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth2_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth2_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth2_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far 84959218 reads; of these: 84959218 (100.00%) were paired; of these: 84727143 (99.73%) aligned concordantly 0 times 212616 (0.25%) aligned concordantly exactly 1 time 19459 (0.02%) aligned concordantly >1 times 0.27% overall alignment rate 84959218 reads; of these: 84959218 (100.00%) were paired; of these: 84726125 (99.73%) aligned concordantly 0 times 213206 (0.25%) aligned concordantly exactly 1 time 19887 (0.02%) aligned concordantly >1 times 0.27% overall alignment rate 84959218 reads; of these: 84959218 (100.00%) were paired; of these: 84775420 (99.78%) aligned concordantly 0 times 167733 (0.20%) aligned concordantly exactly 1 time 16065 (0.02%) aligned concordantly >1 times 0.22% overall alignment rate 84959218 reads; of these: 84959218 (100.00%) were paired; of these: 84773716 (99.78%) aligned concordantly 0 times 169298 (0.20%) aligned concordantly exactly 1 time 16204 (0.02%) aligned concordantly >1 times 0.22% overall alignment rate Processed 84959218 sequences in total Successfully deleted the temporary files Meth2_R1_001_val_1.fq.gz_C_to_T.fastq, Meth2_R1_001_val_1.fq.gz_G_to_A.fastq, Meth2_R2_001_val_2.fq.gz_C_to_T.fastq and Meth2_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 84959218 Number of paired-end alignments with a unique best hit: 743448 Mapping efficiency: 0.9% Sequence pairs with no alignments under any condition: 84169773 Sequence pairs did not map uniquely: 45997 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 164405 ((converted) top strand) GA/CT/CT: 208669 (complementary to (converted) top strand) GA/CT/GA: 207583 (complementary to (converted) bottom strand) CT/GA/GA: 162791 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 37683048 Total methylated C's in CpG context: 134444 Total methylated C's in CHG context: 117238 Total methylated C's in CHH context: 330378 Total methylated C's in Unknown context: 15261 Total unmethylated C's in CpG context: 11164684 Total unmethylated C's in CHG context: 9325315 Total unmethylated C's in CHH context: 16610989 Total unmethylated C's in Unknown context: 90565 C methylated in CpG context: 1.2% C methylated in CHG context: 1.2% C methylated in CHH context: 2.0% C methylated in unknown context (CN or CHN): 14.4% Bismark completed in 0d 1h 22m 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/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth3_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth3_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth3_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth3_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth3_R1_001_val_1.fq.gz to Meth3_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth3_R1_001_val_1.fq.gz to Meth3_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth3_R1_001_val_1.fq.gz (77672273 sequences in total) Writing a C -> T converted version of the input file Meth3_R2_001_val_2.fq.gz to Meth3_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth3_R2_001_val_2.fq.gz to Meth3_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth3_R2_001_val_2.fq.gz (77672273 sequences in total) Input files are Meth3_R1_001_val_1.fq.gz_C_to_T.fastq and Meth3_R1_001_val_1.fq.gz_G_to_A.fastq and Meth3_R2_001_val_2.fq.gz_C_to_T.fastq and Meth3_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth3_R1_001_val_1.fq.gz_C_to_T.fastq and Meth3_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21377:1000_1:N:0:GGACTTGG+NGCAGACG/1 77 * 0 0 * * 0 0 TTTAAAATAAATAAATTAAAAATTATTAAATAAAAATTTATAAATTTAATAAATTAAATTTTTTTATTAATAAAATTAATTTAAATAATTATTATTATTATTAAATTATATATATAAAATTAATAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F,FFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21377:1000_2:N:0:GGACTTGG+NGCAGACG/2 141 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth3_R1_001_val_1.fq.gz_G_to_A.fastq and Meth3_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21377:1000_1:N:0:GGACTTGG+NGCAGACG/1 77 * 0 0 * * 0 0 TCTAAAACAAACAAATTAAAAACCATTAAATAAAAACTTACAAACCCAATAAACTAAATTTTCTCATCAATAAAACTAACTTAAACAACTACTACTATTACCAAATCACATACACAAAATCAACAAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F,FFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21377:1000_2:N:0:GGACTTGG+NGCAGACG/2 141 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth3_R1_001_val_1.fq.gz_G_to_A.fastq and Meth3_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21377:1000_1:N:0:GGACTTGG+NGCAGACG/1 77 * 0 0 * * 0 0 TCTAAAACAAACAAATTAAAAACCATTAAATAAAAACTTACAAACCCAATAAACTAAATTTTCTCATCAATAAAACTAACTTAAACAACTACTACTATTACCAAATCACATACACAAAATCAACAAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F,FFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21377:1000_2:N:0:GGACTTGG+NGCAGACG/2 141 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth3_R1_001_val_1.fq.gz_C_to_T.fastq and Meth3_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21377:1000_1:N:0:GGACTTGG+NGCAGACG/1 77 * 0 0 * * 0 0 TTTAAAATAAATAAATTAAAAATTATTAAATAAAAATTTATAAATTTAATAAATTAAATTTTTTTATTAATAAAATTAATTTAAATAATTATTATTATTATTAAATTATATATATAAAATTAATAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F,FFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21377:1000_2:N:0:GGACTTGG+NGCAGACG/2 141 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth3_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth3_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth3_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far 77672273 reads; of these: 77672273 (100.00%) were paired; of these: 77144698 (99.32%) aligned concordantly 0 times 498230 (0.64%) aligned concordantly exactly 1 time 29345 (0.04%) aligned concordantly >1 times 0.68% overall alignment rate 77672273 reads; of these: 77672273 (100.00%) were paired; of these: 77145238 (99.32%) aligned concordantly 0 times 497127 (0.64%) aligned concordantly exactly 1 time 29908 (0.04%) aligned concordantly >1 times 0.68% overall alignment rate 77672273 reads; of these: 77672273 (100.00%) were paired; of these: 77249742 (99.46%) aligned concordantly 0 times 398985 (0.51%) aligned concordantly exactly 1 time 23546 (0.03%) aligned concordantly >1 times 0.54% overall alignment rate 77672273 reads; of these: 77672273 (100.00%) were paired; of these: 77252018 (99.46%) aligned concordantly 0 times 397514 (0.51%) aligned concordantly exactly 1 time 22741 (0.03%) aligned concordantly >1 times 0.54% overall alignment rate Processed 77672273 sequences in total Successfully deleted the temporary files Meth3_R1_001_val_1.fq.gz_C_to_T.fastq, Meth3_R1_001_val_1.fq.gz_G_to_A.fastq, Meth3_R2_001_val_2.fq.gz_C_to_T.fastq and Meth3_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 77672273 Number of paired-end alignments with a unique best hit: 1783822 Mapping efficiency: 2.3% Sequence pairs with no alignments under any condition: 75831912 Sequence pairs did not map uniquely: 56539 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 397064 ((converted) top strand) GA/CT/CT: 495438 (complementary to (converted) top strand) GA/CT/GA: 496118 (complementary to (converted) bottom strand) CT/GA/GA: 395202 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 98521353 Total methylated C's in CpG context: 334021 Total methylated C's in CHG context: 287617 Total methylated C's in CHH context: 514004 Total methylated C's in Unknown context: 44912 Total unmethylated C's in CpG context: 29379291 Total unmethylated C's in CHG context: 24594546 Total unmethylated C's in CHH context: 43411874 Total unmethylated C's in Unknown context: 246301 C methylated in CpG context: 1.1% C methylated in CHG context: 1.2% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 15.4% Bismark completed in 0d 1h 24m 20s ==================== 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/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth4_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth4_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth4_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth4_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth4_R1_001_val_1.fq.gz to Meth4_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth4_R1_001_val_1.fq.gz to Meth4_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth4_R1_001_val_1.fq.gz (149828789 sequences in total) Writing a C -> T converted version of the input file Meth4_R2_001_val_2.fq.gz to Meth4_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth4_R2_001_val_2.fq.gz to Meth4_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth4_R2_001_val_2.fq.gz (149828789 sequences in total) Input files are Meth4_R1_001_val_1.fq.gz_C_to_T.fastq and Meth4_R1_001_val_1.fq.gz_G_to_A.fastq and Meth4_R2_001_val_2.fq.gz_C_to_T.fastq and Meth4_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth4_R1_001_val_1.fq.gz_C_to_T.fastq and Meth4_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21522:1000_1:N:0:AAGTCCAA+NATGAGTA/1 99 NC_000913.3_CT_converted 422181 42 72M = 422181 -72 TNGGTGGGGTAGTAATGATTATTGGTGGGTTGATTTTTTTGTTTTTTATTATTGGGTTGATTGGTTATTATT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-1 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:1G70 YS:i:0 YT:Z:CP A00387:192:GW191111360th:4:1101:21522:1000_2:N:0:AAGTCCAA+NATGAGTA/2 147 NC_000913.3_CT_converted 422181 42 72M = 422181 -72 TGGGTGGGGTAGTAATGATTATTGGTGGGTTGATTTTTTTGTTTTTTATTATTGGGTTGATTGGTTATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:72 YS:i:-1 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth4_R1_001_val_1.fq.gz_G_to_A.fastq and Meth4_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21522:1000_1:N:0:AAGTCCAA+NATGAGTA/1 77 * 0 0 * * 0 0 TNAATAAAATAATAATAATTATTAATAAATTAATTTTTTTATTTTTTATTATTAAATTAATTAATTATTATT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21522:1000_2:N:0:AAGTCCAA+NATGAGTA/2 141 * 0 0 * * 0 0 AATAATAATTAATTAATTTAATAATAAAAAATAAAAAAATTAATTTATTAATAATTATTATTATTTTATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth4_R1_001_val_1.fq.gz_G_to_A.fastq and Meth4_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21522:1000_1:N:0:AAGTCCAA+NATGAGTA/1 77 * 0 0 * * 0 0 TNAATAAAATAATAATAATTATTAATAAATTAATTTTTTTATTTTTTATTATTAAATTAATTAATTATTATT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21522:1000_2:N:0:AAGTCCAA+NATGAGTA/2 141 * 0 0 * * 0 0 AATAATAATTAATTAATTTAATAATAAAAAATAAAAAAATTAATTTATTAATAATTATTATTATTTTATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth4_R1_001_val_1.fq.gz_C_to_T.fastq and Meth4_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21522:1000_1:N:0:AAGTCCAA+NATGAGTA/1 77 * 0 0 * * 0 0 TNGGTGGGGTAGTAATGATTATTGGTGGGTTGATTTTTTTGTTTTTTATTATTGGGTTGATTGGTTATTATT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21522:1000_2:N:0:AAGTCCAA+NATGAGTA/2 141 * 0 0 * * 0 0 AATAATAACCAATCAACCCAATAATAAAAAACAAAAAAATCAACCCACCAATAATCATTACTACCCCACCCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth4_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth4_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth4_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Processed 107000000 sequence pairs so far Processed 108000000 sequence pairs so far Processed 109000000 sequence pairs so far Processed 110000000 sequence pairs so far Processed 111000000 sequence pairs so far Processed 112000000 sequence pairs so far Processed 113000000 sequence pairs so far Processed 114000000 sequence pairs so far Processed 115000000 sequence pairs so far Processed 116000000 sequence pairs so far Processed 117000000 sequence pairs so far Processed 118000000 sequence pairs so far Processed 119000000 sequence pairs so far Processed 120000000 sequence pairs so far Processed 121000000 sequence pairs so far Processed 122000000 sequence pairs so far Processed 123000000 sequence pairs so far Processed 124000000 sequence pairs so far Processed 125000000 sequence pairs so far Processed 126000000 sequence pairs so far Processed 127000000 sequence pairs so far Processed 128000000 sequence pairs so far Processed 129000000 sequence pairs so far Processed 130000000 sequence pairs so far Processed 131000000 sequence pairs so far Processed 132000000 sequence pairs so far Processed 133000000 sequence pairs so far Processed 134000000 sequence pairs so far Processed 135000000 sequence pairs so far Processed 136000000 sequence pairs so far Processed 137000000 sequence pairs so far Processed 138000000 sequence pairs so far Processed 139000000 sequence pairs so far Processed 140000000 sequence pairs so far Processed 141000000 sequence pairs so far Processed 142000000 sequence pairs so far Processed 143000000 sequence pairs so far Processed 144000000 sequence pairs so far Processed 145000000 sequence pairs so far Processed 146000000 sequence pairs so far Processed 147000000 sequence pairs so far Processed 148000000 sequence pairs so far Processed 149000000 sequence pairs so far 149828789 reads; of these: 149828789 (100.00%) were paired; of these: 144002552 (96.11%) aligned concordantly 0 times 5307960 (3.54%) aligned concordantly exactly 1 time 518277 (0.35%) aligned concordantly >1 times 3.89% overall alignment rate 149828789 reads; of these: 149828789 (100.00%) were paired; of these: 143960029 (96.08%) aligned concordantly 0 times 5346450 (3.57%) aligned concordantly exactly 1 time 522310 (0.35%) aligned concordantly >1 times 3.92% overall alignment rate 149828789 reads; of these: 149828789 (100.00%) were paired; of these: 144212487 (96.25%) aligned concordantly 0 times 5109925 (3.41%) aligned concordantly exactly 1 time 506377 (0.34%) aligned concordantly >1 times 3.75% overall alignment rate 149828789 reads; of these: 149828789 (100.00%) were paired; of these: 144190509 (96.24%) aligned concordantly 0 times 5126475 (3.42%) aligned concordantly exactly 1 time 511805 (0.34%) aligned concordantly >1 times 3.76% overall alignment rate Processed 149828789 sequences in total Successfully deleted the temporary files Meth4_R1_001_val_1.fq.gz_C_to_T.fastq, Meth4_R1_001_val_1.fq.gz_G_to_A.fastq, Meth4_R2_001_val_2.fq.gz_C_to_T.fastq and Meth4_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 149828789 Number of paired-end alignments with a unique best hit: 20858855 Mapping efficiency: 13.9% Sequence pairs with no alignments under any condition: 127883369 Sequence pairs did not map uniquely: 1086565 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5100860 ((converted) top strand) GA/CT/CT: 5294939 (complementary to (converted) top strand) GA/CT/GA: 5337577 (complementary to (converted) bottom strand) CT/GA/GA: 5125479 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1037373553 Total methylated C's in CpG context: 10755342 Total methylated C's in CHG context: 1572545 Total methylated C's in CHH context: 3716965 Total methylated C's in Unknown context: 48018 Total unmethylated C's in CpG context: 325751508 Total unmethylated C's in CHG context: 269623303 Total unmethylated C's in CHH context: 425953890 Total unmethylated C's in Unknown context: 137875 C methylated in CpG context: 3.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 25.8% Bismark completed in 0d 4h 41m 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/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth5_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth5_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth5_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth5_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth5_R1_001_val_1.fq.gz to Meth5_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth5_R1_001_val_1.fq.gz to Meth5_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth5_R1_001_val_1.fq.gz (284116370 sequences in total) Writing a C -> T converted version of the input file Meth5_R2_001_val_2.fq.gz to Meth5_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth5_R2_001_val_2.fq.gz to Meth5_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth5_R2_001_val_2.fq.gz (284116370 sequences in total) Input files are Meth5_R1_001_val_1.fq.gz_C_to_T.fastq and Meth5_R1_001_val_1.fq.gz_G_to_A.fastq and Meth5_R2_001_val_2.fq.gz_C_to_T.fastq and Meth5_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth5_R1_001_val_1.fq.gz_C_to_T.fastq and Meth5_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21829:1000_1:N:0:ATCCACTG+NGGTGCGT/1 77 * 0 0 * * 0 0 TNATAAAAATTATTTATATATATTTATAATTAATTTATAATAAAAATTATATTATATATTATAATATAAATAAATTATTAAAAATTATATTATATTATT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21829:1000_2:N:0:ATCCACTG+NGGTGCGT/2 141 * 0 0 * * 0 0 TAAATAATATAATATAATTTTTAATAATTTATTTATATTATAATATATAATATAATTTTTATTATAAATTAATTATAAATATATATAAATAATTTTTCTCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF,FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth5_R1_001_val_1.fq.gz_G_to_A.fastq and Meth5_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21829:1000_1:N:0:ATCCACTG+NGGTGCGT/1 77 * 0 0 * * 0 0 CNATAAAAATCACCCACATACATCTACAACTAACCCATAATAAAAACCATACTACACACCACAACATAAATAAACTACTAAAAATTACACCACACCATC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21829:1000_2:N:0:ATCCACTG+NGGTGCGT/2 141 * 0 0 * * 0 0 TGGATGGTGTGGTGTAATTTTTAGTAGTTTATTTATGTTGTGGTGTGTAGTATGGTTTTTATTATGGGTTAGTTGTAGATGTATGTGGGTGATTTTTTTTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF,FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth5_R1_001_val_1.fq.gz_G_to_A.fastq and Meth5_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21829:1000_1:N:0:ATCCACTG+NGGTGCGT/1 83 NC_000913.3_CT_converted 3987324 42 99M = 3987322 -101 GATGGTGTGGTGTAATTTTTAGTAGTTTATTTATGTTGTGGTGTGTAGTATGGTTTTTATTATGGGTTAGTTGTAGATGTATGTGGGTGATTTTTATNG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-1 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:97T1 YS:i:-6 YT:Z:CP A00387:192:GW191111360th:4:1101:21829:1000_2:N:0:ATCCACTG+NGGTGCGT/2 163 NC_000913.3_CT_converted 3987322 42 101M = 3987324 101 TGGATGGTGTGGTGTAATTTTTAGTAGTTTATTTATGTTGTGGTGTGTAGTATGGTTTTTATTATGGGTTAGTTGTAGATGTATGTGGGTGATTTTTTTTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF,FFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:97A3 YS:i:-1 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth5_R1_001_val_1.fq.gz_C_to_T.fastq and Meth5_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21829:1000_1:N:0:ATCCACTG+NGGTGCGT/1 77 * 0 0 * * 0 0 TNATAAAAATTATTTATATATATTTATAATTAATTTATAATAAAAATTATATTATATATTATAATATAAATAAATTATTAAAAATTATATTATATTATT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21829:1000_2:N:0:ATCCACTG+NGGTGCGT/2 141 * 0 0 * * 0 0 TAAATAATATAATATAATTTTTAATAATTTATTTATATTATAATATATAATATAATTTTTATTATAAATTAATTATAAATATATATAAATAATTTTTCTCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF,FFF YT:Z:UP >>> Writing bisulfite mapping results to Meth5_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth5_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth5_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Processed 107000000 sequence pairs so far Processed 108000000 sequence pairs so far Processed 109000000 sequence pairs so far Processed 110000000 sequence pairs so far Processed 111000000 sequence pairs so far Processed 112000000 sequence pairs so far Processed 113000000 sequence pairs so far Processed 114000000 sequence pairs so far Processed 115000000 sequence pairs so far Processed 116000000 sequence pairs so far Processed 117000000 sequence pairs so far Processed 118000000 sequence pairs so far Processed 119000000 sequence pairs so far Processed 120000000 sequence pairs so far Processed 121000000 sequence pairs so far Processed 122000000 sequence pairs so far Processed 123000000 sequence pairs so far Processed 124000000 sequence pairs so far Processed 125000000 sequence pairs so far Processed 126000000 sequence pairs so far Processed 127000000 sequence pairs so far Processed 128000000 sequence pairs so far Processed 129000000 sequence pairs so far Processed 130000000 sequence pairs so far Processed 131000000 sequence pairs so far Processed 132000000 sequence pairs so far Processed 133000000 sequence pairs so far Processed 134000000 sequence pairs so far Processed 135000000 sequence pairs so far Processed 136000000 sequence pairs so far Processed 137000000 sequence pairs so far Processed 138000000 sequence pairs so far Processed 139000000 sequence pairs so far Processed 140000000 sequence pairs so far Processed 141000000 sequence pairs so far Processed 142000000 sequence pairs so far Processed 143000000 sequence pairs so far Processed 144000000 sequence pairs so far Processed 145000000 sequence pairs so far Processed 146000000 sequence pairs so far Processed 147000000 sequence pairs so far Processed 148000000 sequence pairs so far Processed 149000000 sequence pairs so far Processed 150000000 sequence pairs so far Processed 151000000 sequence pairs so far Processed 152000000 sequence pairs so far Processed 153000000 sequence pairs so far Processed 154000000 sequence pairs so far Processed 155000000 sequence pairs so far Processed 156000000 sequence pairs so far Processed 157000000 sequence pairs so far Processed 158000000 sequence pairs so far Processed 159000000 sequence pairs so far Processed 160000000 sequence pairs so far Processed 161000000 sequence pairs so far Processed 162000000 sequence pairs so far Processed 163000000 sequence pairs so far Processed 164000000 sequence pairs so far Processed 165000000 sequence pairs so far Processed 166000000 sequence pairs so far Processed 167000000 sequence pairs so far Processed 168000000 sequence pairs so far Processed 169000000 sequence pairs so far Processed 170000000 sequence pairs so far Processed 171000000 sequence pairs so far Processed 172000000 sequence pairs so far Processed 173000000 sequence pairs so far Processed 174000000 sequence pairs so far Processed 175000000 sequence pairs so far Processed 176000000 sequence pairs so far Processed 177000000 sequence pairs so far Processed 178000000 sequence pairs so far Processed 179000000 sequence pairs so far Processed 180000000 sequence pairs so far Processed 181000000 sequence pairs so far Processed 182000000 sequence pairs so far Processed 183000000 sequence pairs so far Processed 184000000 sequence pairs so far Processed 185000000 sequence pairs so far Processed 186000000 sequence pairs so far Processed 187000000 sequence pairs so far Processed 188000000 sequence pairs so far Processed 189000000 sequence pairs so far Processed 190000000 sequence pairs so far Processed 191000000 sequence pairs so far Processed 192000000 sequence pairs so far Processed 193000000 sequence pairs so far Processed 194000000 sequence pairs so far Processed 195000000 sequence pairs so far Processed 196000000 sequence pairs so far Processed 197000000 sequence pairs so far Processed 198000000 sequence pairs so far Processed 199000000 sequence pairs so far Processed 200000000 sequence pairs so far Processed 201000000 sequence pairs so far Processed 202000000 sequence pairs so far Processed 203000000 sequence pairs so far Processed 204000000 sequence pairs so far Processed 205000000 sequence pairs so far Processed 206000000 sequence pairs so far Processed 207000000 sequence pairs so far Processed 208000000 sequence pairs so far Processed 209000000 sequence pairs so far Processed 210000000 sequence pairs so far Processed 211000000 sequence pairs so far Processed 212000000 sequence pairs so far Processed 213000000 sequence pairs so far Processed 214000000 sequence pairs so far Processed 215000000 sequence pairs so far Processed 216000000 sequence pairs so far Processed 217000000 sequence pairs so far Processed 218000000 sequence pairs so far Processed 219000000 sequence pairs so far Processed 220000000 sequence pairs so far Processed 221000000 sequence pairs so far Processed 222000000 sequence pairs so far Processed 223000000 sequence pairs so far Processed 224000000 sequence pairs so far Processed 225000000 sequence pairs so far Processed 226000000 sequence pairs so far Processed 227000000 sequence pairs so far Processed 228000000 sequence pairs so far Processed 229000000 sequence pairs so far Processed 230000000 sequence pairs so far Processed 231000000 sequence pairs so far Processed 232000000 sequence pairs so far Processed 233000000 sequence pairs so far Processed 234000000 sequence pairs so far Processed 235000000 sequence pairs so far Processed 236000000 sequence pairs so far Processed 237000000 sequence pairs so far Processed 238000000 sequence pairs so far Processed 239000000 sequence pairs so far Processed 240000000 sequence pairs so far Processed 241000000 sequence pairs so far Processed 242000000 sequence pairs so far Processed 243000000 sequence pairs so far Processed 244000000 sequence pairs so far Processed 245000000 sequence pairs so far Processed 246000000 sequence pairs so far Processed 247000000 sequence pairs so far Processed 248000000 sequence pairs so far Processed 249000000 sequence pairs so far Processed 250000000 sequence pairs so far Processed 251000000 sequence pairs so far Processed 252000000 sequence pairs so far Processed 253000000 sequence pairs so far Processed 254000000 sequence pairs so far Processed 255000000 sequence pairs so far Processed 256000000 sequence pairs so far Processed 257000000 sequence pairs so far Processed 258000000 sequence pairs so far Processed 259000000 sequence pairs so far Processed 260000000 sequence pairs so far Processed 261000000 sequence pairs so far Processed 262000000 sequence pairs so far Processed 263000000 sequence pairs so far Processed 264000000 sequence pairs so far Processed 265000000 sequence pairs so far Processed 266000000 sequence pairs so far Processed 267000000 sequence pairs so far Processed 268000000 sequence pairs so far Processed 269000000 sequence pairs so far Processed 270000000 sequence pairs so far Processed 271000000 sequence pairs so far Processed 272000000 sequence pairs so far Processed 273000000 sequence pairs so far Processed 274000000 sequence pairs so far Processed 275000000 sequence pairs so far Processed 276000000 sequence pairs so far Processed 277000000 sequence pairs so far Processed 278000000 sequence pairs so far Processed 279000000 sequence pairs so far Processed 280000000 sequence pairs so far Processed 281000000 sequence pairs so far Processed 282000000 sequence pairs so far Processed 283000000 sequence pairs so far Processed 284000000 sequence pairs so far 284116370 reads; of these: 284116370 (100.00%) were paired; of these: 276693467 (97.39%) aligned concordantly 0 times 6701877 (2.36%) aligned concordantly exactly 1 time 721026 (0.25%) aligned concordantly >1 times 2.61% overall alignment rate 284116370 reads; of these:284116370 reads; of these: 284116370 (284116370 (100.00100.00%%) were paired; of these:) were paired; of these: 277463629277350000 ( (97.6697.62%%) aligned concordantly 0 times) aligned concordantly 0 times284116370 reads; of these: 60246086130924 ( (2841163702.122.16 (%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time 100.00 % 628133) were paired; of these:635446 ( (0.22 0.22%276772656%) aligned concordantly >1 times () aligned concordantly >1 times 97.42 2.34%2.38%) aligned concordantly 0 times% overall alignment rate overall alignment rate 6627759 (2.33%) aligned concordantly exactly 1 time 715955 (0.25%) aligned concordantly >1 times 2.58% overall alignment rate Processed 284116370 sequences in total Successfully deleted the temporary files Meth5_R1_001_val_1.fq.gz_C_to_T.fastq, Meth5_R1_001_val_1.fq.gz_G_to_A.fastq, Meth5_R2_001_val_2.fq.gz_C_to_T.fastq and Meth5_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 284116370 Number of paired-end alignments with a unique best hit: 25385835 Mapping efficiency: 8.9% Sequence pairs with no alignments under any condition: 257285362 Sequence pairs did not map uniquely: 1445173 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5994921 ((converted) top strand) GA/CT/CT: 6598162 (complementary to (converted) top strand) GA/CT/GA: 6682164 (complementary to (converted) bottom strand) CT/GA/GA: 6110588 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1216049206 Total methylated C's in CpG context: 13356129 Total methylated C's in CHG context: 1864120 Total methylated C's in CHH context: 5809569 Total methylated C's in Unknown context: 49159 Total unmethylated C's in CpG context: 380588107 Total unmethylated C's in CHG context: 315213718 Total unmethylated C's in CHH context: 499217563 Total unmethylated C's in Unknown context: 166287 C methylated in CpG context: 3.4% C methylated in CHG context: 0.6% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 22.8% Bismark completed in 0d 7h 10m 50s ==================== 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/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth6_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth6_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth6_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth6_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth6_R1_001_val_1.fq.gz to Meth6_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth6_R1_001_val_1.fq.gz to Meth6_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth6_R1_001_val_1.fq.gz (140382105 sequences in total) Writing a C -> T converted version of the input file Meth6_R2_001_val_2.fq.gz to Meth6_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth6_R2_001_val_2.fq.gz to Meth6_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth6_R2_001_val_2.fq.gz (140382105 sequences in total) Input files are Meth6_R1_001_val_1.fq.gz_C_to_T.fastq and Meth6_R1_001_val_1.fq.gz_G_to_A.fastq and Meth6_R2_001_val_2.fq.gz_C_to_T.fastq and Meth6_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth6_R1_001_val_1.fq.gz_C_to_T.fastq and Meth6_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21992:1000_1:N:0:GCTTGTCA+NAACATAC/1 77 * 0 0 * * 0 0 TNGGTTGAAGTTTATTTGGATTTATGTTATTTGTTGGTGGTGTTAAAGAGGTTGAAAATGGTTGTTAAAGGGTTTTTTTAATTTAAGAAAAAGTGGTTTTTTGGTGTTGGTTGTATGAGGATTGGATTTAAGATGTTGATGTTT F#FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF: YT:Z:UP A00387:192:GW191111360th:4:1101:21992:1000_2:N:0:GCTTGTCA+NAACATAC/2 141 * 0 0 * * 0 0 AAACATCAACATCTTAAATCCAATCCTCATACAACCAACACCAAAAAACCACTTTTTCTTAAATTAAAAAAACCCTTTAACAACCATTTTCAACCTCTTTAACACCACCAACAAATAACATAAATCCAAATAAACTTCAACCCA F,FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth6_R1_001_val_1.fq.gz_G_to_A.fastq and Meth6_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21992:1000_1:N:0:GCTTGTCA+NAACATAC/1 77 * 0 0 * * 0 0 TNAATTAAAATTTATTTAAATTTATATTATTTATTAATAATATTAAAAAAATTAAAAATAATTATTAAAAAATTTTTTTAATTTAAAAAAAAATAATTTTTTAATATTAATTATATAAAAATTAAATTTAAAATATTAATATTT F#FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF: YT:Z:UP A00387:192:GW191111360th:4:1101:21992:1000_2:N:0:GCTTGTCA+NAACATAC/2 141 * 0 0 * * 0 0 AAATATTAATATTTTAAATTTAATTTTTATATAATTAATATTAAAAAATTATTTTTTTTTAAATTAAAAAAATTTTTTAATAATTATTTTTAATTTTTTTAATATTATTAATAAATAATATAAATTTAAATAAATTTTAATTTA F,FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth6_R1_001_val_1.fq.gz_G_to_A.fastq and Meth6_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21992:1000_1:N:0:GCTTGTCA+NAACATAC/1 77 * 0 0 * * 0 0 TNAATTAAAATTTATTTAAATTTATATTATTTATTAATAATATTAAAAAAATTAAAAATAATTATTAAAAAATTTTTTTAATTTAAAAAAAAATAATTTTTTAATATTAATTATATAAAAATTAAATTTAAAATATTAATATTT F#FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF: YT:Z:UP A00387:192:GW191111360th:4:1101:21992:1000_2:N:0:GCTTGTCA+NAACATAC/2 141 * 0 0 * * 0 0 AAATATTAATATTTTAAATTTAATTTTTATATAATTAATATTAAAAAATTATTTTTTTTTAAATTAAAAAAATTTTTTAATAATTATTTTTAATTTTTTTAATATTATTAATAAATAATATAAATTTAAATAAATTTTAATTTA F,FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth6_R1_001_val_1.fq.gz_C_to_T.fastq and Meth6_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21992:1000_1:N:0:GCTTGTCA+NAACATAC/1 77 * 0 0 * * 0 0 TNGGTTGAAGTTTATTTGGATTTATGTTATTTGTTGGTGGTGTTAAAGAGGTTGAAAATGGTTGTTAAAGGGTTTTTTTAATTTAAGAAAAAGTGGTTTTTTGGTGTTGGTTGTATGAGGATTGGATTTAAGATGTTGATGTTT F#FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF: YT:Z:UP A00387:192:GW191111360th:4:1101:21992:1000_2:N:0:GCTTGTCA+NAACATAC/2 141 * 0 0 * * 0 0 AAACATCAACATCTTAAATCCAATCCTCATACAACCAACACCAAAAAACCACTTTTTCTTAAATTAAAAAAACCCTTTAACAACCATTTTCAACCTCTTTAACACCACCAACAAATAACATAAATCCAAATAAACTTCAACCCA F,FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth6_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth6_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth6_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Processed 107000000 sequence pairs so far Processed 108000000 sequence pairs so far Processed 109000000 sequence pairs so far Processed 110000000 sequence pairs so far Processed 111000000 sequence pairs so far Processed 112000000 sequence pairs so far Processed 113000000 sequence pairs so far Processed 114000000 sequence pairs so far Processed 115000000 sequence pairs so far Processed 116000000 sequence pairs so far Processed 117000000 sequence pairs so far Processed 118000000 sequence pairs so far Processed 119000000 sequence pairs so far Processed 120000000 sequence pairs so far Processed 121000000 sequence pairs so far Processed 122000000 sequence pairs so far Processed 123000000 sequence pairs so far Processed 124000000 sequence pairs so far Processed 125000000 sequence pairs so far Processed 126000000 sequence pairs so far Processed 127000000 sequence pairs so far Processed 128000000 sequence pairs so far Processed 129000000 sequence pairs so far Processed 130000000 sequence pairs so far Processed 131000000 sequence pairs so far Processed 132000000 sequence pairs so far Processed 133000000 sequence pairs so far Processed 134000000 sequence pairs so far Processed 135000000 sequence pairs so far Processed 136000000 sequence pairs so far Processed 137000000 sequence pairs so far Processed 138000000 sequence pairs so far Processed 139000000 sequence pairs so far Processed 140000000 sequence pairs so far 140382105 reads; of these: 140382105 (100.00%) were paired; of these: 135448732 (96.49%) aligned concordantly 0 times 4475996 (3.19%) aligned concordantly exactly 1 time 457377 (0.33%) aligned concordantly >1 times 3.51% overall alignment rate 140382105 reads; of these: 140382105 (100.00%) were paired; of these: 135825791 (96.75%) aligned concordantly 0 times 4134083 (2.94%) aligned concordantly exactly 1 time 422231 (0.30%) aligned concordantly >1 times 3.25% overall alignment rate 140382105 reads; of these: 140382105 (100.00%) were paired; of these: 135413098 (96.46%) aligned concordantly 0 times 4507498 (3.21%) aligned concordantly exactly 1 time 461509 (0.33%) aligned concordantly >1 times 3.54% overall alignment rate 140382105 reads; of these: 140382105 (100.00%) were paired; of these: 135803557 (96.74%) aligned concordantly 0 times 4152112 (2.96%) aligned concordantly exactly 1 time 426436 (0.30%) aligned concordantly >1 times 3.26% overall alignment rate Processed 140382105 sequences in total Successfully deleted the temporary files Meth6_R1_001_val_1.fq.gz_C_to_T.fastq, Meth6_R1_001_val_1.fq.gz_G_to_A.fastq, Meth6_R2_001_val_2.fq.gz_C_to_T.fastq and Meth6_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 140382105 Number of paired-end alignments with a unique best hit: 17223714 Mapping efficiency: 12.3% Sequence pairs with no alignments under any condition: 122221927 Sequence pairs did not map uniquely: 936464 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4120918 ((converted) top strand) GA/CT/CT: 4460507 (complementary to (converted) top strand) GA/CT/GA: 4497161 (complementary to (converted) bottom strand) CT/GA/GA: 4145128 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 837822086 Total methylated C's in CpG context: 8969121 Total methylated C's in CHG context: 1269417 Total methylated C's in CHH context: 3356012 Total methylated C's in Unknown context: 38087 Total unmethylated C's in CpG context: 262346185 Total unmethylated C's in CHG context: 217295520 Total unmethylated C's in CHH context: 344585831 Total unmethylated C's in Unknown context: 114427 C methylated in CpG context: 3.3% C methylated in CHG context: 0.6% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 25.0% Bismark completed in 0d 4h 4m 23s ==================== 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/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth7_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth7_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth7_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth7_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth7_R1_001_val_1.fq.gz to Meth7_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth7_R1_001_val_1.fq.gz to Meth7_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth7_R1_001_val_1.fq.gz (95537325 sequences in total) Writing a C -> T converted version of the input file Meth7_R2_001_val_2.fq.gz to Meth7_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth7_R2_001_val_2.fq.gz to Meth7_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth7_R2_001_val_2.fq.gz (95537325 sequences in total) Input files are Meth7_R1_001_val_1.fq.gz_C_to_T.fastq and Meth7_R1_001_val_1.fq.gz_G_to_A.fastq and Meth7_R2_001_val_2.fq.gz_C_to_T.fastq and Meth7_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth7_R1_001_val_1.fq.gz_C_to_T.fastq and Meth7_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:22209:1000_1:N:0:CAAGCTAG+NCATAGCG/1 77 * 0 0 * * 0 0 TTTATATAATAAATAATGTATTATATTTTATATTGAAATTTAAATTAAATATGAAAAAAAATATTTTGTTATATATATATATTTTTTGATAATTAAATATAATAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:22209:1000_2:N:0:CAAGCTAG+NCATAGCG/2 141 * 0 0 * * 0 0 TAATTATTATATTTAATTATCAAAAAATATATATATATAACAAAATATTTTTTTTCATATTTAATTTAAATTTCAATATAAAATATAATACATTATTTATTATATAAA FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:,FFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth7_R1_001_val_1.fq.gz_G_to_A.fastq and Meth7_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:22209:1000_1:N:0:CAAGCTAG+NCATAGCG/1 77 * 0 0 * * 0 0 CTTACACAATAAACAACACACTACATTCTACATCAAAACTTAAATCAAATACAAAAAAAAACATCTCACCATATATACATACCCTCCAATAATCAAACATAACAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:22209:1000_2:N:0:CAAGCTAG+NCATAGCG/2 141 * 0 0 * * 0 0 TAATTGTTATGTTTGATTATTGGAGGGTATGTATATATGGTGAGATGTTTTTTTTTGTATTTGATTTAAGTTTTGATGTAGAATGTAGTGTGTTGTTTATTGTGTAAG FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:,FFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth7_R1_001_val_1.fq.gz_G_to_A.fastq and Meth7_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:22209:1000_1:N:0:CAAGCTAG+NCATAGCG/1 77 * 0 0 * * 0 0 CTTACACAATAAACAACACACTACATTCTACATCAAAACTTAAATCAAATACAAAAAAAAACATCTCACCATATATACATACCCTCCAATAATCAAACATAACAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:22209:1000_2:N:0:CAAGCTAG+NCATAGCG/2 141 * 0 0 * * 0 0 TAATTGTTATGTTTGATTATTGGAGGGTATGTATATATGGTGAGATGTTTTTTTTTGTATTTGATTTAAGTTTTGATGTAGAATGTAGTGTGTTGTTTATTGTGTAAG FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:,FFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth7_R1_001_val_1.fq.gz_C_to_T.fastq and Meth7_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:22209:1000_1:N:0:CAAGCTAG+NCATAGCG/1 77 * 0 0 * * 0 0 TTTATATAATAAATAATGTATTATATTTTATATTGAAATTTAAATTAAATATGAAAAAAAATATTTTGTTATATATATATATTTTTTGATAATTAAATATAATAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:22209:1000_2:N:0:CAAGCTAG+NCATAGCG/2 141 * 0 0 * * 0 0 TAATTATTATATTTAATTATCAAAAAATATATATATATAACAAAATATTTTTTTTCATATTTAATTTAAATTTCAATATAAAATATAATACATTATTTATTATATAAA FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:,FFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth7_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth7_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth7_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1220:28592:15280_1:N:0:CAAGCTAG+ACATAGCG NC_000913.3 4641543 Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1220:29396:16454_1:N:0:CAAGCTAG+ACATAGCG NC_000913.3 4641543 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1539:16242:35196_1:N:0:CAAGCTAG+ACATAGCG NC_000913.3 4641543 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far 95537325 reads; of these: 95537325 (100.00%) were paired; of these: 9510828995537325 ( reads; of these:99.55%) aligned concordantly 0 times 40324395537325 ( (0.42%) aligned concordantly exactly 1 time 25793 (0.03%) aligned concordantly >1 times 0.45% overall alignment rate 100.0095537325% reads; of these:) were paired; of these: 9553732594999546 ( (99.44100.00%%) aligned concordantly 0 times) were paired; of these: 50463294995049 ( (0.5399.43%%) aligned concordantly exactly 1 time) aligned concordantly 0 times 3314750904695537325 ( ( reads; of these:0.030.53 %% ) aligned concordantly >1 times) aligned concordantly exactly 1 time95537325 (0.56 %33230100.00 overall alignment rate (% 0.03) were paired; of these:% ) aligned concordantly >1 times 951049150.57 (%99.55 overall alignment rate% ) aligned concordantly 0 times 405934 (0.42%) aligned concordantly exactly 1 time 26476 (0.03%) aligned concordantly >1 times 0.45% overall alignment rate Processed 95537325 sequences in total Successfully deleted the temporary files Meth7_R1_001_val_1.fq.gz_C_to_T.fastq, Meth7_R1_001_val_1.fq.gz_G_to_A.fastq, Meth7_R2_001_val_2.fq.gz_C_to_T.fastq and Meth7_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 95537325 Number of paired-end alignments with a unique best hit: 1807479 Mapping efficiency: 1.9% Sequence pairs with no alignments under any condition: 93662468 Sequence pairs did not map uniquely: 67378 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 402279 ((converted) top strand) GA/CT/CT: 505170 (complementary to (converted) top strand) GA/CT/GA: 500747 (complementary to (converted) bottom strand) CT/GA/GA: 399280 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 100752645 Total methylated C's in CpG context: 355102 Total methylated C's in CHG context: 292359 Total methylated C's in CHH context: 599722 Total methylated C's in Unknown context: 50479 Total unmethylated C's in CpG context: 29666526 Total unmethylated C's in CHG context: 24937022 Total unmethylated C's in CHH context: 44901914 Total unmethylated C's in Unknown context: 270504 C methylated in CpG context: 1.2% C methylated in CHG context: 1.2% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 15.7% Bismark completed in 0d 1h 39m 59s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth8_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth8_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth8_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth8_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth8_R1_001_val_1.fq.gz to Meth8_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth8_R1_001_val_1.fq.gz to Meth8_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth8_R1_001_val_1.fq.gz (85174300 sequences in total) Writing a C -> T converted version of the input file Meth8_R2_001_val_2.fq.gz to Meth8_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth8_R2_001_val_2.fq.gz to Meth8_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth8_R2_001_val_2.fq.gz (85174300 sequences in total) Input files are Meth8_R1_001_val_1.fq.gz_C_to_T.fastq and Meth8_R1_001_val_1.fq.gz_G_to_A.fastq and Meth8_R2_001_val_2.fq.gz_C_to_T.fastq and Meth8_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth8_R1_001_val_1.fq.gz_C_to_T.fastq and Meth8_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:23674:1000_1:N:0:TGGATCGA+NTGCGATA/1 77 * 0 0 * * 0 0 TTATTTTTTTTTATAAAAATTTTTTAAATAAAAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23674:1000_2:N:0:TGGATCGA+NTGCGATA/2 141 * 0 0 * * 0 0 ATTTTTTTATTTAAAAAATTTTTATAAAAAAAAATAA FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth8_R1_001_val_1.fq.gz_G_to_A.fastq and Meth8_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:23674:1000_1:N:0:TGGATCGA+NTGCGATA/1 77 * 0 0 * * 0 0 CTATCTCTCTCTACAAAAACCCCCCAAATAAAAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23674:1000_2:N:0:TGGATCGA+NTGCGATA/2 141 * 0 0 * * 0 0 ATTTTTTTATTTGGGGGGTTTTTGTAGAGAGAGATAG FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth8_R1_001_val_1.fq.gz_G_to_A.fastq and Meth8_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:23674:1000_1:N:0:TGGATCGA+NTGCGATA/1 77 * 0 0 * * 0 0 CTATCTCTCTCTACAAAAACCCCCCAAATAAAAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23674:1000_2:N:0:TGGATCGA+NTGCGATA/2 141 * 0 0 * * 0 0 ATTTTTTTATTTGGGGGGTTTTTGTAGAGAGAGATAG FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth8_R1_001_val_1.fq.gz_C_to_T.fastq and Meth8_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:23674:1000_1:N:0:TGGATCGA+NTGCGATA/1 77 * 0 0 * * 0 0 TTATTTTTTTTTATAAAAATTTTTTAAATAAAAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:23674:1000_2:N:0:TGGATCGA+NTGCGATA/2 141 * 0 0 * * 0 0 ATTTTTTTATTTAAAAAATTTTTATAAAAAAAAATAA FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to Meth8_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth8_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth8_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:1432:20256:9204_1:N:0:TGGATCGA+GTGCGATA NC_000913.3 1 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:192:GW191111360th:4:2432:22580:15828_1:N:0:TGGATCGA+GTGCGATA NC_000913.3 1 Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far 85174300 reads; of these: 85174300 (100.00%) were paired; of these: 84727184 (99.48%) aligned concordantly 0 times 418803 (0.49%) aligned concordantly exactly 1 time 28313 (0.03%) aligned concordantly >1 times 0.52% overall alignment rate 85174300 reads; of these: 85174300 (100.00%) were paired; of these: 84633542 (99.37%) aligned concordantly 0 times 505522 (0.59%) aligned concordantly exactly 1 time 35236 (0.04%) aligned concordantly >1 times 0.63% overall alignment rate 85174300 reads; of these: 85174300 (100.00%) were paired; of these: 84630469 (99.36%) aligned concordantly 0 times 508158 (0.60%) aligned concordantly exactly 1 time 35673 (0.04%) aligned concordantly >1 times 0.64% overall alignment rate 85174300 reads; of these: 85174300 (100.00%) were paired; of these: 84727351 (99.48%) aligned concordantly 0 times 417950 (0.49%) aligned concordantly exactly 1 time 28999 (0.03%) aligned concordantly >1 times 0.52% overall alignment rate Processed 85174300 sequences in total Successfully deleted the temporary files Meth8_R1_001_val_1.fq.gz_C_to_T.fastq, Meth8_R1_001_val_1.fq.gz_G_to_A.fastq, Meth8_R2_001_val_2.fq.gz_C_to_T.fastq and Meth8_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 85174300 Number of paired-end alignments with a unique best hit: 1830106 Mapping efficiency: 2.1% Sequence pairs with no alignments under any condition: 83269883 Sequence pairs did not map uniquely: 74311 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 413048 ((converted) top strand) GA/CT/CT: 503358 (complementary to (converted) top strand) GA/CT/GA: 500356 (complementary to (converted) bottom strand) CT/GA/GA: 413342 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 101987599 Total methylated C's in CpG context: 408609 Total methylated C's in CHG context: 332944 Total methylated C's in CHH context: 674102 Total methylated C's in Unknown context: 60803 Total unmethylated C's in CpG context: 29942775 Total unmethylated C's in CHG context: 25190219 Total unmethylated C's in CHH context: 45438950 Total unmethylated C's in Unknown context: 279460 C methylated in CpG context: 1.3% C methylated in CHG context: 1.3% C methylated in CHH context: 1.5% C methylated in unknown context (CN or CHN): 17.9% Bismark completed in 0d 1h 31m 26s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/ecoli-MG1655/ (absolute path is '/gscratch/srlab/sr320/data/ecoli-MG1655/)' 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/sr320/032820-lambda'): /gscratch/scrubbed/sr320/031520-TG-bs/Meth9_R1_001_val_1.fq.gz /gscratch/scrubbed/sr320/031520-TG-bs/Meth9_R2_001_val_2.fq.gz 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 Output will be written into the directory: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/032820-lambda Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/031520-TG-bs/Meth9_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth9_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Meth9_R1_001_val_1.fq.gz to Meth9_R1_001_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth9_R1_001_val_1.fq.gz to Meth9_R1_001_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth9_R1_001_val_1.fq.gz (87033711 sequences in total) Writing a C -> T converted version of the input file Meth9_R2_001_val_2.fq.gz to Meth9_R2_001_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file Meth9_R2_001_val_2.fq.gz to Meth9_R2_001_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file Meth9_R2_001_val_2.fq.gz (87033711 sequences in total) Input files are Meth9_R1_001_val_1.fq.gz_C_to_T.fastq and Meth9_R1_001_val_1.fq.gz_G_to_A.fastq and Meth9_R2_001_val_2.fq.gz_C_to_T.fastq and Meth9_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Meth9_R1_001_val_1.fq.gz_C_to_T.fastq and Meth9_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21612:1000_1:N:0:AGTTCAGG+NCAACAGA/1 77 * 0 0 * * 0 0 TTTTTAAAATATTAAATTTAAAATTTTTTATAATAATTAATTTATATTATTAATTTATTAATAATATTAAATTATTTTATTATATTT FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21612:1000_2:N:0:AGTTCAGG+NCAACAGA/2 141 * 0 0 * * 0 0 CAATCTCTCTATAAAAAAATATAATAAAATAATTTAATATTATTAATAAATTAATAATATAAATTAATTATTATAAAAAATTTTAAATTTAATATTTTAAAAA FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFF:FFFF:FFFF:FFFFFFFFFFFFFFFFF,:FFFFFFFFFFF,FFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Meth9_R1_001_val_1.fq.gz_G_to_A.fastq and Meth9_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00387:192:GW191111360th:4:1101:21612:1000_1:N:0:AGTTCAGG+NCAACAGA/1 77 * 0 0 * * 0 0 TTTTCAAAACATCAAATTTAAAACTCTTTACAACAACCAATTTACATTATCAACTCATTAATAATACTAAATTACCTTATCATACTC FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21612:1000_2:N:0:AGTTCAGG+NCAACAGA/2 141 * 0 0 * * 0 0 TGATTTTTTTGTGAGAGAGTATGATAAGGTAATTTAGTATTATTAATGAGTTGATAATGTAAATTGGTTGTTGTAAAGAGTTTTAAATTTGATGTTTTGAAAA FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFF:FFFF:FFFF:FFFFFFFFFFFFFFFFF,:FFFFFFFFFFF,FFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Meth9_R1_001_val_1.fq.gz_G_to_A.fastq and Meth9_R2_001_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21612:1000_1:N:0:AGTTCAGG+NCAACAGA/1 77 * 0 0 * * 0 0 TTTTCAAAACATCAAATTTAAAACTCTTTACAACAACCAATTTACATTATCAACTCATTAATAATACTAAATTACCTTATCATACTC FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21612:1000_2:N:0:AGTTCAGG+NCAACAGA/2 141 * 0 0 * * 0 0 TGATTTTTTTGTGAGAGAGTATGATAAGGTAATTTAGTATTATTAATGAGTTGATAATGTAAATTGGTTGTTGTAAAGAGTTTTAAATTTGATGTTTTGAAAA FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFF:FFFF:FFFF:FFFFFFFFFFFFFFFFF,:FFFFFFFFFFF,FFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Meth9_R1_001_val_1.fq.gz_C_to_T.fastq and Meth9_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00387:192:GW191111360th:4:1101:21612:1000_1:N:0:AGTTCAGG+NCAACAGA/1 77 * 0 0 * * 0 0 TTTTTAAAATATTAAATTTAAAATTTTTTATAATAATTAATTTATATTATTAATTTATTAATAATATTAAATTATTTTATTATATTT FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00387:192:GW191111360th:4:1101:21612:1000_2:N:0:AGTTCAGG+NCAACAGA/2 141 * 0 0 * * 0 0 CAATCTCTCTATAAAAAAATATAATAAAATAATTTAATATTATTAATAAATTAATAATATAAATTAATTATTATAAAAAATTTTAAATTTAATATTTTAAAAA FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFF:FFFF:FFFF:FFFFFFFFFFFFFFFFF,:FFFFFFFFFFF,FFFFFFFF:FFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Meth9_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/031520-TG-bs/Meth9_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth9_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far 87033711 reads; of these: 87033711 (100.00%) were paired; of these: 86622482 (99.53%) aligned concordantly 0 times 386595 (0.44%) aligned concordantly exactly 1 time 24634 (0.03%) aligned concordantly >1 times 0.47% overall alignment rate 87033711 reads; of these: 87033711 (100.00%) were paired; of these: 86625941 (99.53%) aligned concordantly 0 times 382945 (0.44%) aligned concordantly exactly 1 time 24825 (0.03%) aligned concordantly >1 times 0.47% overall alignment rate 87033711 reads; of these: 87033711 (100.00%) were paired; of these: 86528525 (99.42%) aligned concordantly 0 times 474970 (0.55%) aligned concordantly exactly 1 time 30216 (0.03%) aligned concordantly >1 times 0.58% overall alignment rate 87033711 reads; of these: 87033711 (100.00%) were paired; of these: 86528666 (99.42%) aligned concordantly 0 times 474535 (0.55%) aligned concordantly exactly 1 time 30510 (0.04%) aligned concordantly >1 times 0.58% overall alignment rate Processed 87033711 sequences in total Successfully deleted the temporary files Meth9_R1_001_val_1.fq.gz_C_to_T.fastq, Meth9_R1_001_val_1.fq.gz_G_to_A.fastq, Meth9_R2_001_val_2.fq.gz_C_to_T.fastq and Meth9_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 87033711 Number of paired-end alignments with a unique best hit: 1702838 Mapping efficiency: 2.0% Sequence pairs with no alignments under any condition: 85267224 Sequence pairs did not map uniquely: 63649 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 382342 ((converted) top strand) GA/CT/CT: 470912 (complementary to (converted) top strand) GA/CT/GA: 470618 (complementary to (converted) bottom strand) CT/GA/GA: 378966 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 93339251 Total methylated C's in CpG context: 371121 Total methylated C's in CHG context: 318297 Total methylated C's in CHH context: 604062 Total methylated C's in Unknown context: 61561 Total unmethylated C's in CpG context: 27272922 Total unmethylated C's in CHG context: 22972831 Total unmethylated C's in CHH context: 41800018 Total unmethylated C's in Unknown context: 286558 C methylated in CpG context: 1.3% C methylated in CHG context: 1.4% C methylated in CHH context: 1.4% C methylated in unknown context (CN or CHN): 17.7% Bismark completed in 0d 1h 31m 30s ==================== Bismark run complete ==================== /var/spool/slurm/d/job2441667/slurm_script: line 60: --------------------------------------------------------: command not found mkdir: cannot create directory ‘lambda_tg’: File exists Processing paired-end Bismark output file(s) (SAM format): Meth10_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>Meth10_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in Meth10_R1_001_val_1_bismark_bt2_pe.bam: 2253301 Total number duplicated alignments removed: 1431781 (63.54%) Duplicated alignments were found at: 519605 different position(s) Total count of deduplicated leftover sequences: 821520 (36.46% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_R2_001_val_2.fq.gz -o lambda_tg" Processing paired-end Bismark output file(s) (SAM format): Meth11_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>Meth11_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in Meth11_R1_001_val_1_bismark_bt2_pe.bam: 676715 Total number duplicated alignments removed: 327926 (48.46%) Duplicated alignments were found at: 170367 different position(s) Total count of deduplicated leftover sequences: 348789 (51.54% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_R2_001_val_2.fq.gz -o lambda_tg" Processing paired-end Bismark output file(s) (SAM format): Meth12_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>Meth12_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in Meth12_R1_001_val_1_bismark_bt2_pe.bam: 2013003 Total number duplicated alignments removed: 1063002 (52.81%) Duplicated alignments were found at: 499991 different position(s) Total count of deduplicated leftover sequences: 950001 (47.19% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R2_001_val_2.fq.gz -o lambda_tg" Processing paired-end Bismark output file(s) (SAM format): Meth16_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>Meth16_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in Meth16_R1_001_val_1_bismark_bt2_pe.bam: 13777973 Total number duplicated alignments removed: 10194942 (73.99%) Duplicated alignments were found at: 2576498 different position(s) Total count of deduplicated leftover sequences: 3583031 (26.01% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth16_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth16_R2_001_val_2.fq.gz -o lambda_tg" Processing paired-end Bismark output file(s) (SAM format): Meth17_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>Meth17_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in Meth17_R1_001_val_1_bismark_bt2_pe.bam: 12928057 Total number duplicated alignments removed: 10830494 (83.78%) Duplicated alignments were found at: 1704214 different position(s) Total count of deduplicated leftover sequences: 2097563 (16.22% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth17_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth17_R2_001_val_2.fq.gz -o lambda_tg" Processing paired-end Bismark output file(s) (SAM format): Meth18_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>Meth18_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in Meth18_R1_001_val_1_bismark_bt2_pe.bam: 14475529 Total number duplicated alignments removed: 11937389 (82.47%) Duplicated alignments were found at: 2012642 different position(s) Total count of deduplicated leftover sequences: 2538140 (17.53% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R2_001_val_2.fq.gz -o lambda_tg" *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 14 Output will be written to the current directory ('/gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup') 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 >>Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_R2_001_val_2.fq.gz -o lambda_tg" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 821520 lines in total Total number of methylation call strings processed: 1643040 Final Cytosine Methylation Report ================================= Total number of C's analysed: 27579975 Total methylated C's in CpG context: 118759 Total methylated C's in CHG context: 98771 Total methylated C's in CHH context: 174341 Total C to T conversions in CpG context: 8172986 Total C to T conversions in CHG context: 6839460 Total C to T conversions in CHH context: 12175658 C methylated in CpG context: 1.4% C methylated in CHG context: 1.4% C methylated in CHH context: 1.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 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_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_R2_001_val_2.fq.gz -o lambda_tg" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 348789 lines in total Total number of methylation call strings processed: 697578 Final Cytosine Methylation Report ================================= Total number of C's analysed: 11708431 Total methylated C's in CpG context: 45279 Total methylated C's in CHG context: 37472 Total methylated C's in CHH context: 77761 Total C to T conversions in CpG context: 3481432 Total C to T conversions in CHG context: 2913371 Total C to T conversions in CHH context: 5153116 C methylated in CpG context: 1.3% C methylated in CHG context: 1.3% C methylated in CHH context: 1.5% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 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_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R2_001_val_2.fq.gz -o lambda_tg" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 950001 lines in total Total number of methylation call strings processed: 1900002 Final Cytosine Methylation Report ================================= Total number of C's analysed: 34519213 Total methylated C's in CpG context: 146627 Total methylated C's in CHG context: 122297 Total methylated C's in CHH context: 200851 Total C to T conversions in CpG context: 10123232 Total C to T conversions in CHG context: 8533012 Total C to T conversions in CHH context: 15393194 C methylated in CpG context: 1.4% C methylated in CHG context: 1.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 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_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth16_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth16_R2_001_val_2.fq.gz -o lambda_tg" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Finished processing child process. Exiting.. Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Finished processing child process. Exiting.. Processed lines: 3500000 Processed lines: 3500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 3500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 3583031 lines in total Total number of methylation call strings processed: 7166062 Final Cytosine Methylation Report ================================= Total number of C's analysed: 134501269 Total methylated C's in CpG context: 605151 Total methylated C's in CHG context: 503911 Total methylated C's in CHH context: 754133 Total C to T conversions in CpG context: 39415955 Total C to T conversions in CHG context: 33158830 Total C to T conversions in CHH context: 60063289 C methylated in CpG context: 1.5% C methylated in CHG context: 1.5% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 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_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth17_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth17_R2_001_val_2.fq.gz -o lambda_tg" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Finished processing child process. Exiting.. Finished 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: 'Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 2097563 lines in total Total number of methylation call strings processed: 4195126 Final Cytosine Methylation Report ================================= Total number of C's analysed: 77952543 Total methylated C's in CpG context: 327089 Total methylated C's in CHG context: 272009 Total methylated C's in CHH context: 424309 Total C to T conversions in CpG context: 22901611 Total C to T conversions in CHG context: 19251799 Total C to T conversions in CHH context: 34775726 C methylated in CpG context: 1.4% C methylated in CHG context: 1.4% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 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_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R2_001_val_2.fq.gz -o lambda_tg" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Finished processing child process. Exiting.. Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Finished processing child process. Exiting.. Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 2500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 2538140 lines in total Total number of methylation call strings processed: 5076280 Final Cytosine Methylation Report ================================= Total number of C's analysed: 94365749 Total methylated C's in CpG context: 410583 Total methylated C's in CHG context: 343612 Total methylated C's in CHH context: 542767 Total C to T conversions in CpG context: 27514997 Total C to T conversions in CHG context: 23190708 Total C to T conversions in CHH context: 42363082 C methylated in CpG context: 1.5% C methylated in CHG context: 1.5% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 130 Maximum read length of Read 2: 130 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_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_CTOB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/CpG_OB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found no potential alignment reports in the current directory. Please specify a single Bismark alignment report file using the option '--alignment_report FILE' SYNOPSIS: This script uses a Bismark alignment report to generate a graphical HTML report page. Optionally, further reports of the Bismark suite such as deduplication, methylation extractor splitting or M-bias reports can be specified as well. If several Bismark reports are found in the same folder, a separate report will be generated for each of these, whereby the output filename will be derived from the Bismark alignment report file. bismark2report attempts to find optional reports automatically based on the file basename. USAGE: bismark2report [options] -o/--output Name of the output file (optional). If not specified explicitly, the output filename will be derived from the Bismark alignment report file. Specifying an output filename only works if the HTML report is to be generated for a single Bismark alignment report (and potentially additional reports). --dir Output directory. Output is written to the current directory if not specified explicitly. --alignment_report FILE If not specified explicitly, bismark2report attempts to find Bismark report file(s) in the current directory and produces a separate HTML report for each mapping report file. Based on the basename of the Bismark mapping report, bismark2report will also attempt to find the other Bismark reports (see below) for inclusion into the HTML report. Specifying a Bismark alignment report file is mandatory. --dedup_report FILE If not specified explicitly, bismark2report attempts to find a deduplication report file with the same basename as the Bismark mapping report (generated by deduplicate_bismark) in the current working directory. Including a deduplication report is optional, and using the FILE 'none' will skip this step entirely. --splitting_report FILE If not specified explicitly, bismark2report attempts to find a splitting report file with the same basename as the Bismark mapping report (generated by the Bismark methylation extractor) in the current working directory. Including a splitting report is optional, and using the FILE 'none' will skip this step entirely. --mbias_report FILE If not specified explicitly, bismark2report attempts to find a single M-bias report file with the same basename as the Bismark mapping report (generated by the Bismark methylation extractor) in the current working directory. Including an M-Bias report is optional, and using the FILE 'none' will skip this step entirely. --nucleotide_report FILE If not specified explicitly, bismark2report attempts to find a single nucleotide coverage report file with the same basename as the Bismark mapping report (generated by Bismark with the option '--nucleotide_coverage') in the current working directory. Including a nucleotide coverage statistics report is optional, and using the FILE 'none' will skip this report entirely. Script last modified: 07 August 2018 No Bismark/Bowtie2 single-end BAM files detected Found Bismark/Bowtie2 paired-end files No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 6 Bismark BAM file(s)... Could not find Bismark report (Meth10_R1_001_val_1_bismark_bt2_PE_report.txt) to open [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: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/< Genome directory: >/gscratch/srlab/sr320/data/ecoli-MG1655/< 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/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Stored sequence information of 1 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: Meth10_R1_001_val_1_bismark_bt2_pe..CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_000913.3 Writing cytosine report for last chromosome NC_000913.3 (stored 699962 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 1 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 >>Meth10_R1_001_val_1_bismark_bt2_pe..CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Meth10_R1_001_val_1_bismark_bt2_pe..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: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/< Genome directory: >/gscratch/srlab/sr320/data/ecoli-MG1655/< 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/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Stored sequence information of 1 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: Meth11_R1_001_val_1_bismark_bt2_pe..CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_000913.3 Writing cytosine report for last chromosome NC_000913.3 (stored 671844 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 1 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 >>Meth11_R1_001_val_1_bismark_bt2_pe..CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Meth11_R1_001_val_1_bismark_bt2_pe..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: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/< Genome directory: >/gscratch/srlab/sr320/data/ecoli-MG1655/< 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/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Stored sequence information of 1 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: Meth12_R1_001_val_1_bismark_bt2_pe..CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_000913.3 Writing cytosine report for last chromosome NC_000913.3 (stored 702840 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 1 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 >>Meth12_R1_001_val_1_bismark_bt2_pe..CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Meth12_R1_001_val_1_bismark_bt2_pe..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: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/< Genome directory: >/gscratch/srlab/sr320/data/ecoli-MG1655/< 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/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Stored sequence information of 1 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: Meth16_R1_001_val_1_bismark_bt2_pe..CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_000913.3 Writing cytosine report for last chromosome NC_000913.3 (stored 749733 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 1 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 >>Meth16_R1_001_val_1_bismark_bt2_pe..CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Meth16_R1_001_val_1_bismark_bt2_pe..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: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/< Genome directory: >/gscratch/srlab/sr320/data/ecoli-MG1655/< 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/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Stored sequence information of 1 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: Meth17_R1_001_val_1_bismark_bt2_pe..CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_000913.3 Writing cytosine report for last chromosome NC_000913.3 (stored 724045 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 1 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 >>Meth17_R1_001_val_1_bismark_bt2_pe..CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Meth17_R1_001_val_1_bismark_bt2_pe..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: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/032820-lambda/lambda_tg/dedup/< Genome directory: >/gscratch/srlab/sr320/data/ecoli-MG1655/< 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/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Stored sequence information of 1 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: Meth18_R1_001_val_1_bismark_bt2_pe..CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_000913.3 Writing cytosine report for last chromosome NC_000913.3 (stored 731704 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 1 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 >>Meth18_R1_001_val_1_bismark_bt2_pe..CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Meth18_R1_001_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! /var/spool/slurm/d/job2441667/slurm_script: line 178: ------------------------: command not found *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file Meth13_R1_001_val_1_bismark_bt2_pe.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 14 Output will be written to the current directory ('/gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup') 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 >>Meth13_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file >Meth13_R1_001_val_1_bismark_bt2_pe.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Meth13_R1_001_val_1_bismark_bt2_pe.txt Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth13_R1_001_val_1_bismark_bt2_pe.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth13_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth13_R2_001_val_2.fq.gz -o lambda_tg" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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: 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Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt' Merging from these individual files: Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.1 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.2 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.3 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.4 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.5 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.6 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.7 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.8 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.9 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.10 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.11 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.12 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.13 Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.14 Processed 6361993 lines in total Total number of methylation call strings processed: 12723986 Final Cytosine Methylation Report ================================= Total number of C's analysed: 197973815 Total methylated C's in CpG context: 585262 Total methylated C's in CHG context: 306599 Total methylated C's in CHH context: 647534 Total C to T conversions in CpG context: 61558063 Total C to T conversions in CHG context: 51070651 Total C to T conversions in CHH context: 83805706 C methylated in CpG context: 0.9% C methylated in CHG context: 0.6% C methylated in CHH context: 0.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.1.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.2.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.3.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.4.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.5.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.6.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.7.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.8.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.9.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.10.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.11.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.12.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.13.mbias Meth13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 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_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CpG_CTOT_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CpG_CTOB_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CpG_OB_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_OT_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_CTOT_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_CTOB_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_OB_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_OT_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_CTOT_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_CTOB_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_OB_Meth13_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept Using these input files: CpG_OT_Meth13_R1_001_val_1_bismark_bt2_pe.txt CpG_CTOT_Meth13_R1_001_val_1_bismark_bt2_pe.txt CpG_CTOB_Meth13_R1_001_val_1_bismark_bt2_pe.txt CpG_OB_Meth13_R1_001_val_1_bismark_bt2_pe.txt CHG_OT_Meth13_R1_001_val_1_bismark_bt2_pe.txt CHG_CTOT_Meth13_R1_001_val_1_bismark_bt2_pe.txt CHG_CTOB_Meth13_R1_001_val_1_bismark_bt2_pe.txt CHG_OB_Meth13_R1_001_val_1_bismark_bt2_pe.txt CHH_OT_Meth13_R1_001_val_1_bismark_bt2_pe.txt CHH_CTOT_Meth13_R1_001_val_1_bismark_bt2_pe.txt CHH_CTOB_Meth13_R1_001_val_1_bismark_bt2_pe.txt CHH_OB_Meth13_R1_001_val_1_bismark_bt2_pe.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Meth13_R1_001_val_1_bismark_bt2_pe.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/sr320/032820-lambda/lambda_tg/nodedup/CpG_OT_Meth13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/CpG_CTOT_Meth13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/CpG_CTOB_Meth13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/CpG_OB_Meth13_R1_001_val_1_bismark_bt2_pe.txt Writing bedGraph to file: Meth13_R1_001_val_1_bismark_bt2_pe.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Meth13_R1_001_val_1_bismark_bt2_pe.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 Meth13_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Meth13_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Finished writing methylation calls from CpG_CTOT_Meth13_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Finished writing methylation calls from CpG_CTOB_Meth13_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Finished writing methylation calls from CpG_OB_Meth13_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Sorting input file Meth13_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Meth13_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>Meth14_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file >Meth14_R1_001_val_1_bismark_bt2_pe.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Meth14_R1_001_val_1_bismark_bt2_pe.txt Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth14_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth14_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth14_R2_001_val_2.fq.gz -o lambda_tg" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. 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: 'Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt' Merging from these individual files: Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.1 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.2 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.3 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.4 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.5 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.6 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.7 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.8 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.9 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.10 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.11 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.12 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.13 Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.14 Processed 4416160 lines in total Total number of methylation call strings processed: 8832320 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128934623 Total methylated C's in CpG context: 384872 Total methylated C's in CHG context: 183684 Total methylated C's in CHH context: 444482 Total C to T conversions in CpG context: 40522459 Total C to T conversions in CHG context: 33542592 Total C to T conversions in CHH context: 53856534 C methylated in CpG context: 0.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.1.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.2.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.3.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.4.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.5.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.6.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.7.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.8.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.9.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.10.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.11.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.12.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.13.mbias Meth14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 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_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CpG_CTOT_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CpG_CTOB_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CpG_OB_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_OT_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_CTOT_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_CTOB_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_OB_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_OT_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_CTOT_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_CTOB_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_OB_Meth14_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept Using these input files: CpG_OT_Meth14_R1_001_val_1_bismark_bt2_pe.txt CpG_CTOT_Meth14_R1_001_val_1_bismark_bt2_pe.txt CpG_CTOB_Meth14_R1_001_val_1_bismark_bt2_pe.txt CpG_OB_Meth14_R1_001_val_1_bismark_bt2_pe.txt CHG_OT_Meth14_R1_001_val_1_bismark_bt2_pe.txt CHG_CTOT_Meth14_R1_001_val_1_bismark_bt2_pe.txt CHG_CTOB_Meth14_R1_001_val_1_bismark_bt2_pe.txt CHG_OB_Meth14_R1_001_val_1_bismark_bt2_pe.txt CHH_OT_Meth14_R1_001_val_1_bismark_bt2_pe.txt CHH_CTOT_Meth14_R1_001_val_1_bismark_bt2_pe.txt CHH_CTOB_Meth14_R1_001_val_1_bismark_bt2_pe.txt CHH_OB_Meth14_R1_001_val_1_bismark_bt2_pe.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Meth14_R1_001_val_1_bismark_bt2_pe.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/sr320/032820-lambda/lambda_tg/nodedup/CpG_OT_Meth14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/CpG_CTOT_Meth14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/CpG_CTOB_Meth14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/CpG_OB_Meth14_R1_001_val_1_bismark_bt2_pe.txt Writing bedGraph to file: Meth14_R1_001_val_1_bismark_bt2_pe.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Meth14_R1_001_val_1_bismark_bt2_pe.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 Meth14_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Meth14_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Finished writing methylation calls from CpG_CTOT_Meth14_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Finished writing methylation calls from CpG_CTOB_Meth14_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Finished writing methylation calls from CpG_OB_Meth14_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Sorting input file Meth14_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Meth14_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>Meth15_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file >Meth15_R1_001_val_1_bismark_bt2_pe.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Meth15_R1_001_val_1_bismark_bt2_pe.txt Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Now reading in Bismark result file Meth15_R1_001_val_1_bismark_bt2_pe.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_000913.3 LN:4641652 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/ecoli-MG1655/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/scrubbed/sr320/031520-TG-bs/Meth15_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/sr320/031520-TG-bs/Meth15_R2_001_val_2.fq.gz -o lambda_tg" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed 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lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt' Merging from these individual files: Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.1 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.2 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.3 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.4 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.5 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.6 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.7 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.8 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.9 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.10 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.11 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.12 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.13 Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.14 Processed 9108570 lines in total Total number of methylation call strings processed: 18217140 Final Cytosine Methylation Report ================================= Total number of C's analysed: 275160369 Total methylated C's in CpG context: 796796 Total methylated C's in CHG context: 419293 Total methylated C's in CHH context: 919614 Total C to T conversions in CpG context: 85816235 Total C to T conversions in CHG context: 71099224 Total C to T conversions in CHH context: 116109207 C methylated in CpG context: 0.9% C methylated in CHG context: 0.6% C methylated in CHH context: 0.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.1.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.2.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.3.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.4.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.5.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.6.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.7.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.8.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.9.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.10.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.11.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.12.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.13.mbias Meth15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 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_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CpG_CTOT_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CpG_CTOB_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CpG_OB_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_OT_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_CTOT_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_CTOB_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHG_OB_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_OT_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_CTOT_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_CTOB_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept CHH_OB_Meth15_R1_001_val_1_bismark_bt2_pe.txt contains data -> kept Using these input files: CpG_OT_Meth15_R1_001_val_1_bismark_bt2_pe.txt CpG_CTOT_Meth15_R1_001_val_1_bismark_bt2_pe.txt CpG_CTOB_Meth15_R1_001_val_1_bismark_bt2_pe.txt CpG_OB_Meth15_R1_001_val_1_bismark_bt2_pe.txt CHG_OT_Meth15_R1_001_val_1_bismark_bt2_pe.txt CHG_CTOT_Meth15_R1_001_val_1_bismark_bt2_pe.txt CHG_CTOB_Meth15_R1_001_val_1_bismark_bt2_pe.txt CHG_OB_Meth15_R1_001_val_1_bismark_bt2_pe.txt CHH_OT_Meth15_R1_001_val_1_bismark_bt2_pe.txt CHH_CTOT_Meth15_R1_001_val_1_bismark_bt2_pe.txt CHH_CTOB_Meth15_R1_001_val_1_bismark_bt2_pe.txt CHH_OB_Meth15_R1_001_val_1_bismark_bt2_pe.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Meth15_R1_001_val_1_bismark_bt2_pe.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/sr320/032820-lambda/lambda_tg/nodedup/CpG_OT_Meth15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/CpG_CTOT_Meth15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/CpG_CTOB_Meth15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/CpG_OB_Meth15_R1_001_val_1_bismark_bt2_pe.txt Writing bedGraph to file: Meth15_R1_001_val_1_bismark_bt2_pe.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Meth15_R1_001_val_1_bismark_bt2_pe.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 Meth15_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Meth15_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Finished writing methylation calls from CpG_CTOT_Meth15_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Finished writing methylation calls from CpG_CTOB_Meth15_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Finished writing methylation calls from CpG_OB_Meth15_R1_001_val_1_bismark_bt2_pe.txt to merged temp file Sorting input file Meth15_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Meth15_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found no potential alignment reports in the current directory. Please specify a single Bismark alignment report file using the option '--alignment_report FILE' SYNOPSIS: This script uses a Bismark alignment report to generate a graphical HTML report page. Optionally, further reports of the Bismark suite such as deduplication, methylation extractor splitting or M-bias reports can be specified as well. If several Bismark reports are found in the same folder, a separate report will be generated for each of these, whereby the output filename will be derived from the Bismark alignment report file. bismark2report attempts to find optional reports automatically based on the file basename. USAGE: bismark2report [options] -o/--output Name of the output file (optional). If not specified explicitly, the output filename will be derived from the Bismark alignment report file. Specifying an output filename only works if the HTML report is to be generated for a single Bismark alignment report (and potentially additional reports). --dir Output directory. Output is written to the current directory if not specified explicitly. --alignment_report FILE If not specified explicitly, bismark2report attempts to find Bismark report file(s) in the current directory and produces a separate HTML report for each mapping report file. Based on the basename of the Bismark mapping report, bismark2report will also attempt to find the other Bismark reports (see below) for inclusion into the HTML report. Specifying a Bismark alignment report file is mandatory. --dedup_report FILE If not specified explicitly, bismark2report attempts to find a deduplication report file with the same basename as the Bismark mapping report (generated by deduplicate_bismark) in the current working directory. Including a deduplication report is optional, and using the FILE 'none' will skip this step entirely. --splitting_report FILE If not specified explicitly, bismark2report attempts to find a splitting report file with the same basename as the Bismark mapping report (generated by the Bismark methylation extractor) in the current working directory. Including a splitting report is optional, and using the FILE 'none' will skip this step entirely. --mbias_report FILE If not specified explicitly, bismark2report attempts to find a single M-bias report file with the same basename as the Bismark mapping report (generated by the Bismark methylation extractor) in the current working directory. Including an M-Bias report is optional, and using the FILE 'none' will skip this step entirely. --nucleotide_report FILE If not specified explicitly, bismark2report attempts to find a single nucleotide coverage report file with the same basename as the Bismark mapping report (generated by Bismark with the option '--nucleotide_coverage') in the current working directory. Including a nucleotide coverage statistics report is optional, and using the FILE 'none' will skip this report entirely. Script last modified: 07 August 2018 No Bismark/Bowtie2 single-end BAM files detected Found Bismark/Bowtie2 paired-end files No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 3 Bismark BAM file(s)... Could not find Bismark report (Meth13_R1_001_val_1_bismark_bt2_PE_report.txt) to open [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: Meth13_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/< Genome directory: >/gscratch/srlab/sr320/data/ecoli-MG1655/< 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/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Stored sequence information of 1 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: Meth13_R1_001_val_1_bismark_bt2_pe..CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_000913.3 Writing cytosine report for last chromosome NC_000913.3 (stored 494965 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 1 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 >>Meth13_R1_001_val_1_bismark_bt2_pe..CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Meth13_R1_001_val_1_bismark_bt2_pe..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: Meth14_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/< Genome directory: >/gscratch/srlab/sr320/data/ecoli-MG1655/< 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/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Stored sequence information of 1 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: Meth14_R1_001_val_1_bismark_bt2_pe..CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_000913.3 Writing cytosine report for last chromosome NC_000913.3 (stored 474645 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 1 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 >>Meth14_R1_001_val_1_bismark_bt2_pe..CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Meth14_R1_001_val_1_bismark_bt2_pe..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: Meth15_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/032820-lambda/lambda_tg/nodedup/< Genome directory: >/gscratch/srlab/sr320/data/ecoli-MG1655/< 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/ecoli-MG1655/ chr NC_000913.3 (4641652 bp) Stored sequence information of 1 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: Meth15_R1_001_val_1_bismark_bt2_pe..CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_000913.3 Writing cytosine report for last chromosome NC_000913.3 (stored 496185 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 1 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 >>Meth15_R1_001_val_1_bismark_bt2_pe..CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Meth15_R1_001_val_1_bismark_bt2_pe..CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq!