Path to genome folder specified as: /gscratch/srlab/sr320/data/phiX174/ Using 28 threads for the top and bottom strand indexing processes each, so using 56 cores in total Aligner to be used: >> Bowtie 2 << (default) Writing bisulfite genomes out into a single MFA (multi FastA) file Bismark Genome Preparation - Step I: Preparing folders Path to Bowtie 2 specified as: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ Bisulfite Genome Indexer version v0.21.0 (last modified: 05 Feb 2019) A directory called /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/ already exists. Already existing converted sequences and/or already existing Bowtie 2 or HISAT2) indices will be overwritten! Step I - Prepare genome folders - completed Bismark Genome Preparation - Step II: Bisulfite converting reference genome conversions performed: chromosome C->T G->A NC_001422.1 1157 1254 Total number of conversions performed: C->T: 1157 G->A: 1254 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/phiX174/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: 48 Using parameters --bmax 36 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 36 --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 308 sample suffixes Generating random suffixes QSorting 308 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 302 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 38, merged 128; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 15, merged 23; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 8, merged 5; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 5, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 4; iterating... Avg bucket size: 25.278 (target: 35) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 12 of 205 Getting block 18 of 205 Getting block 19 of 205 Getting block 20 of 205 Getting block 21 of 205 Getting block 22 of 205 Getting block 13 of 205 Getting block 15 of 205 Getting block 14 of 205 Getting block 1 of 205 Getting block 3 of 205 Getting block 7 of 205 Reserving size (36) for bucket 12 Reserving size (36) for bucket 18 Getting block 9 of 205 Reserving size (36) for bucket 19 Reserving size (36) for bucket 20 Reserving size (36) for bucket 21 Getting block 8 of 205 Reserving size (36) for bucket 22 Reserving size (36) for bucket 13 Reserving size (36) for bucket 15 Getting block 17 of 205 Reserving size (36) for bucket 14 Getting block 4 of 205 Getting block 6 of 205 Getting block 5 of 205 Getting block 11 of 205 Reserving size (36) for bucket 1 Reserving size (36) for bucket 3 Reserving size (36) for bucket 7 Getting block 23 of 205 Getting block 2 of 205 Getting block 16 of 205 Getting block 10 of 205 Calculating Z arrays for bucket 12 Calculating Z arrays for bucket 18 Reserving size (36) for bucket 9 Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 21 Reserving size (36) for bucket 8 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 13 Calculating Z arrays for bucket 15 Reserving size (36) for bucket 17 Calculating Z arrays for bucket 14 Getting block 24 of 205 Getting block 26 of 205 Getting block 25 of 205 Reserving size (36) for bucket 4 Reserving size (36) for bucket 6 Reserving size (36) for bucket 5 Reserving size (36) for bucket 11 Getting block 27 of 205 Calculating Z arrays for bucket 1 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 7 Reserving size (36) for bucket 23 Reserving size (36) for bucket 2 Reserving size (36) for bucket 16 Reserving size (36) for bucket 10 Calculating Z arrays for bucket 9 Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Calculating Z arrays for bucket 8 Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 22: Calculating Z arrays for bucket 17 Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 14: Reserving size (36) for bucket 24 Reserving size (36) for bucket 26 Reserving size (36) for bucket 25 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 11 Reserving size (36) for bucket 27 Entering block accumulator loop for bucket 1: Entering block accumulator loop for bucket 3: Calculating Z arrays for bucket 23 Entering block accumulator loop for bucket 7: Calculating Z arrays for bucket 2 Calculating Z arrays for bucket 16 Calculating Z arrays for bucket 10 Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 17: Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 26 Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 6: Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 2: Entering block accumulator loop for bucket 16: bucket 12: 10% Entering block accumulator loop for bucket 10: bucket 18: 10% bucket 19: 10% bucket 21: 10% bucket 20: 10% bucket 13: 10% bucket 22: 10% bucket 15: 10% bucket 14: 10% Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 25: bucket 1: 10% Entering block accumulator loop for bucket 27: bucket 3: 10% bucket 7: 10% bucket 12: 20% bucket 9: 10% bucket 18: 20% bucket 19: 20% bucket 21: 20% bucket 20: 20% bucket 8: 10% bucket 13: 20% bucket 22: 20% bucket 17: 10% bucket 15: 20% bucket 14: 20% bucket 4: 10% bucket 6: 10% bucket 5: 10% bucket 1: 20% bucket 11: 10% bucket 3: 20% bucket 7: 20% bucket 16: 10% bucket 2: 10% bucket 23: 10% bucket 12: 30% bucket 9: 20% bucket 10: 10% bucket 18: 30% bucket 19: 30% bucket 21: 30% bucket 20: 30% bucket 8: 20% bucket 13: 30% bucket 22: 30% bucket 17: 20% bucket 15: 30% bucket 14: 30% bucket 24: 10% bucket 26: 10% bucket 4: 20% bucket 25: 10% bucket 6: 20% bucket 5: 20% bucket 1: 30% bucket 27: 10% bucket 11: 20% bucket 3: 30% bucket 7: 30% bucket 16: 20% bucket 2: 20% bucket 23: 20% bucket 12: 40% bucket 9: 30% bucket 10: 20% bucket 18: 40% bucket 19: 40% bucket 21: 40% bucket 20: 40% bucket 8: 30% bucket 13: 40% bucket 22: 40% bucket 17: 30% bucket 15: 40% bucket 14: 40% bucket 24: 20% bucket 26: 20% bucket 4: 30% bucket 25: 20% bucket 6: 30% bucket 5: 30% bucket 1: 40% bucket 27: 20% bucket 11: 30% bucket 3: 40% bucket 7: 40% bucket 16: 30% bucket 2: 30% bucket 23: 30% bucket 12: 50% bucket 9: 40% bucket 10: 30% bucket 18: 50% bucket 19: 50% bucket 21: 50% bucket 20: 50% bucket 8: 40% bucket 13: 50% bucket 22: 50% bucket 17: 40% bucket 15: 50% bucket 14: 50% bucket 24: 30% bucket 26: 30% bucket 4: 40% bucket 25: 30% bucket 6: 40% bucket 5: 40% bucket 1: 50% bucket 27: 30% bucket 11: 40% bucket 3: 50% bucket 7: 50% bucket 16: 40% bucket 2: 40% bucket 23: 40% bucket 12: 60% bucket 9: 50% bucket 10: 40% bucket 18: 60% bucket 19: 60% bucket 21: 60% bucket 20: 60% bucket 8: 50% bucket 13: 60% bucket 22: 60% bucket 17: 50% bucket 15: 60% bucket 14: 60% bucket 24: 40% bucket 26: 40% bucket 4: 50% bucket 25: 40% bucket 6: 50% bucket 5: 50% bucket 1: 60% bucket 27: 40% bucket 11: 50% bucket 3: 60% bucket 7: 60% bucket 16: 50% bucket 2: 50% bucket 23: 50% bucket 12: 70% bucket 9: 60% bucket 10: 50% bucket 18: 70% bucket 19: 70% bucket 21: 70% bucket 20: 70% bucket 8: 60% bucket 13: 70% bucket 22: 70% bucket 17: 60% bucket 15: 70% bucket 14: 70% bucket 24: 50% bucket 26: 50% bucket 4: 60% bucket 25: 50% bucket 6: 60% bucket 5: 60% bucket 1: 70% bucket 27: 50% bucket 11: 60% bucket 3: 70% bucket 7: 70% bucket 16: 60% bucket 2: 60% bucket 23: 60% bucket 12: 80% bucket 9: 70% bucket 10: 60% bucket 18: 80% bucket 19: 80% bucket 21: 80% bucket 20: 80% bucket 8: 70% bucket 13: 80% bucket 22: 80% bucket 17: 70% bucket 15: 80% bucket 14: 80% bucket 24: 60% bucket 26: 60% bucket 4: 70% bucket 25: 60% bucket 6: 70% bucket 5: 70% bucket 1: 80% bucket 27: 60% bucket 11: 70% bucket 3: 80% bucket 7: 80% bucket 16: 70% bucket 2: 70% bucket 23: 70% bucket 12: 90% bucket 9: 80% bucket 10: 70% bucket 18: 90% bucket 19: 90% bucket 21: 90% bucket 20: 90% bucket 8: 80% bucket 13: 90% bucket 22: 90% bucket 17: 80% bucket 15: 90% bucket 14: 90% bucket 24: 70% bucket 26: 70% bucket 4: 80% bucket 25: 70% bucket 6: 80% bucket 5: 80% bucket 1: 90% bucket 27: 70% bucket 11: 80% bucket 3: 90% bucket 7: 90% bucket 16: 80% bucket 2: 80% bucket 23: 80% bucket 12: 100% bucket 9: 90% bucket 10: 80% bucket 18: 100% bucket 19: 100% bucket 21: 100% bucket 20: 100% bucket 8: 90% bucket 13: 100% bucket 22: 100% bucket 17: 90% bucket 15: 100% bucket 14: 100% bucket 24: 80% bucket 26: 80% bucket 4: 90% bucket 25: 80% bucket 6: 90% bucket 5: 90% bucket 1: 100% bucket 27: 80% bucket 11: 90% bucket 3: 100% bucket 7: 100% bucket 16: 90% bucket 2: 90% bucket 23: 90% Sorting block of length 12 for bucket 12 (Using difference cover) bucket 9: 100% bucket 10: 90% Sorting block of length 33 for bucket 18 (Using difference cover) Sorting block of length 21 for bucket 19 (Using difference cover) Sorting block of length 26 for bucket 21 (Using difference cover) Sorting block of length 29 for bucket 20 bucket 8: 100% (Using difference cover) Sorting block of length 34 for bucket 13 (Using difference cover) Sorting block of length 10 for bucket 22 (Using difference cover) bucket 17: 100% Sorting block of length 18 for bucket 15 (Using difference cover) Sorting block of length 18 for bucket 14 bucket 24: 90% (Using difference cover) bucket 26: 90% bucket 4: 100% bucket 25: 90% bucket 6: 100% bucket 5: 100% Sorting block of length 34 for bucket 1 (Using difference cover) bucket 27: 90% bucket 11: 100% Sorting block of length 29 for bucket 3 (Using difference cover) Sorting block of length 35 for bucket 7 bucket 16: 100% (Using difference cover) bucket 2: 100% bucket 23: 100% Sorting block of length 19 for bucket 9 (Using difference cover) bucket 10: 100% Sorting block of length 16 for bucket 8 (Using difference cover) Sorting block of length 11 for bucket 17 (Using difference cover) bucket 24: 100% bucket 26: 100% Sorting block of length 26 for bucket 4 (Using difference cover) bucket 25: 100% Sorting block of length 21 for bucket 6 (Using difference cover) Sorting block of length 17 for bucket 5 bucket 27: 100% (Using difference cover) Sorting block of length 33 for bucket 11 (Using difference cover) Sorting block of length 27 for bucket 16 (Using difference cover) Sorting block of length 26 for bucket 2 (Using difference cover) Sorting block of length 26 for bucket 23 (Using difference cover) Sorting block of length 30 for bucket 10 (Using difference cover) Sorting block of length 17 for bucket 24 (Using difference cover) Sorting block of length 12 for bucket 26 (Using difference cover) Sorting block of length 30 for bucket 25 (Using difference cover) Sorting block of length 32 for bucket 27 (Using difference cover) Sorting block time: 00:00:00 Returning block of 13 for bucket 12 Sorting block time: 00:00:00 Returning block of 27 for bucket 21 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 34 for bucket 11 Returning block of 35 for bucket 1 Returning block of 19 for bucket 15 Sorting block time: 00:00:00 Returning block of 19 for bucket 14 Sorting block time: 00:00:00 Returning block of 30 for bucket 20 Sorting block time: 00:00:00 Returning block of 35 for bucket 13 Sorting block time: 00:00:00 Returning block of 11 for bucket 22 Returning block of 34 for bucket 18 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 17 for bucket 8 Returning block of 30 for bucket 3 Sorting block time: 00:00:00 Returning block of 36 for bucket 7 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 22 for bucket 6 Sorting block time: 00:00:00 Returning block of 27 for bucket 23 Sorting block time: 00:00:00 Returning block of 20 for bucket 9 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 22 for bucket 19 Returning block of 33 for bucket 27 Sorting block time: 00:00:00 Returning block of 18 for bucket 5 Returning block of 13 for bucket 26 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 12 for bucket 17 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 28 for bucket 16 Returning block of 27 for bucket 2 Sorting block time: 00:00:00 Returning block of 31 for bucket 10 Sorting block time: 00:00:00 Returning block of 27 for bucket 4 Returning block of 31 for bucket 25 Returning block of 18 for bucket 24 Getting block 28 of 205 Reserving size (36) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 28: 10% bucket 28: 20% bucket 28: 30% bucket 28: 40% bucket 28: 50% bucket 28: 60% bucket 28: 70% bucket 28: 80% bucket 28: 90% bucket 28: 100% Sorting block of length 31 for bucket 28 (Using difference cover) Getting block 29 of 205 Reserving size (36) for bucket 29 Calculating Z arrays for bucket 29 Sorting block time: 00:00:00 Returning block of 32 for bucket 28 Entering block accumulator loop for bucket 29: bucket 29: 10% bucket 29: 20% bucket 29: 30% bucket 29: 40% bucket 29: 50% bucket 29: 60% bucket 29: 70% bucket 29: 80% bucket 29: 90% bucket 29: 100% Sorting block of length 24 for bucket 29 (Using difference cover) Getting block 30 of 205 Reserving size (36) for bucket 30 Calculating Z arrays for bucket 30 Sorting block time: 00:00:00 Returning block of 25 for bucket 29 Entering block accumulator loop for bucket 30: bucket 30: 10% bucket 30: 20% bucket 30: 30% bucket 30: 40% bucket 30: 50% bucket 30: 60% bucket 30: 70% bucket 30: 80% bucket 30: 90% bucket 30: 100% Sorting block of length 28 for bucket 30 (Using difference cover) Getting block 31 of 205 Reserving size (36) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: bucket 31: 10% bucket 31: 20% bucket 31: 30% bucket 31: 40% bucket 31: 50% bucket 31: 60% bucket 31: 70% bucket 31: 80% bucket 31: 90% bucket 31: 100% Sorting block of length 28 for bucket 31 (Using difference cover) Sorting block time: 00:00:00 Returning block of 29 for bucket 30 Getting block 32 of 205 Reserving size (36) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: bucket 32: 10% bucket 32: 20% bucket 32: 30% bucket 32: 40% bucket 32: 50% bucket 32: 60% bucket 32: 70% bucket 32: 80% Sorting block time: 00:00:00 Returning block of 29 for bucket 31 bucket 32: 90% bucket 32: 100% Sorting block of length 25 for bucket 32 (Using difference cover) Getting block 33 of 205 Reserving size (36) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: bucket 33: 10% bucket 33: 20% bucket 33: 30% bucket 33: 40% bucket 33: 50% bucket 33: 60% bucket 33: 70% bucket 33: 80% bucket 33: 90% bucket 33: 100% Sorting block of length 34 for bucket 33 (Using difference cover) Sorting block time: 00:00:00 Getting block 34 of 205 Returning block of 26 for bucket 32 Reserving size (36) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: bucket 34: 10% bucket 34: 20% bucket 34: 30% bucket 34: 40% bucket 34: 50% bucket 34: 60% bucket 34: 70% bucket 34: 80% bucket 34: 90% bucket 34: 100% Sorting block of length 33 for bucket 34 (Using difference cover) Sorting block time: 00:00:00 Returning block of 35 for bucket 33 Getting block 35 of 205 Reserving size (36) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: bucket 35: 10% bucket 35: 20% bucket 35: 30% bucket 35: 40% bucket 35: 50% bucket 35: 60% bucket 35: 70% bucket 35: 80% Sorting block time: 00:00:00 Returning block of 34 for bucket 34 bucket 35: 90% bucket 35: 100% Sorting block of length 26 for bucket 35 (Using difference cover) Getting block 36 of 205 Reserving size (36) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Sorting block time: 00:00:00 Returning block of 27 for bucket 35 bucket 36: 10% bucket 36: 20% bucket 36: 30% bucket 36: 40% bucket 36: 50% bucket 36: 60% bucket 36: 70% bucket 36: 80% bucket 36: 90% bucket 36: 100% Sorting block of length 19 for bucket 36 (Using difference cover) Getting block 37 of 205 Reserving size (36) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: bucket 37: 10% bucket 37: 20% bucket 37: 30% bucket 37: 40% bucket 37: 50% bucket 37: 60% bucket 37: 70% bucket 37: 80% Sorting block time: 00:00:00 Returning block of 20 for bucket 36 bucket 37: 90% bucket 37: 100% Sorting block of length 25 for bucket 37 (Using difference cover) Getting block 38 of 205 Reserving size (36) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: bucket 38: 10% bucket 38: 20% bucket 38: 30% bucket 38: 40% bucket 38: 50% bucket 38: 60% bucket 38: 70% bucket 38: 80% Getting block 39 of 205 bucket 38: 90% Reserving size (36) for bucket 39 Sorting block time: 00:00:00 bucket 38: 100% Calculating Z arrays for bucket 39 Returning block of 26 for bucket 37 Sorting block of length 15 for bucket 38 (Using difference cover) Entering block accumulator loop for bucket 39: bucket 39: 10% bucket 39: 20% bucket 39: 30% bucket 39: 40% bucket 39: 50% bucket 39: 60% bucket 39: 70% bucket 39: 80% bucket 39: 90% bucket 39: 100% Sorting block of length 30 for bucket 39 (Using difference cover) Getting block 40 of 205 Reserving size (36) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: bucket 40: 10% bucket 40: 20% bucket 40: 30% bucket 40: 40% bucket 40: 50% bucket 40: 60% bucket 40: 70% bucket 40: 80% bucket 40: 90% bucket 40: 100% Sorting block of length 29 for bucket 40 Sorting block time: 00:00:01 (Using difference cover) Returning block of 16 for bucket 38 Getting block 41 of 205 Reserving size (36) for bucket 41 Calculating Z arrays for bucket 41 Sorting block time: 00:00:01 Returning block of 31 for bucket 39 Entering block accumulator loop for bucket 41: bucket 41: 10% bucket 41: 20% bucket 41: 30% bucket 41: 40% bucket 41: 50% bucket 41: 60% bucket 41: 70% bucket 41: 80% bucket 41: 90% bucket 41: 100% Sorting block of length 29 for bucket 41 (Using difference cover) Getting block 42 of 205 Sorting block time: 00:00:00 Reserving size (36) for bucket 42 Returning block of 30 for bucket 40 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: bucket 42: 10% bucket 42: 20% bucket 42: 30% bucket 42: 40% bucket 42: 50% bucket 42: 60% bucket 42: 70% bucket 42: 80% bucket 42: 90% bucket 42: 100% Sorting block of length 26 for bucket 42 (Using difference cover) Sorting block time: 00:00:00 Returning block of 30 for bucket 41 Getting block 43 of 205 Reserving size (36) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: bucket 43: 10% bucket 43: 20% bucket 43: 30% bucket 43: 40% bucket 43: 50% bucket 43: 60% bucket 43: 70% bucket 43: 80% bucket 43: 90% bucket 43: 100% Sorting block of length 21 for bucket 43 (Using difference cover) Sorting block time: 00:00:00 Returning block of 27 for bucket 42 Getting block 44 of 205 Reserving size (36) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: bucket 44: 10% bucket 44: 20% bucket 44: 30% bucket 44: 40% bucket 44: 50% bucket 44: 60% bucket 44: 70% bucket 44: 80% Getting block 45 of 205 Sorting block time: 00:00:00 bucket 44: 90% Reserving size (36) for bucket 45 Returning block of 22 for bucket 43 bucket 44: 100% Calculating Z arrays for bucket 45 Sorting block of length 31 for bucket 44 (Using difference cover) Entering block accumulator loop for bucket 45: bucket 45: 10% bucket 45: 20% bucket 45: 30% bucket 45: 40% bucket 45: 50% bucket 45: 60% bucket 45: 70% bucket 45: 80% bucket 45: 90% bucket 45: 100% Sorting block of length 15 for bucket 45 (Using difference cover) Getting block 46 of 205 Reserving size (36) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: bucket 46: 10% bucket 46: 20% bucket 46: 30% bucket 46: 40% bucket 46: 50% bucket 46: 60% bucket 46: 70% bucket 46: 80% bucket 46: 90% bucket 46: 100% Sorting block of length 20 for bucket 46 (Using difference cover) Getting block 47 of 205 Reserving size (36) for bucket 47 Calculating Z arrays for bucket 47 Sorting block time: 00:00:00 Returning block of 32 for bucket 44 Entering block accumulator loop for bucket 47: bucket 47: 10% bucket 47: 20% bucket 47: 30% bucket 47: 40% bucket 47: 50% bucket 47: 60% bucket 47: 70% bucket 47: 80% bucket 47: 90% bucket 47: 100% Sorting block of length 29 for bucket 47 (Using difference cover) Sorting block time: 00:00:00 Returning block of 16 for bucket 45 Getting block 48 of 205 Reserving size (36) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: bucket 48: 10% bucket 48: 20% bucket 48: 30% bucket 48: 40% bucket 48: 50% bucket 48: 60% bucket 48: 70% bucket 48: 80% bucket 48: 90% Sorting block time: 00:00:00 Returning block of 21 for bucket 46 bucket 48: 100% Sorting block time: 00:00:00 Sorting block of length 33 for bucket 48 (Using difference cover) Returning block of 30 for bucket 47 Getting block 49 of 205 Reserving size (36) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: bucket 49: 10% bucket 49: 20% bucket 49: 30% bucket 49: 40% bucket 49: 50% bucket 49: 60% bucket 49: 70% bucket 49: 80% bucket 49: 90% Sorting block time: 00:00:00 Returning block of 34 for bucket 48 bucket 49: 100% Sorting block of length 15 for bucket 49 (Using difference cover) Getting block 50 of 205 Reserving size (36) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 50: 10% bucket 50: 20% bucket 50: 30% bucket 50: 40% bucket 50: 50% bucket 50: 60% bucket 50: 70% bucket 50: 80% Getting block 51 of 205 bucket 50: 90% Reserving size (36) for bucket 51 bucket 50: 100% Calculating Z arrays for bucket 51 Sorting block of length 21 for bucket 50 (Using difference cover) Sorting block time: 00:00:00 Returning block of 16 for bucket 49 Entering block accumulator loop for bucket 51: bucket 51: 10% bucket 51: 20% bucket 51: 30% bucket 51: 40% bucket 51: 50% bucket 51: 60% bucket 51: 70% bucket 51: 80% bucket 51: 90% bucket 51: 100% Sorting block of length 23 for bucket 51 (Using difference cover) Getting block 52 of 205 Reserving size (36) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 52: 10% bucket 52: 20% bucket 52: 30% bucket 52: 40% bucket 52: 50% bucket 52: 60% bucket 52: 70% bucket 52: 80% bucket 52: 90% bucket 52: 100% Sorting block of length 25 for bucket 52 (Using difference cover) Sorting block time: 00:00:00 Returning block of 22 for bucket 50 Sorting block time: 00:00:00 Returning block of 24 for bucket 51 Getting block 53 of 205 Reserving size (36) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 53: 10% bucket 53: 20% bucket 53: 30% bucket 53: 40% bucket 53: 50% bucket 53: 60% bucket 53: 70% bucket 53: 80% Sorting block time: 00:00:00 Returning block of 26 for bucket 52 bucket 53: 90% bucket 53: 100% Sorting block of length 26 for bucket 53 (Using difference cover) Getting block 54 of 205 Reserving size (36) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 54: 10% Sorting block time: 00:00:00 Returning block of 27 for bucket 53 bucket 54: 20% bucket 54: 30% bucket 54: 40% bucket 54: 50% bucket 54: 60% bucket 54: 70% bucket 54: 80% Getting block 55 of 205 bucket 54: 90% Reserving size (36) for bucket 55 bucket 54: 100% Calculating Z arrays for bucket 55 Sorting block of length 27 for bucket 54 (Using difference cover) Entering block accumulator loop for bucket 55: bucket 55: 10% bucket 55: 20% bucket 55: 30% bucket 55: 40% bucket 55: 50% bucket 55: 60% bucket 55: 70% bucket 55: 80% bucket 55: 90% bucket 55: 100% Sorting block of length 35 for bucket 55 (Using difference cover) Getting block 56 of 205 Reserving size (36) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 56: 10% bucket 56: 20% bucket 56: 30% bucket 56: 40% bucket 56: 50% bucket 56: 60% bucket 56: 70% bucket 56: 80% bucket 56: 90% bucket 56: 100% Sorting block of length 21 for bucket 56 (Using difference cover) Getting block 57 of 205 Sorting block time: 00:00:00 Reserving size (36) for bucket 57 Returning block of 28 for bucket 54 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 57: 10% bucket 57: 20% bucket 57: 30% bucket 57: 40% bucket 57: 50% bucket 57: 60% bucket 57: 70% bucket 57: 80% bucket 57: 90% bucket 57: 100% Sorting block of length 32 for bucket 57 (Using difference cover) Getting block 58 of 205 Sorting block time: 00:00:00 Returning block of 36 for bucket 55 Reserving size (36) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: bucket 58: 10% bucket 58: 20% bucket 58: 30% bucket 58: 40% bucket 58: 50% bucket 58: 60% bucket 58: 70% bucket 58: 80% bucket 58: 90% bucket 58: 100% Sorting block of length 34 for bucket 58 (Using difference cover) Sorting block time: 00:00:00 Returning block of 22 for bucket 56 Getting block 59 of 205 Reserving size (36) for bucket 59 Calculating Z arrays for bucket 59 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 59: Returning block of 33 for bucket 57 bucket 59: 10% Sorting block time: 00:00:00 Returning block of 35 for bucket 58 bucket 59: 20% Getting block 60 of 205 bucket 59: 30% Reserving size (36) for bucket 60 bucket 59: 40% Calculating Z arrays for bucket 60 bucket 59: 50% bucket 59: 60% Entering block accumulator loop for bucket 60: bucket 59: 70% bucket 59: 80% bucket 60: 10% bucket 59: 90% bucket 60: 20% bucket 59: 100% bucket 60: 30% Sorting block of length 12 for bucket 59 (Using difference cover) bucket 60: 40% Getting block 61 of 205 bucket 60: 50% Reserving size (36) for bucket 61 bucket 60: 60% Calculating Z arrays for bucket 61 bucket 60: 70% Entering block accumulator loop for bucket 61: bucket 60: 80% bucket 60: 90% bucket 61: 10% bucket 60: 100% bucket 61: 20% Sorting block of length 25 for bucket 60 (Using difference cover) bucket 61: 30% bucket 61: 40% bucket 61: 50% bucket 61: 60% bucket 61: 70% bucket 61: 80% bucket 61: 90% bucket 61: 100% Sorting block of length 16 for bucket 61 (Using difference cover) Getting block 62 of 205 Reserving size (36) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 62: 10% bucket 62: 20% bucket 62: 30% bucket 62: 40% bucket 62: 50% bucket 62: 60% Sorting block time: 00:00:00 Returning block of 13 for bucket 59 bucket 62: 70% bucket 62: 80% bucket 62: 90% bucket 62: 100% Sorting block of length 35 for bucket 62 (Using difference cover) Getting block 63 of 205 Reserving size (36) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 63: 10% bucket 63: 20% bucket 63: 30% bucket 63: 40% bucket 63: 50% bucket 63: 60% bucket 63: 70% bucket 63: 80% Sorting block time: 00:00:00 Returning block of 26 for bucket 60 bucket 63: 90% bucket 63: 100% Sorting block of length 22 for bucket 63 (Using difference cover) Getting block 64 of 205 Reserving size (36) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 64: 10% bucket 64: 20% bucket 64: 30% bucket 64: 40% bucket 64: 50% bucket 64: 60% Sorting block time: 00:00:00 Returning block of 17 for bucket 61 bucket 64: 70% bucket 64: 80% bucket 64: 90% bucket 64: 100% Sorting block of length 28 for bucket 64 (Using difference cover) Getting block 65 of 205 Reserving size (36) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: bucket 65: 10% bucket 65: 20% bucket 65: 30% bucket 65: 40% bucket 65: 50% bucket 65: 60% bucket 65: 70% Sorting block time: 00:00:00 Returning block of 36 for bucket 62 bucket 65: 80% bucket 65: 90% bucket 65: 100% Sorting block of length 10 for bucket 65 (Using difference cover) Getting block 66 of 205 Reserving size (36) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: bucket 66: 10% bucket 66: 20% bucket 66: 30% bucket 66: 40% bucket 66: 50% bucket 66: 60% bucket 66: 70% bucket 66: 80% Sorting block time: 00:00:00 Returning block of 23 for bucket 63 bucket 66: 90% bucket 66: 100% Sorting block of length 28 for bucket 66 (Using difference cover) Getting block 67 of 205 Reserving size (36) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: bucket 67: 10% bucket 67: 20% bucket 67: 30% bucket 67: 40% bucket 67: 50% bucket 67: 60% bucket 67: 70% bucket 67: 80% bucket 67: 90% Sorting block time: 00:00:00 Returning block of 29 for bucket 64 bucket 67: 100% Sorting block of length 34 for bucket 67 (Using difference cover) Getting block 68 of 205 Reserving size (36) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 68: 10% bucket 68: 20% bucket 68: 30% bucket 68: 40% bucket 68: 50% bucket 68: 60% bucket 68: 70% bucket 68: 80% bucket 68: 90% Sorting block time: 00:00:00 Returning block of 11 for bucket 65 bucket 68: 100% Sorting block of length 23 for bucket 68 (Using difference cover) Getting block 69 of 205 Reserving size (36) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: bucket 69: 10% bucket 69: 20% bucket 69: 30% bucket 69: 40% bucket 69: 50% bucket 69: 60% bucket 69: 70% bucket 69: 80% Sorting block time: 00:00:00 Returning block of 29 for bucket 66 bucket 69: 90% bucket 69: 100% Sorting block of length 31 for bucket 69 (Using difference cover) Getting block 70 of 205 Reserving size (36) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: bucket 70: 10% bucket 70: 20% bucket 70: 30% bucket 70: 40% bucket 70: 50% bucket 70: 60% bucket 70: 70% bucket 70: 80% Sorting block time: 00:00:00 Returning block of 35 for bucket 67 bucket 70: 90% bucket 70: 100% Sorting block of length 2 for bucket 70 (Using difference cover) Getting block 71 of 205 Reserving size (36) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: bucket 71: 10% bucket 71: 20% bucket 71: 30% bucket 71: 40% bucket 71: 50% bucket 71: 60% bucket 71: 70% bucket 71: 80% Sorting block time: 00:00:00 Returning block of 24 for bucket 68 bucket 71: 90% Getting block 72 of 205 bucket 71: 100% Reserving size (36) for bucket 72 Sorting block of length 38 for bucket 71 (Using difference cover) Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 72: 10% bucket 72: 20% bucket 72: 30% bucket 72: 40% bucket 72: 50% bucket 72: 60% bucket 72: 70% bucket 72: 80% Sorting block time: 00:00:00 Returning block of 32 for bucket 69 bucket 72: 90% Sorting block time: 00:00:00 Returning block of 3 for bucket 70 bucket 72: 100% Sorting block of length 32 for bucket 72 (Using difference cover) Getting block 73 of 205 Reserving size (36) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: bucket 73: 10% bucket 73: 20% bucket 73: 30% bucket 73: 40% bucket 73: 50% bucket 73: 60% bucket 73: 70% bucket 73: 80% bucket 73: 90% bucket 73: 100% Sorting block of length 24 for bucket 73 (Using difference cover) Sorting block time: 00:00:00 Returning block of 39 for bucket 71 Sorting block time: 00:00:00 Returning block of 33 for bucket 72 Sorting block time: 00:00:00 Returning block of 25 for bucket 73 Getting block 74 of 205 Reserving size (36) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: bucket 74: 10% bucket 74: 20% bucket 74: 30% bucket 74: 40% bucket 74: 50% bucket 74: 60% bucket 74: 70% bucket 74: 80% bucket 74: 90% bucket 74: 100% Sorting block of length 20 for bucket 74 (Using difference cover) Getting block 75 of 205 Reserving size (36) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 75: 10% bucket 75: 20% bucket 75: 30% bucket 75: 40% bucket 75: 50% bucket 75: 60% bucket 75: 70% bucket 75: 80% bucket 75: 90% bucket 75: 100% Sorting block of length 35 for bucket 75 (Using difference cover) Getting block 76 of 205 Reserving size (36) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 76: 10% bucket 76: 20% bucket 76: 30% bucket 76: 40% bucket 76: 50% bucket 76: 60% bucket 76: 70% bucket 76: 80% bucket 76: 90% Sorting block time: 00:00:00 Returning block of 21 for bucket 74 bucket 76: 100% Sorting block of length 13 for bucket 76 (Using difference cover) Sorting block time: 00:00:00 Returning block of 36 for bucket 75 Getting block 77 of 205 Reserving size (36) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 77: 10% bucket 77: 20% bucket 77: 30% bucket 77: 40% bucket 77: 50% bucket 77: 60% bucket 77: 70% bucket 77: 80% bucket 77: 90% bucket 77: 100% Sorting block of length 29 for bucket 77 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14 for bucket 76 Getting block 78 of 205 Reserving size (36) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 78: 10% bucket 78: 20% bucket 78: 30% bucket 78: 40% bucket 78: 50% bucket 78: 60% bucket 78: 70% bucket 78: 80% bucket 78: 90% bucket 78: 100% Sorting block of length 7 for bucket 78 (Using difference cover) Sorting block time: 00:00:00 Getting block 79 of 205 Returning block of 30 for bucket 77 Reserving size (36) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 79: 10% bucket 79: 20% bucket 79: 30% bucket 79: 40% bucket 79: 50% bucket 79: 60% bucket 79: 70% bucket 79: 80% bucket 79: 90% bucket 79: 100% Sorting block of length 29 for bucket 79 (Using difference cover) Sorting block time: 00:00:00 Returning block of 8 for bucket 78 Getting block 80 of 205 Reserving size (36) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 80: 10% bucket 80: 20% bucket 80: 30% bucket 80: 40% bucket 80: 50% Sorting block time: 00:00:00 Returning block of 30 for bucket 79 bucket 80: 60% bucket 80: 70% bucket 80: 80% bucket 80: 90% bucket 80: 100% Sorting block of length 19 for bucket 80 (Using difference cover) Getting block 81 of 205 Reserving size (36) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 81: 10% bucket 81: 20% bucket 81: 30% bucket 81: 40% bucket 81: 50% bucket 81: 60% bucket 81: 70% bucket 81: 80% bucket 81: 90% bucket 81: 100% Sorting block of length 26 for bucket 81 (Using difference cover) Getting block 82 of 205 Reserving size (36) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 82: 10% bucket 82: 20% bucket 82: 30% Sorting block time: 00:00:00 Returning block of 20 for bucket 80 bucket 82: 40% bucket 82: 50% Sorting block time: 00:00:00 Returning block of 27 for bucket 81 bucket 82: 60% bucket 82: 70% Getting block 83 of 205 bucket 82: 80% Reserving size (36) for bucket 83 bucket 82: 90% Calculating Z arrays for bucket 83 bucket 82: 100% Sorting block of length 20 for bucket 82 (Using difference cover) Entering block accumulator loop for bucket 83: bucket 83: 10% bucket 83: 20% bucket 83: 30% bucket 83: 40% bucket 83: 50% bucket 83: 60% bucket 83: 70% bucket 83: 80% bucket 83: 90% bucket 83: 100% Sorting block of length 30 for bucket 83 (Using difference cover) Getting block 84 of 205 Reserving size (36) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 84: 10% bucket 84: 20% Getting block 85 of 205 bucket 84: 30% Reserving size (36) for bucket 85 bucket 84: 40% Calculating Z arrays for bucket 85 bucket 84: 50% Sorting block time: 00:00:00 bucket 84: 60% Returning block of 21 for bucket 82 Entering block accumulator loop for bucket 85: bucket 84: 70% Sorting block time: 00:00:00 Returning block of 31 for bucket 83 bucket 84: 80% bucket 85: 10% bucket 84: 90% bucket 85: 20% bucket 84: 100% bucket 85: 30% Sorting block of length 18 for bucket 84 (Using difference cover) bucket 85: 40% bucket 85: 50% bucket 85: 60% Getting block 86 of 205 bucket 85: 70% Reserving size (36) for bucket 86 bucket 85: 80% Calculating Z arrays for bucket 86 bucket 85: 90% bucket 85: 100% Entering block accumulator loop for bucket 86: Sorting block of length 29 for bucket 85 (Using difference cover) bucket 86: 10% bucket 86: 20% bucket 86: 30% bucket 86: 40% bucket 86: 50% bucket 86: 60% bucket 86: 70% bucket 86: 80% Getting block 87 of 205 bucket 86: 90% Reserving size (36) for bucket 87 bucket 86: 100% Calculating Z arrays for bucket 87 Sorting block of length 31 for bucket 86 (Using difference cover) Entering block accumulator loop for bucket 87: bucket 87: 10% bucket 87: 20% bucket 87: 30% bucket 87: 40% bucket 87: 50% bucket 87: 60% bucket 87: 70% bucket 87: 80% Sorting block time: 00:00:00 Returning block of 19 for bucket 84 bucket 87: 90% bucket 87: 100% Sorting block of length 31 for bucket 87 (Using difference cover) Getting block 88 of 205 Reserving size (36) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 88: 10% bucket 88: 20% bucket 88: 30% bucket 88: 40% bucket 88: 50% bucket 88: 60% bucket 88: 70% bucket 88: 80% bucket 88: 90% Sorting block time: 00:00:00 Returning block of 30 for bucket 85 bucket 88: 100% Sorting block of length 34 for bucket 88 (Using difference cover) Getting block 89 of 205 Reserving size (36) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 89: 10% bucket 89: 20% bucket 89: 30% bucket 89: 40% bucket 89: 50% Sorting block time: 00:00:00 Returning block of 32 for bucket 86 bucket 89: 60% bucket 89: 70% bucket 89: 80% bucket 89: 90% bucket 89: 100% Sorting block of length 28 for bucket 89 (Using difference cover) Getting block 90 of 205 Reserving size (36) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 90: 10% bucket 90: 20% bucket 90: 30% bucket 90: 40% bucket 90: 50% bucket 90: 60% bucket 90: 70% Sorting block time: 00:00:00 bucket 90: 80% Returning block of 32 for bucket 87 bucket 90: 90% bucket 90: 100% Sorting block of length 32 for bucket 90 (Using difference cover) Getting block 91 of 205 Reserving size (36) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 91: 10% bucket 91: 20% bucket 91: 30% bucket 91: 40% bucket 91: 50% bucket 91: 60% bucket 91: 70% bucket 91: 80% Sorting block time: 00:00:00 Returning block of 35 for bucket 88 bucket 91: 90% bucket 91: 100% Sorting block of length 23 for bucket 91 (Using difference cover) Getting block 92 of 205 Reserving size (36) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: bucket 92: 10% bucket 92: 20% bucket 92: 30% bucket 92: 40% bucket 92: 50% bucket 92: 60% bucket 92: 70% bucket 92: 80% bucket 92: 90% Sorting block time: 00:00:00 Returning block of 29 for bucket 89 bucket 92: 100% Sorting block of length 16 for bucket 92 (Using difference cover) Getting block 93 of 205 Reserving size (36) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 93: 10% bucket 93: 20% bucket 93: 30% bucket 93: 40% Sorting block time: 00:00:00 Returning block of 33 for bucket 90 bucket 93: 50% bucket 93: 60% bucket 93: 70% bucket 93: 80% bucket 93: 90% bucket 93: 100% Sorting block of length 33 for bucket 93 (Using difference cover) Getting block 94 of 205 Reserving size (36) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: bucket 94: 10% bucket 94: 20% bucket 94: 30% bucket 94: 40% bucket 94: 50% bucket 94: 60% Sorting block time: 00:00:00 Returning block of 24 for bucket 91 bucket 94: 70% bucket 94: 80% Getting block 95 of 205 bucket 94: 90% Reserving size (36) for bucket 95 Calculating Z arrays for bucket 95 bucket 94: 100% Sorting block of length 26 for bucket 94 (Using difference cover) Entering block accumulator loop for bucket 95: bucket 95: 10% bucket 95: 20% bucket 95: 30% bucket 95: 40% bucket 95: 50% bucket 95: 60% bucket 95: 70% Sorting block time: 00:00:00 Returning block of 17 for bucket 92 bucket 95: 80% bucket 95: 90% bucket 95: 100% Sorting block of length 20 for bucket 95 (Using difference cover) Getting block 96 of 205 Reserving size (36) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 96: 10% bucket 96: 20% bucket 96: 30% bucket 96: 40% bucket 96: 50% bucket 96: 60% bucket 96: 70% Sorting block time: 00:00:00 Returning block of 34 for bucket 93 bucket 96: 80% bucket 96: 90% Getting block 97 of 205 bucket 96: 100% Reserving size (36) for bucket 97 Sorting block of length 30 for bucket 96 (Using difference cover) Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: bucket 97: 10% bucket 97: 20% bucket 97: 30% bucket 97: 40% bucket 97: 50% bucket 97: 60% bucket 97: 70% Sorting block time: 00:00:00 Returning block of 27 for bucket 94 bucket 97: 80% bucket 97: 90% bucket 97: 100% Sorting block of length 21 for bucket 97 (Using difference cover) Getting block 98 of 205 Reserving size (36) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 98: 10% bucket 98: 20% bucket 98: 30% bucket 98: 40% bucket 98: 50% bucket 98: 60% bucket 98: 70% Sorting block time: 00:00:00 Returning block of 21 for bucket 95 bucket 98: 80% Getting block 99 of 205 bucket 98: 90% Reserving size (36) for bucket 99 bucket 98: 100% Calculating Z arrays for bucket 99 Sorting block of length 5 for bucket 98 (Using difference cover) Entering block accumulator loop for bucket 99: bucket 99: 10% bucket 99: 20% bucket 99: 30% bucket 99: 40% bucket 99: 50% bucket 99: 60% Sorting block time: 00:00:00 Returning block of 31 for bucket 96 bucket 99: 70% Getting block 100 of 205 bucket 99: 80% Reserving size (36) for bucket 100 Calculating Z arrays for bucket 100 bucket 99: 90% bucket 99: 100% Entering block accumulator loop for bucket 100: Sorting block of length 41 for bucket 99 (Using difference cover) bucket 100: 10% bucket 100: 20% bucket 100: 30% bucket 100: 40% bucket 100: 50% bucket 100: 60% bucket 100: 70% bucket 100: 80% bucket 100: 90% Sorting block time: 00:00:00 Returning block of 22 for bucket 97 Sorting block time: 00:00:00 bucket 100: 100% Returning block of 6 for bucket 98 Sorting block of length 13 for bucket 100 (Using difference cover) Getting block 101 of 205 Reserving size (36) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 101: 10% bucket 101: 20% bucket 101: 30% bucket 101: 40% bucket 101: 50% bucket 101: 60% bucket 101: 70% bucket 101: 80% bucket 101: 90% bucket 101: 100% Sorting block of length 29 for bucket 101 (Using difference cover) Getting block 102 of 205 Reserving size (36) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 102: 10% bucket 102: 20% bucket 102: 30% bucket 102: 40% Sorting block time: 00:00:00 bucket 102: 50% Returning block of 42 for bucket 99 bucket 102: 60% bucket 102: 70% bucket 102: 80% bucket 102: 90% bucket 102: 100% Sorting block of length 21 for bucket 102 (Using difference cover) Getting block 103 of 205 Reserving size (36) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: bucket 103: 10% bucket 103: 20% bucket 103: 30% bucket 103: 40% bucket 103: 50% Sorting block time: 00:00:00 Returning block of 14 for bucket 100 bucket 103: 60% bucket 103: 70% bucket 103: 80% Getting block 104 of 205 bucket 103: 90% Reserving size (36) for bucket 104 bucket 103: 100% Calculating Z arrays for bucket 104 Sorting block of length 29 for bucket 103 (Using difference cover) Entering block accumulator loop for bucket 104: bucket 104: 10% bucket 104: 20% bucket 104: 30% bucket 104: 40% bucket 104: 50% bucket 104: 60% bucket 104: 70% Sorting block time: 00:00:00 Returning block of 30 for bucket 101 bucket 104: 80% bucket 104: 90% bucket 104: 100% Sorting block of length 12 for bucket 104 (Using difference cover) Getting block 105 of 205 Reserving size (36) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 105: 10% bucket 105: 20% bucket 105: 30% bucket 105: 40% bucket 105: 50% bucket 105: 60% bucket 105: 70% bucket 105: 80% bucket 105: 90% Sorting block time: 00:00:00 Returning block of 22 for bucket 102 bucket 105: 100% Sorting block of length 30 for bucket 105 (Using difference cover) Getting block 106 of 205 Reserving size (36) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 106: 10% bucket 106: 20% bucket 106: 30% bucket 106: 40% bucket 106: 50% bucket 106: 60% bucket 106: 70% Sorting block time: 00:00:00 Returning block of 30 for bucket 103 bucket 106: 80% bucket 106: 90% Getting block 107 of 205 bucket 106: 100% Reserving size (36) for bucket 107 Sorting block of length 14 for bucket 106 (Using difference cover) Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 107: 10% bucket 107: 20% bucket 107: 30% bucket 107: 40% bucket 107: 50% bucket 107: 60% bucket 107: 70% Sorting block time: 00:00:00 Returning block of 13 for bucket 104 bucket 107: 80% bucket 107: 90% bucket 107: 100% Sorting block of length 28 for bucket 107 (Using difference cover) Getting block 108 of 205 Reserving size (36) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 108: 10% bucket 108: 20% bucket 108: 30% bucket 108: 40% bucket 108: 50% bucket 108: 60% bucket 108: 70% Sorting block time: 00:00:00 Returning block of 31 for bucket 105 bucket 108: 80% bucket 108: 90% bucket 108: 100% Sorting block of length 32 for bucket 108 (Using difference cover) Getting block 109 of 205 Reserving size (36) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 109: 10% bucket 109: 20% bucket 109: 30% bucket 109: 40% bucket 109: 50% bucket 109: 60% bucket 109: 70% bucket 109: 80% bucket 109: 90% bucket 109: 100% Sorting block of length 11 for bucket 109 Sorting block time: 00:00:00 (Using difference cover) Returning block of 15 for bucket 106 Getting block 110 of 205 Reserving size (36) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 110: 10% bucket 110: 20% bucket 110: 30% bucket 110: 40% bucket 110: 50% bucket 110: 60% bucket 110: 70% bucket 110: 80% bucket 110: 90% bucket 110: 100% Getting block 111 of 205 Sorting block of length 25 for bucket 110 (Using difference cover) Reserving size (36) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: bucket 111: 10% bucket 111: 20% bucket 111: 30% bucket 111: 40% bucket 111: 50% bucket 111: 60% bucket 111: 70% bucket 111: 80% bucket 111: 90% Getting block 112 of 205 bucket 111: 100% Reserving size (36) for bucket 112 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block of length 20 for bucket 111 (Using difference cover) Returning block of 29 for bucket 107 Calculating Z arrays for bucket 112 Returning block of 33 for bucket 108 Entering block accumulator loop for bucket 112: bucket 112: 10% bucket 112: 20% bucket 112: 30% bucket 112: 40% bucket 112: 50% bucket 112: 60% bucket 112: 70% bucket 112: 80% bucket 112: 90% Getting block 113 of 205 bucket 112: 100% Reserving size (36) for bucket 113 Sorting block of length 27 for bucket 112 (Using difference cover) Calculating Z arrays for bucket 113 Sorting block time: 00:00:00 Returning block of 12 for bucket 109 Entering block accumulator loop for bucket 113: bucket 113: 10% bucket 113: 20% bucket 113: 30% bucket 113: 40% bucket 113: 50% bucket 113: 60% bucket 113: 70% bucket 113: 80% Getting block 114 of 205 bucket 113: 90% Reserving size (36) for bucket 114 bucket 113: 100% Calculating Z arrays for bucket 114 Sorting block of length 29 for bucket 113 (Using difference cover) Sorting block time: 00:00:00 Returning block of 26 for bucket 110 Entering block accumulator loop for bucket 114: bucket 114: 10% bucket 114: 20% bucket 114: 30% bucket 114: 40% bucket 114: 50% bucket 114: 60% bucket 114: 70% bucket 114: 80% Getting block 115 of 205 bucket 114: 90% Reserving size (36) for bucket 115 bucket 114: 100% Calculating Z arrays for bucket 115 Sorting block of length 28 for bucket 114 (Using difference cover) Entering block accumulator loop for bucket 115: Sorting block time: 00:00:00 Returning block of 21 for bucket 111 bucket 115: 10% bucket 115: 20% bucket 115: 30% bucket 115: 40% bucket 115: 50% bucket 115: 60% Getting block 116 of 205 bucket 115: 70% Reserving size (36) for bucket 116 bucket 115: 80% Calculating Z arrays for bucket 116 bucket 115: 90% bucket 115: 100% Sorting block of length 27 for bucket 115 (Using difference cover) Entering block accumulator loop for bucket 116: bucket 116: 10% bucket 116: 20% bucket 116: 30% bucket 116: 40% bucket 116: 50% bucket 116: 60% bucket 116: 70% bucket 116: 80% bucket 116: 90% Getting block 117 of 205 bucket 116: 100% Reserving size (36) for bucket 117 Sorting block of length 29 for bucket 116 (Using difference cover) Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: bucket 117: 10% bucket 117: 20% bucket 117: 30% bucket 117: 40% bucket 117: 50% Sorting block time: 00:00:00 Returning block of 28 for bucket 112 bucket 117: 60% bucket 117: 70% bucket 117: 80% bucket 117: 90% bucket 117: 100% Sorting block of length 14 for bucket 117 (Using difference cover) Getting block 118 of 205 Reserving size (36) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: bucket 118: 10% bucket 118: 20% bucket 118: 30% bucket 118: 40% bucket 118: 50% bucket 118: 60% Sorting block time: 00:00:00 Returning block of 30 for bucket 113 bucket 118: 70% bucket 118: 80% bucket 118: 90% bucket 118: 100% Sorting block of length 31 for bucket 118 (Using difference cover) Getting block 119 of 205 Reserving size (36) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: bucket 119: 10% bucket 119: 20% bucket 119: 30% bucket 119: 40% bucket 119: 50% bucket 119: 60% bucket 119: 70% bucket 119: 80% bucket 119: 90% bucket 119: 100% Sorting block of length 20 for bucket 119 (Using difference cover) Sorting block time: 00:00:00 Returning block of 29 for bucket 114 Getting block 120 of 205 Reserving size (36) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 120: 10% bucket 120: 20% bucket 120: 30% bucket 120: 40% bucket 120: 50% bucket 120: 60% bucket 120: 70% bucket 120: 80% Sorting block time: 00:00:00 Returning block of 28 for bucket 115 bucket 120: 90% bucket 120: 100% Sorting block time: 00:00:00 Sorting block of length 28 for bucket 120 (Using difference cover) Getting block 121 of 205 Returning block of 30 for bucket 116 Reserving size (36) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 121: 10% bucket 121: 20% bucket 121: 30% bucket 121: 40% bucket 121: 50% bucket 121: 60% bucket 121: 70% bucket 121: 80% Sorting block time: 00:00:00 Getting block 122 of 205 Returning block of 32 for bucket 118 bucket 121: 90% Sorting block time: 00:00:00 Reserving size (36) for bucket 122 Returning block of 15 for bucket 117 bucket 121: 100% Calculating Z arrays for bucket 122 Sorting block of length 27 for bucket 121 (Using difference cover) Entering block accumulator loop for bucket 122: bucket 122: 10% bucket 122: 20% bucket 122: 30% bucket 122: 40% bucket 122: 50% bucket 122: 60% bucket 122: 70% Sorting block time: 00:00:00 Returning block of 21 for bucket 119 bucket 122: 80% bucket 122: 90% Getting block 123 of 205 bucket 122: 100% Reserving size (36) for bucket 123 Sorting block of length 34 for bucket 122 (Using difference cover) Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 123: 10% bucket 123: 20% bucket 123: 30% bucket 123: 40% bucket 123: 50% bucket 123: 60% bucket 123: 70% bucket 123: 80% Sorting block time: 00:00:00 bucket 123: 90% Returning block of 29 for bucket 120 bucket 123: 100% Sorting block of length 35 for bucket 123 (Using difference cover) Getting block 124 of 205 Reserving size (36) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 124: 10% bucket 124: 20% bucket 124: 30% bucket 124: 40% bucket 124: 50% bucket 124: 60% bucket 124: 70% bucket 124: 80% bucket 124: 90% Sorting block time: 00:00:00 Returning block of 28 for bucket 121 bucket 124: 100% Getting block 125 of 205 Sorting block of length 23 for bucket 124 (Using difference cover) Reserving size (36) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: bucket 125: 10% bucket 125: 20% bucket 125: 30% bucket 125: 40% bucket 125: 50% bucket 125: 60% bucket 125: 70% bucket 125: 80% bucket 125: 90% bucket 125: 100% Sorting block of length 24 for bucket 125 (Using difference cover) Sorting block time: 00:00:00 Returning block of 35 for bucket 122 Getting block 126 of 205 Reserving size (36) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: bucket 126: 10% bucket 126: 20% bucket 126: 30% bucket 126: 40% bucket 126: 50% bucket 126: 60% bucket 126: 70% bucket 126: 80% Getting block 127 of 205 bucket 126: 90% Reserving size (36) for bucket 127 bucket 126: 100% Calculating Z arrays for bucket 127 Sorting block of length 12 for bucket 126 (Using difference cover) Entering block accumulator loop for bucket 127: bucket 127: 10% bucket 127: 20% bucket 127: 30% bucket 127: 40% bucket 127: 50% bucket 127: 60% bucket 127: 70% Getting block 128 of 205 bucket 127: 80% Reserving size (36) for bucket 128 bucket 127: 90% Calculating Z arrays for bucket 128 bucket 127: 100% Sorting block time: 00:00:00 Sorting block of length 23 for bucket 127 Sorting block time: 00:00:00 (Using difference cover) Returning block of 24 for bucket 124 Entering block accumulator loop for bucket 128: Returning block of 36 for bucket 123 bucket 128: 10% bucket 128: 20% bucket 128: 30% bucket 128: 40% bucket 128: 50% bucket 128: 60% Getting block 129 of 205 bucket 128: 70% Reserving size (36) for bucket 129 bucket 128: 80% Calculating Z arrays for bucket 129 bucket 128: 90% bucket 128: 100% Sorting block of length 34 for bucket 128 (Using difference cover) Entering block accumulator loop for bucket 129: Sorting block time: 00:00:00 Returning block of 25 for bucket 125 bucket 129: 10% bucket 129: 20% bucket 129: 30% bucket 129: 40% bucket 129: 50% bucket 129: 60% bucket 129: 70% bucket 129: 80% Getting block 130 of 205 bucket 129: 90% Reserving size (36) for bucket 130 bucket 129: 100% Calculating Z arrays for bucket 130 Sorting block of length 31 for bucket 129 (Using difference cover) Entering block accumulator loop for bucket 130: Sorting block time: 00:00:00 Returning block of 13 for bucket 126 bucket 130: 10% bucket 130: 20% bucket 130: 30% bucket 130: 40% bucket 130: 50% bucket 130: 60% bucket 130: 70% bucket 130: 80% bucket 130: 90% bucket 130: 100% Sorting block of length 31 for bucket 130 (Using difference cover) Sorting block time: 00:00:00 Returning block of 24 for bucket 127 Getting block 131 of 205 Reserving size (36) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 131: 10% bucket 131: 20% bucket 131: 30% bucket 131: 40% bucket 131: 50% bucket 131: 60% bucket 131: 70% bucket 131: 80% bucket 131: 90% bucket 131: 100% Sorting block of length 26 for bucket 131 (Using difference cover) Getting block 132 of 205 Reserving size (36) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 132: 10% bucket 132: 20% bucket 132: 30% bucket 132: 40% bucket 132: 50% bucket 132: 60% bucket 132: 70% bucket 132: 80% bucket 132: 90% bucket 132: 100% Sorting block of length 13 for bucket 132 Sorting block time: 00:00:00 (Using difference cover) Returning block of 35 for bucket 128 Getting block 133 of 205 Reserving size (36) for bucket 133 Calculating Z arrays for bucket 133 Sorting block time: 00:00:00 Returning block of 32 for bucket 129 Entering block accumulator loop for bucket 133: bucket 133: 10% bucket 133: 20% bucket 133: 30% bucket 133: 40% bucket 133: 50% bucket 133: 60% bucket 133: 70% bucket 133: 80% bucket 133: 90% bucket 133: 100% Sorting block of length 30 for bucket 133 (Using difference cover) Getting block 134 of 205 Reserving size (36) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: Sorting block time: 00:00:00 bucket 134: 10% Returning block of 32 for bucket 130 bucket 134: 20% Getting block 135 of 205 bucket 134: 30% Reserving size (36) for bucket 135 bucket 134: 40% Calculating Z arrays for bucket 135 bucket 134: 50% bucket 134: 60% Entering block accumulator loop for bucket 135: bucket 134: 70% bucket 134: 80% bucket 135: 10% bucket 134: 90% bucket 135: 20% bucket 134: 100% Sorting block of length 32 for bucket 134 (Using difference cover) bucket 135: 30% bucket 135: 40% bucket 135: 50% Sorting block time: 00:00:00 bucket 135: 60% Returning block of 27 for bucket 131 bucket 135: 70% Getting block 136 of 205 Sorting block time: 00:00:00 Returning block of 14 for bucket 132 bucket 135: 80% Reserving size (36) for bucket 136 bucket 135: 90% Calculating Z arrays for bucket 136 bucket 135: 100% Sorting block of length 35 for bucket 135 (Using difference cover) Entering block accumulator loop for bucket 136: bucket 136: 10% bucket 136: 20% bucket 136: 30% bucket 136: 40% bucket 136: 50% bucket 136: 60% bucket 136: 70% bucket 136: 80% bucket 136: 90% Getting block 137 of 205 bucket 136: 100% Reserving size (36) for bucket 137 Sorting block of length 33 for bucket 136 (Using difference cover) Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 137: 10% bucket 137: 20% bucket 137: 30% bucket 137: 40% bucket 137: 50% bucket 137: 60% bucket 137: 70% bucket 137: 80% bucket 137: 90% bucket 137: 100% Sorting block of length 32 for bucket 137 (Using difference cover) Getting block 138 of 205 Reserving size (36) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 138: 10% bucket 138: 20% bucket 138: 30% Sorting block time: 00:00:00 Returning block of 31 for bucket 133 bucket 138: 40% bucket 138: 50% bucket 138: 60% bucket 138: 70% bucket 138: 80% Getting block 139 of 205 bucket 138: 90% Reserving size (36) for bucket 139 bucket 138: 100% Calculating Z arrays for bucket 139 Sorting block of length 13 for bucket 138 (Using difference cover) Entering block accumulator loop for bucket 139: bucket 139: 10% bucket 139: 20% bucket 139: 30% bucket 139: 40% bucket 139: 50% bucket 139: 60% bucket 139: 70% bucket 139: 80% bucket 139: 90% bucket 139: 100% Sorting block of length 29 for bucket 139 (Using difference cover) Getting block 140 of 205 Reserving size (36) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: bucket 140: 10% bucket 140: 20% bucket 140: 30% bucket 140: 40% bucket 140: 50% Sorting block time: 00:00:00 bucket 140: 60% Returning block of 33 for bucket 134 bucket 140: 70% bucket 140: 80% bucket 140: 90% bucket 140: 100% Sorting block of length 30 for bucket 140 (Using difference cover) Getting block 141 of 205 Reserving size (36) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 141: 10% bucket 141: 20% bucket 141: 30% bucket 141: 40% bucket 141: 50% bucket 141: 60% bucket 141: 70% bucket 141: 80% bucket 141: 90% bucket 141: 100% Sorting block of length 28 for bucket 141 (Using difference cover) Getting block 142 of 205 Reserving size (36) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 142: 10% bucket 142: 20% bucket 142: 30% bucket 142: 40% bucket 142: 50% bucket 142: 60% bucket 142: 70% bucket 142: 80% bucket 142: 90% bucket 142: 100% Sorting block of length 27 for bucket 142 (Using difference cover) Getting block 143 of 205 Reserving size (36) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 33 for bucket 137 Returning block of 36 for bucket 135 bucket 143: 10% bucket 143: 20% bucket 143: 30% bucket 143: 40% bucket 143: 50% bucket 143: 60% Getting block 144 of 205 bucket 143: 70% Reserving size (36) for bucket 144 bucket 143: 80% Calculating Z arrays for bucket 144 bucket 143: 90% bucket 143: 100% Sorting block of length 20 for bucket 143 (Using difference cover) Entering block accumulator loop for bucket 144: bucket 144: 10% bucket 144: 20% bucket 144: 30% bucket 144: 40% bucket 144: 50% bucket 144: 60% bucket 144: 70% Getting block 145 of 205 bucket 144: 80% Reserving size (36) for bucket 145 bucket 144: 90% Calculating Z arrays for bucket 145 bucket 144: 100% Sorting block of length 30 for bucket 144 (Using difference cover) Entering block accumulator loop for bucket 145: bucket 145: 10% bucket 145: 20% bucket 145: 30% bucket 145: 40% Sorting block time: 00:00:00 Returning block of 34 for bucket 136 bucket 145: 50% bucket 145: 60% bucket 145: 70% bucket 145: 80% bucket 145: 90% bucket 145: 100% Sorting block of length 7 for bucket 145 (Using difference cover) Getting block 146 of 205 Reserving size (36) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: bucket 146: 10% bucket 146: 20% bucket 146: 30% bucket 146: 40% bucket 146: 50% bucket 146: 60% bucket 146: 70% Sorting block time: 00:00:00 Returning block of 14 for bucket 138 bucket 146: 80% bucket 146: 90% bucket 146: 100% Sorting block of length 32 for bucket 146 (Using difference cover) Sorting block time: 00:00:00 Returning block of 30 for bucket 139 Sorting block time: 00:00:00 Returning block of 31 for bucket 140 Getting block 147 of 205 Reserving size (36) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: Sorting block time: 00:00:00 Returning block of 28 for bucket 142 bucket 147: 10% Sorting block time: 00:00:00 Returning block of 29 for bucket 141 bucket 147: 20% bucket 147: 30% bucket 147: 40% bucket 147: 50% bucket 147: 60% bucket 147: 70% bucket 147: 80% bucket 147: 90% bucket 147: 100% Sorting block of length 31 for bucket 147 (Using difference cover) Getting block 148 of 205 Reserving size (36) for bucket 148 Calculating Z arrays for bucket 148 Sorting block time: 00:00:00 Returning block of 31 for bucket 144 Entering block accumulator loop for bucket 148: Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 21 for bucket 143 Returning block of 8 for bucket 145 bucket 148: 10% bucket 148: 20% bucket 148: 30% bucket 148: 40% bucket 148: 50% bucket 148: 60% bucket 148: 70% bucket 148: 80% bucket 148: 90% Getting block 149 of 205 bucket 148: 100% Reserving size (36) for bucket 149 Sorting block of length 11 for bucket 148 (Using difference cover) Calculating Z arrays for bucket 149 Sorting block time: 00:00:00 Returning block of 33 for bucket 146 Entering block accumulator loop for bucket 149: bucket 149: 10% bucket 149: 20% bucket 149: 30% bucket 149: 40% bucket 149: 50% bucket 149: 60% bucket 149: 70% bucket 149: 80% Getting block 150 of 205 bucket 149: 90% Reserving size (36) for bucket 150 bucket 149: 100% Calculating Z arrays for bucket 150 Sorting block time: 00:00:00 Sorting block of length 24 for bucket 149 (Using difference cover) Returning block of 32 for bucket 147 Entering block accumulator loop for bucket 150: Sorting block time: 00:00:00 Returning block of 12 for bucket 148 bucket 150: 10% bucket 150: 20% bucket 150: 30% bucket 150: 40% bucket 150: 50% bucket 150: 60% bucket 150: 70% bucket 150: 80% bucket 150: 90% bucket 150: 100% Sorting block time: 00:00:00 Sorting block of length 31 for bucket 150 (Using difference cover) Returning block of 25 for bucket 149 Getting block 151 of 205 Reserving size (36) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 151: 10% bucket 151: 20% bucket 151: 30% bucket 151: 40% bucket 151: 50% bucket 151: 60% bucket 151: 70% bucket 151: 80% bucket 151: 90% Sorting block time: 00:00:00 Returning block of 32 for bucket 150 bucket 151: 100% Sorting block of length 31 for bucket 151 (Using difference cover) Getting block 152 of 205 Reserving size (36) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: bucket 152: 10% bucket 152: 20% bucket 152: 30% bucket 152: 40% bucket 152: 50% bucket 152: 60% bucket 152: 70% bucket 152: 80% bucket 152: 90% bucket 152: 100% Sorting block of length 33 for bucket 152 (Using difference cover) Getting block 153 of 205 Reserving size (36) for bucket 153 Calculating Z arrays for bucket 153 Sorting block time: 00:00:00 Returning block of 32 for bucket 151 Entering block accumulator loop for bucket 153: bucket 153: 10% bucket 153: 20% bucket 153: 30% bucket 153: 40% bucket 153: 50% bucket 153: 60% bucket 153: 70% bucket 153: 80% bucket 153: 90% bucket 153: 100% Sorting block of length 21 for bucket 153 (Using difference cover) Getting block 154 of 205 Reserving size (36) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 154: 10% bucket 154: 20% bucket 154: 30% bucket 154: 40% bucket 154: 50% bucket 154: 60% bucket 154: 70% bucket 154: 80% bucket 154: 90% Getting block 155 of 205 bucket 154: 100% Reserving size (36) for bucket 155 Sorting block of length 27 for bucket 154 (Using difference cover) Calculating Z arrays for bucket 155 Sorting block time: 00:00:00 Returning block of 34 for bucket 152 Entering block accumulator loop for bucket 155: bucket 155: 10% bucket 155: 20% bucket 155: 30% bucket 155: 40% bucket 155: 50% bucket 155: 60% bucket 155: 70% bucket 155: 80% bucket 155: 90% bucket 155: 100% Sorting block of length 34 for bucket 155 (Using difference cover) Getting block 156 of 205 Sorting block time: 00:00:00 Reserving size (36) for bucket 156 Returning block of 22 for bucket 153 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 156: 10% bucket 156: 20% bucket 156: 30% bucket 156: 40% bucket 156: 50% bucket 156: 60% bucket 156: 70% bucket 156: 80% Getting block 157 of 205 bucket 156: 90% Reserving size (36) for bucket 157 Calculating Z arrays for bucket 157 bucket 156: 100% Sorting block time: 00:00:00 Sorting block of length 9 for bucket 156 (Using difference cover) Returning block of 28 for bucket 154 Entering block accumulator loop for bucket 157: Sorting block time: 00:00:00 Returning block of 35 for bucket 155 bucket 157: 10% bucket 157: 20% bucket 157: 30% bucket 157: 40% Getting block 158 of 205 bucket 157: 50% Reserving size (36) for bucket 158 bucket 157: 60% Calculating Z arrays for bucket 158 bucket 157: 70% bucket 157: 80% Entering block accumulator loop for bucket 158: bucket 157: 90% bucket 157: 100% bucket 158: 10% Sorting block of length 34 for bucket 157 (Using difference cover) bucket 158: 20% bucket 158: 30% Sorting block time: 00:00:00 Returning block of 10 for bucket 156 bucket 158: 40% bucket 158: 50% bucket 158: 60% bucket 158: 70% bucket 158: 80% Getting block 159 of 205 bucket 158: 90% Reserving size (36) for bucket 159 bucket 158: 100% Calculating Z arrays for bucket 159 Sorting block of length 33 for bucket 158 (Using difference cover) Entering block accumulator loop for bucket 159: bucket 159: 10% bucket 159: 20% bucket 159: 30% bucket 159: 40% bucket 159: 50% bucket 159: 60% bucket 159: 70% bucket 159: 80% bucket 159: 90% bucket 159: 100% Sorting block of length 31 for bucket 159 (Using difference cover) Sorting block time: 00:00:00 Returning block of 35 for bucket 157 Getting block 160 of 205 Reserving size (36) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 160: 10% bucket 160: 20% bucket 160: 30% bucket 160: 40% Getting block 161 of 205 bucket 160: 50% Reserving size (36) for bucket 161 bucket 160: 60% Calculating Z arrays for bucket 161 bucket 160: 70% Sorting block time: 00:00:00 Returning block of 34 for bucket 158 bucket 160: 80% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 161: Returning block of 32 for bucket 159 bucket 160: 90% bucket 160: 100% bucket 161: 10% Sorting block of length 34 for bucket 160 (Using difference cover) bucket 161: 20% Getting block 162 of 205 bucket 161: 30% Reserving size (36) for bucket 162 Calculating Z arrays for bucket 162 bucket 161: 40% bucket 161: 50% Entering block accumulator loop for bucket 162: bucket 161: 60% bucket 161: 70% bucket 162: 10% bucket 161: 80% bucket 162: 20% bucket 161: 90% bucket 162: 30% bucket 161: 100% Sorting block of length 6 for bucket 161 (Using difference cover) bucket 162: 40% bucket 162: 50% bucket 162: 60% bucket 162: 70% bucket 162: 80% bucket 162: 90% Getting block 163 of 205 bucket 162: 100% Reserving size (36) for bucket 163 Sorting block of length 32 for bucket 162 (Using difference cover) Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: bucket 163: 10% bucket 163: 20% bucket 163: 30% bucket 163: 40% bucket 163: 50% bucket 163: 60% bucket 163: 70% Sorting block time: 00:00:00 bucket 163: 80% Returning block of 35 for bucket 160 Sorting block time: 00:00:00 bucket 163: 90% Returning block of 7 for bucket 161 Getting block 164 of 205 bucket 163: 100% Reserving size (36) for bucket 164 Sorting block of length 31 for bucket 163 (Using difference cover) Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 164: 10% bucket 164: 20% bucket 164: 30% bucket 164: 40% bucket 164: 50% bucket 164: 60% bucket 164: 70% bucket 164: 80% bucket 164: 90% bucket 164: 100% Sorting block of length 27 for bucket 164 (Using difference cover) Getting block 165 of 205 Reserving size (36) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 165: 10% bucket 165: 20% bucket 165: 30% bucket 165: 40% bucket 165: 50% bucket 165: 60% bucket 165: 70% bucket 165: 80% bucket 165: 90% Sorting block time: 00:00:00 Returning block of 33 for bucket 162 bucket 165: 100% Sorting block of length 29 for bucket 165 (Using difference cover) Getting block 166 of 205 Reserving size (36) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 166: 10% bucket 166: 20% bucket 166: 30% bucket 166: 40% bucket 166: 50% bucket 166: 60% bucket 166: 70% bucket 166: 80% Getting block 167 of 205 Sorting block time: 00:00:00 bucket 166: 90% Reserving size (36) for bucket 167 Returning block of 32 for bucket 163 bucket 166: 100% Calculating Z arrays for bucket 167 Sorting block of length 30 for bucket 166 (Using difference cover) Entering block accumulator loop for bucket 167: bucket 167: 10% bucket 167: 20% bucket 167: 30% bucket 167: 40% bucket 167: 50% Getting block 168 of 205 bucket 167: 60% Reserving size (36) for bucket 168 bucket 167: 70% Calculating Z arrays for bucket 168 bucket 167: 80% bucket 167: 90% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 168: Returning block of 28 for bucket 164 bucket 167: 100% Sorting block of length 22 for bucket 167 (Using difference cover) bucket 168: 10% bucket 168: 20% bucket 168: 30% bucket 168: 40% bucket 168: 50% Getting block 169 of 205 bucket 168: 60% Reserving size (36) for bucket 169 bucket 168: 70% Calculating Z arrays for bucket 169 bucket 168: 80% bucket 168: 90% Entering block accumulator loop for bucket 169: bucket 168: 100% Sorting block of length 14 for bucket 168 (Using difference cover) bucket 169: 10% Sorting block time: 00:00:00 Returning block of 30 for bucket 165 bucket 169: 20% bucket 169: 30% bucket 169: 40% bucket 169: 50% bucket 169: 60% bucket 169: 70% bucket 169: 80% bucket 169: 90% bucket 169: 100% Sorting block of length 23 for bucket 169 (Using difference cover) Getting block 170 of 205 Reserving size (36) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 170: 10% bucket 170: 20% Sorting block time: 00:00:00 bucket 170: 30% Returning block of 31 for bucket 166 bucket 170: 40% bucket 170: 50% bucket 170: 60% bucket 170: 70% bucket 170: 80% Getting block 171 of 205 bucket 170: 90% Reserving size (36) for bucket 171 bucket 170: 100% Calculating Z arrays for bucket 171 Sorting block of length 32 for bucket 170 (Using difference cover) Entering block accumulator loop for bucket 171: bucket 171: 10% bucket 171: 20% bucket 171: 30% bucket 171: 40% bucket 171: 50% bucket 171: 60% bucket 171: 70% Sorting block time: 00:00:00 Returning block of 15 for bucket 168 bucket 171: 80% Sorting block time: 00:00:00 Getting block 172 of 205 Returning block of 23 for bucket 167 bucket 171: 90% Reserving size (36) for bucket 172 bucket 171: 100% Calculating Z arrays for bucket 172 Sorting block of length 18 for bucket 171 (Using difference cover) Entering block accumulator loop for bucket 172: bucket 172: 10% bucket 172: 20% bucket 172: 30% bucket 172: 40% bucket 172: 50% bucket 172: 60% bucket 172: 70% bucket 172: 80% Getting block 173 of 205 bucket 172: 90% Sorting block time: 00:00:00 Reserving size (36) for bucket 173 Returning block of 24 for bucket 169 bucket 172: 100% Calculating Z arrays for bucket 173 Sorting block of length 25 for bucket 172 (Using difference cover) Entering block accumulator loop for bucket 173: bucket 173: 10% bucket 173: 20% bucket 173: 30% bucket 173: 40% bucket 173: 50% bucket 173: 60% bucket 173: 70% bucket 173: 80% bucket 173: 90% bucket 173: 100% Sorting block of length 30 for bucket 173 (Using difference cover) Getting block 174 of 205 Reserving size (36) for bucket 174 Calculating Z arrays for bucket 174 Sorting block time: 00:00:00 Returning block of 33 for bucket 170 Entering block accumulator loop for bucket 174: bucket 174: 10% bucket 174: 20% bucket 174: 30% bucket 174: 40% bucket 174: 50% bucket 174: 60% bucket 174: 70% bucket 174: 80% bucket 174: 90% bucket 174: 100% Sorting block of length 15 for bucket 174 (Using difference cover) Getting block 175 of 205 Reserving size (36) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 175: 10% bucket 175: 20% bucket 175: 30% bucket 175: 40% bucket 175: 50% bucket 175: 60% bucket 175: 70% bucket 175: 80% bucket 175: 90% bucket 175: 100% Sorting block of length 31 for bucket 175 (Using difference cover) Getting block 176 of 205 Reserving size (36) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: bucket 176: 10% bucket 176: 20% bucket 176: 30% bucket 176: 40% bucket 176: 50% bucket 176: 60% bucket 176: 70% bucket 176: 80% bucket 176: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 19 for bucket 171 Returning block of 26 for bucket 172 Sorting block time: 00:00:00 bucket 176: 100% Returning block of 31 for bucket 173 Sorting block of length 25 for bucket 176 (Using difference cover) Getting block 177 of 205 Reserving size (36) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 177: 10% bucket 177: 20% bucket 177: 30% bucket 177: 40% bucket 177: 50% bucket 177: 60% bucket 177: 70% Sorting block time: 00:00:00 Returning block of 16 for bucket 174 bucket 177: 80% bucket 177: 90% bucket 177: 100% Sorting block of length 31 for bucket 177 (Using difference cover) Getting block 178 of 205 Reserving size (36) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: bucket 178: 10% bucket 178: 20% bucket 178: 30% bucket 178: 40% bucket 178: 50% Sorting block time: 00:00:00 Returning block of 32 for bucket 175 bucket 178: 60% bucket 178: 70% bucket 178: 80% bucket 178: 90% bucket 178: 100% Sorting block of length 23 for bucket 178 (Using difference cover) Getting block 179 of 205 Reserving size (36) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 179: 10% bucket 179: 20% bucket 179: 30% bucket 179: 40% bucket 179: 50% Sorting block time: 00:00:00 Returning block of 26 for bucket 176 bucket 179: 60% bucket 179: 70% bucket 179: 80% bucket 179: 90% bucket 179: 100% Sorting block of length 30 for bucket 179 (Using difference cover) Getting block 180 of 205 Reserving size (36) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 180: 10% bucket 180: 20% bucket 180: 30% bucket 180: 40% bucket 180: 50% Sorting block time: 00:00:00 Returning block of 32 for bucket 177 bucket 180: 60% bucket 180: 70% bucket 180: 80% bucket 180: 90% bucket 180: 100% Sorting block of length 27 for bucket 180 (Using difference cover) Sorting block time: 00:00:00 Getting block 181 of 205 Returning block of 24 for bucket 178 Reserving size (36) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: bucket 181: 10% bucket 181: 20% bucket 181: 30% bucket 181: 40% bucket 181: 50% bucket 181: 60% Getting block 182 of 205 bucket 181: 70% Reserving size (36) for bucket 182 bucket 181: 80% Calculating Z arrays for bucket 182 bucket 181: 90% bucket 181: 100% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 182: Sorting block of length 32 for bucket 181 (Using difference cover) Returning block of 31 for bucket 179 Sorting block time: 00:00:00 Returning block of 28 for bucket 180 bucket 182: 10% bucket 182: 20% bucket 182: 30% bucket 182: 40% bucket 182: 50% bucket 182: 60% bucket 182: 70% bucket 182: 80% bucket 182: 90% bucket 182: 100% Sorting block of length 22 for bucket 182 (Using difference cover) Getting block 183 of 205 Reserving size (36) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: bucket 183: 10% bucket 183: 20% bucket 183: 30% bucket 183: 40% bucket 183: 50% bucket 183: 60% bucket 183: 70% bucket 183: 80% Getting block 184 of 205 bucket 183: 90% Reserving size (36) for bucket 184 bucket 183: 100% Calculating Z arrays for bucket 184 Sorting block of length 33 for bucket 183 Sorting block time: 00:00:00 (Using difference cover) Entering block accumulator loop for bucket 184: Returning block of 33 for bucket 181 Sorting block time: 00:00:00 Returning block of 23 for bucket 182 bucket 184: 10% bucket 184: 20% bucket 184: 30% bucket 184: 40% bucket 184: 50% bucket 184: 60% bucket 184: 70% Getting block 185 of 205 bucket 184: 80% Reserving size (36) for bucket 185 bucket 184: 90% Calculating Z arrays for bucket 185 bucket 184: 100% Sorting block of length 21 for bucket 184 (Using difference cover) Entering block accumulator loop for bucket 185: bucket 185: 10% bucket 185: 20% bucket 185: 30% bucket 185: 40% bucket 185: 50% bucket 185: 60% bucket 185: 70% bucket 185: 80% Getting block 186 of 205 bucket 185: 90% Reserving size (36) for bucket 186 bucket 185: 100% Calculating Z arrays for bucket 186 Sorting block of length 20 for bucket 185 (Using difference cover) Entering block accumulator loop for bucket 186: bucket 186: 10% bucket 186: 20% bucket 186: 30% bucket 186: 40% Sorting block time: 00:00:00 Returning block of 34 for bucket 183 bucket 186: 50% bucket 186: 60% bucket 186: 70% bucket 186: 80% bucket 186: 90% bucket 186: 100% Sorting block of length 31 for bucket 186 (Using difference cover) Getting block 187 of 205 Reserving size (36) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: bucket 187: 10% bucket 187: 20% bucket 187: 30% Sorting block time: 00:00:00 Returning block of 22 for bucket 184 bucket 187: 40% bucket 187: 50% bucket 187: 60% bucket 187: 70% bucket 187: 80% bucket 187: 90% Getting block 188 of 205 bucket 187: 100% Reserving size (36) for bucket 188 Sorting block of length 20 for bucket 187 (Using difference cover) Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 188: 10% bucket 188: 20% Sorting block time: 00:00:00 Returning block of 21 for bucket 185 bucket 188: 30% bucket 188: 40% bucket 188: 50% bucket 188: 60% bucket 188: 70% bucket 188: 80% bucket 188: 90% bucket 188: 100% Sorting block of length 18 for bucket 188 (Using difference cover) Getting block 189 of 205 Reserving size (36) for bucket 189 Calculating Z arrays for bucket 189 Sorting block time: 00:00:00 Returning block of 32 for bucket 186 Entering block accumulator loop for bucket 189: bucket 189: 10% bucket 189: 20% bucket 189: 30% bucket 189: 40% bucket 189: 50% bucket 189: 60% bucket 189: 70% bucket 189: 80% bucket 189: 90% bucket 189: 100% Sorting block of length 33 for bucket 189 (Using difference cover) Getting block 190 of 205 Reserving size (36) for bucket 190 Calculating Z arrays for bucket 190 Sorting block time: 00:00:00 Returning block of 21 for bucket 187 Entering block accumulator loop for bucket 190: bucket 190: 10% bucket 190: 20% bucket 190: 30% bucket 190: 40% bucket 190: 50% bucket 190: 60% bucket 190: 70% Getting block 191 of 205 bucket 190: 80% Reserving size (36) for bucket 191 bucket 190: 90% Calculating Z arrays for bucket 191 bucket 190: 100% Sorting block of length 34 for bucket 190 (Using difference cover) Entering block accumulator loop for bucket 191: bucket 191: 10% Sorting block time: 00:00:00 Returning block of 19 for bucket 188 bucket 191: 20% bucket 191: 30% bucket 191: 40% bucket 191: 50% bucket 191: 60% bucket 191: 70% bucket 191: 80% bucket 191: 90% bucket 191: 100% Sorting block of length 35 for bucket 191 (Using difference cover) Getting block 192 of 205 Sorting block time: 00:00:00 Reserving size (36) for bucket 192 Returning block of 34 for bucket 189 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 192: 10% bucket 192: 20% bucket 192: 30% bucket 192: 40% bucket 192: 50% bucket 192: 60% bucket 192: 70% bucket 192: 80% bucket 192: 90% Getting block 193 of 205 bucket 192: 100% Reserving size (36) for bucket 193 Sorting block of length 25 for bucket 192 (Using difference cover) Calculating Z arrays for bucket 193 Sorting block time: 00:00:00 Returning block of 35 for bucket 190 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 193: Returning block of 36 for bucket 191 bucket 193: 10% bucket 193: 20% bucket 193: 30% bucket 193: 40% bucket 193: 50% Getting block 194 of 205 bucket 193: 60% Reserving size (36) for bucket 194 bucket 193: 70% Calculating Z arrays for bucket 194 bucket 193: 80% bucket 193: 90% Entering block accumulator loop for bucket 194: bucket 193: 100% Sorting block of length 32 for bucket 193 (Using difference cover) bucket 194: 10% bucket 194: 20% Sorting block time: 00:00:00 Returning block of 26 for bucket 192 bucket 194: 30% bucket 194: 40% bucket 194: 50% bucket 194: 60% bucket 194: 70% bucket 194: 80% bucket 194: 90% bucket 194: 100% Sorting block of length 6 for bucket 194 (Using difference cover) Getting block 195 of 205 Reserving size (36) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 195: 10% bucket 195: 20% bucket 195: 30% bucket 195: 40% bucket 195: 50% bucket 195: 60% bucket 195: 70% bucket 195: 80% bucket 195: 90% bucket 195: 100% Sorting block of length 35 for bucket 195 (Using difference cover) Getting block 196 of 205 Reserving size (36) for bucket 196 Calculating Z arrays for bucket 196 Sorting block time: 00:00:00 Returning block of 33 for bucket 193 Entering block accumulator loop for bucket 196: Sorting block time: 00:00:00 Returning block of 7 for bucket 194 bucket 196: 10% bucket 196: 20% bucket 196: 30% bucket 196: 40% bucket 196: 50% bucket 196: 60% bucket 196: 70% bucket 196: 80% bucket 196: 90% Getting block 197 of 205 bucket 196: 100% Reserving size (36) for bucket 197 Sorting block of length 31 for bucket 196 (Using difference cover) Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: bucket 197: 10% bucket 197: 20% bucket 197: 30% bucket 197: 40% bucket 197: 50% bucket 197: 60% bucket 197: 70% bucket 197: 80% bucket 197: 90% Getting block 198 of 205 bucket 197: 100% Reserving size (36) for bucket 198 Sorting block of length 33 for bucket 197 (Using difference cover) Calculating Z arrays for bucket 198 Sorting block time: 00:00:00 Returning block of 36 for bucket 195 Entering block accumulator loop for bucket 198: bucket 198: 10% bucket 198: 20% bucket 198: 30% bucket 198: 40% bucket 198: 50% Getting block 199 of 205 bucket 198: 60% Reserving size (36) for bucket 199 bucket 198: 70% Calculating Z arrays for bucket 199 bucket 198: 80% bucket 198: 90% Entering block accumulator loop for bucket 199: bucket 198: 100% Sorting block of length 5 for bucket 198 (Using difference cover) bucket 199: 10% bucket 199: 20% Sorting block time: 00:00:00 Returning block of 32 for bucket 196 bucket 199: 30% bucket 199: 40% bucket 199: 50% bucket 199: 60% bucket 199: 70% bucket 199: 80% bucket 199: 90% bucket 199: 100% Sorting block of length 35 for bucket 199 (Using difference cover) Getting block 200 of 205 Reserving size (36) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 200: 10% bucket 200: 20% bucket 200: 30% Sorting block time: 00:00:00 Returning block of 34 for bucket 197 bucket 200: 40% bucket 200: 50% Sorting block time: 00:00:00 Returning block of 6 for bucket 198 bucket 200: 60% bucket 200: 70% Getting block 201 of 205 bucket 200: 80% Reserving size (36) for bucket 201 bucket 200: 90% Calculating Z arrays for bucket 201 bucket 200: 100% Sorting block of length 35 for bucket 200 (Using difference cover) Entering block accumulator loop for bucket 201: bucket 201: 10% bucket 201: 20% bucket 201: 30% bucket 201: 40% bucket 201: 50% bucket 201: 60% bucket 201: 70% bucket 201: 80% bucket 201: 90% bucket 201: 100% Sorting block of length 17 for bucket 201 (Using difference cover) Getting block 202 of 205 Reserving size (36) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 202: 10% bucket 202: 20% bucket 202: 30% bucket 202: 40% bucket 202: 50% bucket 202: 60% bucket 202: 70% bucket 202: 80% bucket 202: 90% Sorting block time: 00:00:00 Returning block of 36 for bucket 199 bucket 202: 100% Sorting block of length 32 for bucket 202 (Using difference cover) Getting block 203 of 205 Reserving size (36) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: bucket 203: 10% bucket 203: 20% bucket 203: 30% bucket 203: 40% bucket 203: 50% bucket 203: 60% bucket 203: 70% bucket 203: 80% bucket 203: 90% bucket 203: 100% Sorting block of length 25 for bucket 203 (Using difference cover) Sorting block time: 00:00:00 Getting block 204 of 205 Returning block of 36 for bucket 200 Reserving size (36) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: bucket 204: 10% bucket 204: 20% bucket 204: 30% bucket 204: 40% bucket 204: 50% bucket 204: 60% bucket 204: 70% bucket 204: 80% bucket 204: 90% bucket 204: 100% Sorting block of length 34 for bucket 204 (Using difference cover) Sorting block time: 00:00:00 Getting block 205 of 205 Returning block of 18 for bucket 201 Reserving size (36) for bucket 205 Calculating Z arrays for bucket 205 Entering block accumulator loop for bucket 205: bucket 205: 10% bucket 205: 20% bucket 205: 30% bucket 205: 40% bucket 205: 50% bucket 205: 60% bucket 205: 70% bucket 205: 80% bucket 205: 90% bucket 205: 100% Sorting block of length 7 for bucket 205 (Using difference cover) Sorting block time: 00:00:00 Returning block of 33 for bucket 202 Sorting block time: 00:00:00 Returning block of 35 for bucket 204 Sorting block time: 00:00:00 Returning block of 26 for bucket 203 Sorting block time: 00:00:00 Returning block of 8 for bucket 205 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1291 fchr[G]: 1291 fchr[T]: 2545 fchr[$]: 5386 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4196346 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 1352 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 5386 bwtLen: 5387 sz: 1347 bwtSz: 1347 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 337 offsSz: 1348 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 29 numLines: 29 ebwtTotLen: 1856 ebwtTotSz: 1856 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:01 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 48 Using parameters --bmax 36 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 36 --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 308 sample suffixes Generating random suffixes QSorting 308 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 302 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 36, merged 134; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 21, merged 20; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 7, merged 9; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 4, merged 4; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 25.6683 (target: 35) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 202 Reserving size (36) for bucket 1 Getting block 2 of 202 Getting block 3 of 202 Getting block 4 of 202 Getting block 5 of 202 Getting block 6 of 202 Getting block 7 of 202 Getting block 8 of 202 Getting block 9 of 202 Getting block 10 of 202 Getting block 11 of 202 Calculating Z arrays for bucket 1 Reserving size (36) for bucket 2 Reserving size (36) for bucket 3 Getting block 12 of 202 Getting block 13 of 202 Reserving size (36) for bucket 4 Reserving size (36) for bucket 5 Getting block 14 of 202 Getting block 15 of 202 Reserving size (36) for bucket 6 Reserving size (36) for bucket 7 Reserving size (36) for bucket 8 Getting block 16 of 202 Reserving size (36) for bucket 9 Getting block 17 of 202 Reserving size (36) for bucket 10 Reserving size (36) for bucket 11 Getting block 18 of 202 Getting block 19 of 202 Getting block 20 of 202 Getting block 21 of 202 Getting block 22 of 202 Getting block 23 of 202 Getting block 24 of 202 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 2 Getting block 25 of 202 Getting block 26 of 202 Calculating Z arrays for bucket 3 Reserving size (36) for bucket 12 Reserving size (36) for bucket 13 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Reserving size (36) for bucket 14 Reserving size (36) for bucket 15 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 8 Reserving size (36) for bucket 16 Calculating Z arrays for bucket 9 Reserving size (36) for bucket 17 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 11 Reserving size (36) for bucket 18 Reserving size (36) for bucket 19 Reserving size (36) for bucket 20 Reserving size (36) for bucket 21 Reserving size (36) for bucket 22 Reserving size (36) for bucket 23 Reserving size (36) for bucket 24 Entering block accumulator loop for bucket 2: Reserving size (36) for bucket 25 Reserving size (36) for bucket 26 Calculating Z arrays for bucket 12 Entering block accumulator loop for bucket 3: Calculating Z arrays for bucket 13 Entering block accumulator loop for bucket 4: Calculating Z arrays for bucket 14 Entering block accumulator loop for bucket 5: Calculating Z arrays for bucket 15 Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 8: Calculating Z arrays for bucket 16 Entering block accumulator loop for bucket 9: Calculating Z arrays for bucket 17 Entering block accumulator loop for bucket 10: Calculating Z arrays for bucket 18 Entering block accumulator loop for bucket 11: Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 24 bucket 1: 10% Calculating Z arrays for bucket 25 Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 23: bucket 1: 20% bucket 2: 10% Entering block accumulator loop for bucket 24: bucket 3: 10% Entering block accumulator loop for bucket 25: bucket 4: 10% Entering block accumulator loop for bucket 26: bucket 5: 10% bucket 6: 10% bucket 7: 10% bucket 8: 10% bucket 9: 10% bucket 10: 10% bucket 11: 10% bucket 1: 30% bucket 2: 20% bucket 3: 20% bucket 12: 10% bucket 4: 20% bucket 13: 10% bucket 5: 20% bucket 14: 10% bucket 6: 20% bucket 15: 10% bucket 7: 20% bucket 8: 20% bucket 9: 20% bucket 16: 10% bucket 10: 20% bucket 17: 10% bucket 11: 20% bucket 23: 10% bucket 18: 10% bucket 19: 10% bucket 20: 10% bucket 22: 10% bucket 21: 10% bucket 1: 40% bucket 2: 30% bucket 24: 10% bucket 3: 30% bucket 12: 20% bucket 25: 10% bucket 4: 30% bucket 13: 20% bucket 26: 10% bucket 5: 30% bucket 14: 20% bucket 6: 30% bucket 15: 20% bucket 7: 30% bucket 8: 30% bucket 9: 30% bucket 16: 20% bucket 10: 30% bucket 17: 20% bucket 11: 30% bucket 23: 20% bucket 18: 20% bucket 19: 20% bucket 20: 20% bucket 22: 20% bucket 21: 20% bucket 1: 50% bucket 2: 40% bucket 24: 20% bucket 3: 40% bucket 12: 30% bucket 25: 20% bucket 4: 40% bucket 13: 30% bucket 26: 20% bucket 5: 40% bucket 14: 30% bucket 6: 40% bucket 15: 30% bucket 7: 40% bucket 8: 40% bucket 9: 40% bucket 16: 30% bucket 10: 40% bucket 17: 30% bucket 11: 40% bucket 23: 30% bucket 18: 30% bucket 19: 30% bucket 20: 30% bucket 22: 30% bucket 21: 30% bucket 1: 60% bucket 2: 50% bucket 24: 30% bucket 3: 50% bucket 12: 40% bucket 25: 30% bucket 4: 50% bucket 13: 40% bucket 26: 30% bucket 5: 50% bucket 14: 40% bucket 6: 50% bucket 15: 40% bucket 7: 50% bucket 8: 50% bucket 9: 50% bucket 16: 40% bucket 10: 50% bucket 17: 40% bucket 11: 50% bucket 23: 40% bucket 18: 40% bucket 19: 40% bucket 20: 40% bucket 22: 40% bucket 21: 40% bucket 1: 70% bucket 2: 60% bucket 24: 40% bucket 3: 60% bucket 12: 50% bucket 25: 40% bucket 4: 60% bucket 13: 50% bucket 26: 40% bucket 5: 60% bucket 14: 50% bucket 6: 60% bucket 15: 50% bucket 7: 60% bucket 8: 60% bucket 9: 60% bucket 16: 50% bucket 10: 60% bucket 17: 50% bucket 11: 60% bucket 23: 50% bucket 18: 50% bucket 19: 50% bucket 20: 50% bucket 22: 50% bucket 21: 50% bucket 1: 80% bucket 2: 70% bucket 24: 50% bucket 3: 70% bucket 12: 60% bucket 25: 50% bucket 4: 70% bucket 13: 60% bucket 26: 50% Getting block 27 of 202 bucket 5: 70% bucket 14: 60% bucket 6: 70% bucket 15: 60% bucket 7: 70% bucket 8: 70% bucket 9: 70% bucket 16: 60% bucket 10: 70% bucket 17: 60% bucket 11: 70% bucket 23: 60% bucket 18: 60% bucket 19: 60% bucket 20: 60% bucket 22: 60% bucket 21: 60% bucket 1: 90% bucket 2: 80% bucket 24: 60% bucket 3: 80% bucket 12: 70% bucket 25: 60% bucket 4: 80% bucket 13: 70% bucket 26: 60% Reserving size (36) for bucket 27 bucket 5: 80% bucket 14: 70% bucket 6: 80% bucket 15: 70% bucket 7: 80% bucket 8: 80% bucket 9: 80% bucket 16: 70% bucket 10: 80% bucket 17: 70% bucket 11: 80% bucket 23: 70% bucket 18: 70% bucket 19: 70% bucket 20: 70% bucket 22: 70% bucket 21: 70% bucket 1: 100% bucket 2: 90% bucket 24: 70% bucket 3: 90% bucket 12: 80% bucket 25: 70% bucket 4: 90% bucket 13: 80% bucket 26: 70% Calculating Z arrays for bucket 27 bucket 5: 90% bucket 14: 80% bucket 6: 90% bucket 15: 80% bucket 7: 90% bucket 8: 90% bucket 9: 90% bucket 16: 80% bucket 10: 90% bucket 17: 80% bucket 11: 90% bucket 23: 80% bucket 18: 80% bucket 19: 80% bucket 20: 80% bucket 22: 80% bucket 21: 80% Sorting block of length 26 for bucket 1 (Using difference cover) bucket 2: 100% bucket 24: 80% bucket 3: 100% bucket 12: 90% bucket 25: 80% bucket 4: 100% bucket 13: 90% bucket 26: 80% bucket 5: 100% Entering block accumulator loop for bucket 27: bucket 14: 90% bucket 6: 100% bucket 15: 90% bucket 7: 100% bucket 8: 100% bucket 9: 100% bucket 16: 90% bucket 10: 100% bucket 17: 90% bucket 11: 100% bucket 23: 90% Sorting block time: 00:00:00 bucket 18: 90% bucket 19: 90% bucket 20: 90% bucket 22: 90% bucket 21: 90% Sorting block of length 18 for bucket 2 (Using difference cover) bucket 24: 90% Sorting block of length 20 for bucket 3 (Using difference cover) bucket 12: 100% bucket 25: 90% Sorting block of length 33 for bucket 4 (Using difference cover) bucket 13: 100% bucket 26: 90% Sorting block of length 24 for bucket 5 (Using difference cover) bucket 14: 100% Sorting block of length 19 for bucket 6 (Using difference cover) bucket 15: 100% Sorting block of length 19 for bucket 7 (Using difference cover) Sorting block of length 25 for bucket 8 (Using difference cover) Sorting block of length 27 for bucket 9 (Using difference cover) bucket 16: 100% Sorting block of length 8 for bucket 10 (Using difference cover) bucket 17: 100% Sorting block of length 34 for bucket 11 (Using difference cover) Returning block of 27 for bucket 1 bucket 23: 100% bucket 18: 100% bucket 19: 100% bucket 20: 100% bucket 22: 100% bucket 21: 100% bucket 24: 100% Sorting block of length 35 for bucket 12 (Using difference cover) bucket 25: 100% Sorting block of length 29 for bucket 13 (Using difference cover) bucket 26: 100% bucket 27: 10% Sorting block of length 16 for bucket 14 (Using difference cover) Sorting block of length 24 for bucket 15 (Using difference cover) Sorting block of length 35 for bucket 16 (Using difference cover) Sorting block of length 19 for bucket 17 Sorting block of length 34 for bucket 23 (Using difference cover) (Using difference cover) Sorting block of length 30 for bucket 18 (Using difference cover) Sorting block of length 26 for bucket 19 (Using difference cover) Sorting block of length 20 for bucket 20 (Using difference cover) Sorting block of length 19 for bucket 22 (Using difference cover) Sorting block of length 23 for bucket 21 (Using difference cover) Sorting block of length 18 for bucket 24 (Using difference cover) Sorting block of length 20 for bucket 25 (Using difference cover) Sorting block of length 26 for bucket 26 (Using difference cover) bucket 27: 20% Getting block 28 of 202 bucket 27: 30% Reserving size (36) for bucket 28 bucket 27: 40% Calculating Z arrays for bucket 28 bucket 27: 50% bucket 27: 60% Entering block accumulator loop for bucket 28: bucket 27: 70% bucket 27: 80% bucket 28: 10% bucket 27: 90% bucket 28: 20% bucket 27: 100% bucket 28: 30% Sorting block of length 30 for bucket 27 (Using difference cover) bucket 28: 40% bucket 28: 50% bucket 28: 60% bucket 28: 70% bucket 28: 80% bucket 28: 90% bucket 28: 100% Sorting block of length 33 for bucket 28 (Using difference cover) Sorting block time: 00:00:00 Returning block of 19 for bucket 2 Getting block 29 of 202 Reserving size (36) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 29: 10% bucket 29: 20% bucket 29: 30% bucket 29: 40% bucket 29: 50% bucket 29: 60% bucket 29: 70% bucket 29: 80% bucket 29: 90% bucket 29: 100% Sorting block of length 16 for bucket 29 (Using difference cover) Sorting block time: 00:00:00 Returning block of 21 for bucket 3 Sorting block time: 00:00:00 Returning block of 25 for bucket 5 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 20 for bucket 7 Sorting block time: 00:00:00 Returning block of 34 for bucket 4 Returning block of 9 for bucket 10 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 30 of 202 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 21 for bucket 20 Returning block of 31 for bucket 18 Sorting block time: 00:00:00 Returning block of 36 for bucket 12 Sorting block time: 00:00:00 Returning block of 28 for bucket 9 Reserving size (36) for bucket 30 Returning block of 30 for bucket 13 Returning block of 20 for bucket 6 Calculating Z arrays for bucket 30 Getting block 31 of 202 Reserving size (36) for bucket 31 Entering block accumulator loop for bucket 30: Calculating Z arrays for bucket 31 Sorting block time: 00:00:00 Returning block of 34 for bucket 28 bucket 30: 10% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 31: Returning block of 20 for bucket 17 bucket 30: 20% bucket 30: 30% bucket 31: 10% bucket 30: 40% bucket 31: 20% bucket 30: 50% bucket 31: 30% bucket 30: 60% bucket 31: 40% Sorting block time: 00:00:00 bucket 30: 70% Returning block of 26 for bucket 8 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 31: 50% Sorting block time: 00:00:00 bucket 30: 80% Returning block of 20 for bucket 22 Sorting block time: 00:00:00 Returning block of 35 for bucket 23 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 17 for bucket 14 bucket 31: 60% bucket 30: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 36 for bucket 16 Getting block 32 of 202 Returning block of 35 for bucket 11 Returning block of 25 for bucket 15 bucket 31: 70% Returning block of 27 for bucket 19 Returning block of 24 for bucket 21 Sorting block time: 00:00:00 bucket 30: 100% Reserving size (36) for bucket 32 Sorting block time: 00:00:00 Getting block 33 of 202 bucket 31: 80% Sorting block time: 00:00:00 Returning block of 19 for bucket 24 Sorting block time: 00:00:00 Sorting block of length 24 for bucket 30 Sorting block time: 00:00:00 (Using difference cover) Calculating Z arrays for bucket 32 Returning block of 21 for bucket 25 Reserving size (36) for bucket 33 Getting block 34 of 202 bucket 31: 90% Returning block of 17 for bucket 29 Returning block of 27 for bucket 26 Getting block 35 of 202 Returning block of 31 for bucket 27 Entering block accumulator loop for bucket 32: Calculating Z arrays for bucket 33 Reserving size (36) for bucket 34 bucket 31: 100% Reserving size (36) for bucket 35 Calculating Z arrays for bucket 34 Sorting block of length 13 for bucket 31 (Using difference cover) Getting block 36 of 202 Entering block accumulator loop for bucket 33: Calculating Z arrays for bucket 35 Getting block 37 of 202 Sorting block time: 00:00:00 bucket 32: 10% Entering block accumulator loop for bucket 34: Reserving size (36) for bucket 36 Reserving size (36) for bucket 37 Entering block accumulator loop for bucket 35: Returning block of 25 for bucket 30 bucket 32: 20% Calculating Z arrays for bucket 36 bucket 33: 10% Calculating Z arrays for bucket 37 bucket 32: 30% bucket 34: 10% bucket 33: 20% Entering block accumulator loop for bucket 36: bucket 35: 10% bucket 32: 40% Entering block accumulator loop for bucket 37: bucket 34: 20% bucket 33: 30% Sorting block time: 00:00:00 bucket 35: 20% bucket 32: 50% bucket 34: 30% Getting block 38 of 202 Returning block of 14 for bucket 31 bucket 33: 40% bucket 36: 10% bucket 35: 30% bucket 32: 60% bucket 37: 10% bucket 34: 40% Reserving size (36) for bucket 38 bucket 33: 50% bucket 36: 20% bucket 35: 40% bucket 32: 70% bucket 37: 20% Getting block 39 of 202 bucket 34: 50% Calculating Z arrays for bucket 38 bucket 33: 60% bucket 36: 30% bucket 35: 50% bucket 32: 80% bucket 37: 30% Reserving size (36) for bucket 39 bucket 34: 60% bucket 33: 70% Entering block accumulator loop for bucket 38: bucket 36: 40% bucket 35: 60% bucket 32: 90% Getting block 40 of 202 bucket 37: 40% Calculating Z arrays for bucket 39 bucket 34: 70% bucket 33: 80% bucket 36: 50% bucket 35: 70% bucket 32: 100% Reserving size (36) for bucket 40 bucket 37: 50% bucket 34: 80% Getting block 41 of 202 Entering block accumulator loop for bucket 39: bucket 33: 90% bucket 38: 10% bucket 36: 60% bucket 35: 80% Sorting block of length 22 for bucket 32 (Using difference cover) Calculating Z arrays for bucket 40 bucket 37: 60% bucket 34: 90% Reserving size (36) for bucket 41 bucket 33: 100% bucket 38: 20% bucket 36: 70% bucket 35: 90% Getting block 42 of 202 bucket 37: 70% Entering block accumulator loop for bucket 40: bucket 34: 100% Calculating Z arrays for bucket 41 bucket 39: 10% Sorting block of length 28 for bucket 33 (Using difference cover) bucket 38: 30% bucket 36: 80% Getting block 43 of 202 bucket 35: 100% Reserving size (36) for bucket 42 bucket 37: 80% Sorting block of length 27 for bucket 34 (Using difference cover) bucket 39: 20% Entering block accumulator loop for bucket 41: bucket 38: 40% bucket 36: 90% Reserving size (36) for bucket 43 Sorting block of length 13 for bucket 35 (Using difference cover) Calculating Z arrays for bucket 42 Getting block 44 of 202 bucket 37: 90% bucket 40: 10% bucket 39: 30% bucket 38: 50% bucket 36: 100% Calculating Z arrays for bucket 43 Getting block 45 of 202 Reserving size (36) for bucket 44 Entering block accumulator loop for bucket 42: bucket 37: 100% bucket 40: 20% bucket 39: 40% bucket 41: 10% bucket 38: 60% Sorting block time: 00:00:00 Sorting block of length 29 for bucket 36 (Using difference cover) Reserving size (36) for bucket 45 Entering block accumulator loop for bucket 43: Calculating Z arrays for bucket 44 Sorting block of length 31 for bucket 37 (Using difference cover) bucket 40: 30% bucket 39: 50% bucket 41: 20% Returning block of 23 for bucket 32 bucket 38: 70% Getting block 46 of 202 Calculating Z arrays for bucket 45 bucket 42: 10% Entering block accumulator loop for bucket 44: bucket 40: 40% bucket 39: 60% bucket 41: 30% Getting block 47 of 202 bucket 38: 80% Reserving size (36) for bucket 46 bucket 43: 10% bucket 42: 20% Entering block accumulator loop for bucket 45: bucket 40: 50% Getting block 48 of 202 bucket 39: 70% bucket 41: 40% Reserving size (36) for bucket 47 bucket 38: 90% Calculating Z arrays for bucket 46 bucket 43: 20% bucket 42: 30% bucket 44: 10% bucket 40: 60% Reserving size (36) for bucket 48 Getting block 49 of 202 bucket 39: 80% Calculating Z arrays for bucket 47 bucket 41: 50% bucket 38: 100% bucket 43: 30% Entering block accumulator loop for bucket 46: bucket 42: 40% bucket 45: 10% bucket 44: 20% Getting block 50 of 202 bucket 40: 70% Calculating Z arrays for bucket 48 Reserving size (36) for bucket 49 bucket 39: 90% Entering block accumulator loop for bucket 47: bucket 41: 60% Sorting block of length 35 for bucket 38 Sorting block time: 00:00:00 (Using difference cover) bucket 43: 40% bucket 42: 50% bucket 45: 20% bucket 44: 30% Reserving size (36) for bucket 50 bucket 40: 80% Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 48: bucket 39: 100% Getting block 51 of 202 bucket 41: 70% Returning block of 29 for bucket 33 bucket 43: 50% bucket 46: 10% bucket 42: 60% bucket 45: 30% bucket 44: 40% Calculating Z arrays for bucket 50 bucket 40: 90% Entering block accumulator loop for bucket 49: Sorting block of length 24 for bucket 39 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 47: 10% Reserving size (36) for bucket 51 (Using difference cover) Getting block 52 of 202 bucket 41: 80% bucket 43: 60% bucket 46: 20% bucket 42: 70% Getting block 53 of 202 bucket 45: 40% bucket 44: 50% bucket 40: 100% Entering block accumulator loop for bucket 50: bucket 48: 10% Returning block of 28 for bucket 34 Returning block of 14 for bucket 35 bucket 47: 20% Calculating Z arrays for bucket 51 Reserving size (36) for bucket 52 bucket 41: 90% bucket 43: 70% bucket 46: 30% Sorting block time: 00:00:00 bucket 42: 80% Reserving size (36) for bucket 53 Getting block 54 of 202 bucket 45: 50% bucket 44: 60% Sorting block time: 00:00:00 Sorting block of length 34 for bucket 40 (Using difference cover) bucket 48: 20% bucket 49: 10% bucket 47: 30% Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 51: bucket 41: 100% Getting block 55 of 202 bucket 43: 80% Returning block of 32 for bucket 37 bucket 46: 40% bucket 42: 90% Calculating Z arrays for bucket 53 Reserving size (36) for bucket 54 Getting block 56 of 202 bucket 45: 60% Returning block of 30 for bucket 36 bucket 44: 70% bucket 50: 10% bucket 48: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 49: 20% bucket 47: 40% Entering block accumulator loop for bucket 52: Sorting block of length 27 for bucket 41 (Using difference cover) Reserving size (36) for bucket 55 bucket 43: 90% bucket 46: 50% bucket 42: 100% Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 53: Reserving size (36) for bucket 56 bucket 45: 70% bucket 44: 80% bucket 50: 20% Returning block of 36 for bucket 38 bucket 48: 40% Returning block of 25 for bucket 39 bucket 47: 50% bucket 51: 10% bucket 49: 30% Calculating Z arrays for bucket 55 Getting block 57 of 202 bucket 43: 100% bucket 46: 60% Sorting block of length 22 for bucket 42 (Using difference cover) Sorting block time: 00:00:00 Entering block accumulator loop for bucket 54: Calculating Z arrays for bucket 56 Getting block 58 of 202 bucket 45: 80% bucket 44: 90% Sorting block time: 00:00:00 bucket 50: 30% bucket 48: 50% Getting block 59 of 202 bucket 47: 60% bucket 51: 20% bucket 52: 10% Getting block 60 of 202 bucket 49: 40% Entering block accumulator loop for bucket 55: Reserving size (36) for bucket 57 Sorting block of length 24 for bucket 43 (Using difference cover) bucket 46: 70% bucket 53: 10% Returning block of 35 for bucket 40 Entering block accumulator loop for bucket 56: Reserving size (36) for bucket 58 bucket 45: 90% Returning block of 28 for bucket 41 bucket 44: 100% bucket 50: 40% bucket 48: 60% Reserving size (36) for bucket 59 Getting block 61 of 202 bucket 47: 70% bucket 51: 30% bucket 52: 20% Reserving size (36) for bucket 60 bucket 49: 50% Calculating Z arrays for bucket 57 bucket 46: 80% Getting block 62 of 202 bucket 53: 20% bucket 54: 10% Sorting block time: 00:00:00 Calculating Z arrays for bucket 58 bucket 45: 100% Sorting block of length 22 for bucket 44 (Using difference cover) Sorting block time: 00:00:00 bucket 50: 50% bucket 48: 70% Calculating Z arrays for bucket 59 Reserving size (36) for bucket 61 bucket 47: 80% bucket 51: 40% bucket 52: 30% Calculating Z arrays for bucket 60 Getting block 63 of 202 bucket 49: 60% bucket 55: 10% bucket 46: 90% Entering block accumulator loop for bucket 57: Reserving size (36) for bucket 62 Getting block 64 of 202 bucket 53: 30% Returning block of 23 for bucket 42 bucket 54: 20% Sorting block time: 00:00:00 bucket 56: 10% Sorting block of length 22 for bucket 45 (Using difference cover) Entering block accumulator loop for bucket 58: Returning block of 25 for bucket 43 bucket 50: 60% bucket 48: 80% Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 59: bucket 47: 90% bucket 51: 50% bucket 52: 40% Entering block accumulator loop for bucket 60: Reserving size (36) for bucket 63 bucket 49: 70% bucket 55: 20% bucket 46: 100% Calculating Z arrays for bucket 62 Reserving size (36) for bucket 64 Getting block 65 of 202 bucket 53: 40% Returning block of 23 for bucket 44 bucket 54: 30% Sorting block time: 00:00:00 bucket 56: 20% Getting block 66 of 202 bucket 50: 70% bucket 48: 90% Entering block accumulator loop for bucket 61: bucket 47: 100% bucket 51: 60% bucket 52: 50% Calculating Z arrays for bucket 63 bucket 49: 80% bucket 55: 30% Sorting block of length 26 for bucket 46 (Using difference cover) bucket 57: 10% Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 62: Reserving size (36) for bucket 65 bucket 53: 50% Returning block of 23 for bucket 45 bucket 54: 40% Getting block 67 of 202 Getting block 68 of 202 bucket 56: 30% bucket 58: 10% Reserving size (36) for bucket 66 bucket 50: 80% bucket 48: 100% bucket 59: 10% Sorting block of length 25 for bucket 47 (Using difference cover) bucket 51: 70% bucket 52: 60% bucket 60: 10% Entering block accumulator loop for bucket 63: bucket 49: 90% bucket 55: 40% bucket 57: 20% Entering block accumulator loop for bucket 64: Calculating Z arrays for bucket 65 bucket 53: 60% bucket 54: 50% Reserving size (36) for bucket 67 Reserving size (36) for bucket 68 bucket 56: 40% bucket 58: 20% Calculating Z arrays for bucket 66 bucket 50: 90% Sorting block of length 32 for bucket 48 (Using difference cover) bucket 59: 20% bucket 61: 10% bucket 51: 80% bucket 52: 70% bucket 60: 20% Sorting block time: 00:00:00 bucket 49: 100% bucket 55: 50% bucket 57: 30% bucket 62: 10% Getting block 69 of 202 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 65: bucket 53: 70% bucket 54: 60% Calculating Z arrays for bucket 67 Calculating Z arrays for bucket 68 bucket 56: 50% bucket 58: 30% Entering block accumulator loop for bucket 66: bucket 50: 100% Sorting block time: 00:00:00 Getting block 70 of 202 bucket 59: 30% bucket 61: 20% bucket 51: 90% bucket 52: 80% Returning block of 27 for bucket 46 bucket 60: 30% bucket 63: 10% Sorting block of length 34 for bucket 49 (Using difference cover) bucket 55: 60% bucket 57: 40% bucket 62: 20% bucket 64: 10% Reserving size (36) for bucket 69 Returning block of 26 for bucket 47 bucket 53: 80% bucket 54: 70% Entering block accumulator loop for bucket 67: Entering block accumulator loop for bucket 68: bucket 56: 60% bucket 58: 40% Sorting block of length 34 for bucket 50 (Using difference cover) Returning block of 33 for bucket 48 Reserving size (36) for bucket 70 Getting block 71 of 202 bucket 59: 40% bucket 61: 30% bucket 51: 100% bucket 52: 90% bucket 60: 40% bucket 63: 20% bucket 55: 70% bucket 57: 50% bucket 62: 30% bucket 64: 20% Calculating Z arrays for bucket 69 bucket 65: 10% bucket 53: 90% bucket 54: 80% Getting block 72 of 202 bucket 56: 70% bucket 58: 50% bucket 66: 10% Calculating Z arrays for bucket 70 Reserving size (36) for bucket 71 bucket 59: 50% bucket 61: 40% Sorting block of length 24 for bucket 51 (Using difference cover) bucket 52: 100% bucket 60: 50% Sorting block time: 00:00:00 bucket 63: 30% Sorting block time: 00:00:00 bucket 55: 80% bucket 57: 60% bucket 62: 40% bucket 64: 30% Entering block accumulator loop for bucket 69: bucket 65: 20% bucket 53: 100% bucket 54: 90% Reserving size (36) for bucket 72 bucket 67: 10% bucket 68: 10% bucket 56: 80% bucket 58: 60% bucket 66: 20% Getting block 73 of 202 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 70: bucket 59: 60% bucket 61: 50% Sorting block of length 15 for bucket 52 Sorting block time: 00:00:00 (Using difference cover) Returning block of 35 for bucket 49 bucket 60: 60% Returning block of 35 for bucket 50 bucket 63: 40% bucket 55: 90% bucket 57: 70% bucket 62: 50% bucket 64: 40% Getting block 74 of 202 bucket 65: 30% Sorting block of length 23 for bucket 53 (Using difference cover) bucket 54: 100% Calculating Z arrays for bucket 72 bucket 67: 20% bucket 68: 20% bucket 56: 90% bucket 58: 70% bucket 66: 30% Reserving size (36) for bucket 73 Entering block accumulator loop for bucket 71: bucket 59: 70% bucket 61: 60% Returning block of 25 for bucket 51 bucket 60: 70% Getting block 75 of 202 bucket 63: 50% bucket 55: 100% bucket 57: 80% bucket 62: 60% bucket 64: 50% bucket 69: 10% Reserving size (36) for bucket 74 bucket 65: 40% Sorting block of length 15 for bucket 54 (Using difference cover) bucket 67: 30% Entering block accumulator loop for bucket 72: bucket 68: 30% bucket 56: 100% bucket 58: 80% Sorting block time: 00:00:00 bucket 66: 40% Calculating Z arrays for bucket 73 bucket 70: 10% bucket 59: 80% bucket 61: 70% bucket 60: 80% Reserving size (36) for bucket 75 bucket 63: 60% Sorting block of length 28 for bucket 55 (Using difference cover) bucket 57: 90% bucket 62: 70% bucket 64: 60% Calculating Z arrays for bucket 74 bucket 69: 20% bucket 65: 50% bucket 67: 40% Getting block 76 of 202 bucket 68: 40% Sorting block of length 15 for bucket 56 (Using difference cover) Returning block of 16 for bucket 52 bucket 58: 90% bucket 66: 50% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 73: bucket 70: 20% bucket 71: 10% bucket 59: 90% Getting block 77 of 202 bucket 61: 80% bucket 60: 90% Calculating Z arrays for bucket 75 bucket 63: 70% bucket 57: 100% bucket 62: 80% bucket 64: 70% Entering block accumulator loop for bucket 74: bucket 69: 30% bucket 65: 60% bucket 72: 10% bucket 67: 50% Reserving size (36) for bucket 76 bucket 68: 50% bucket 58: 100% Returning block of 24 for bucket 53 bucket 66: 60% Getting block 78 of 202 bucket 70: 30% bucket 71: 20% bucket 59: 100% Reserving size (36) for bucket 77 bucket 61: 90% bucket 60: 100% bucket 63: 80% Entering block accumulator loop for bucket 75: Sorting block of length 28 for bucket 57 (Using difference cover) bucket 62: 90% bucket 64: 80% bucket 69: 40% bucket 65: 70% bucket 72: 20% Sorting block time: 00:00:00 bucket 67: 60% Calculating Z arrays for bucket 76 bucket 68: 60% Sorting block of length 31 for bucket 58 (Using difference cover) bucket 66: 70% Sorting block time: 00:00:00 bucket 73: 10% Reserving size (36) for bucket 78 bucket 70: 40% bucket 71: 30% Sorting block of length 35 for bucket 59 (Using difference cover) Calculating Z arrays for bucket 77 bucket 61: 100% Sorting block of length 31 for bucket 60 (Using difference cover) bucket 63: 90% bucket 62: 100% bucket 64: 90% bucket 74: 10% bucket 69: 50% bucket 65: 80% Returning block of 16 for bucket 54 bucket 72: 30% bucket 67: 70% bucket 68: 70% Entering block accumulator loop for bucket 76: Returning block of 16 for bucket 56 bucket 66: 80% bucket 73: 20% Calculating Z arrays for bucket 78 Getting block 79 of 202 bucket 70: 50% bucket 71: 40% Sorting block of length 20 for bucket 61 (Using difference cover) Entering block accumulator loop for bucket 77: bucket 63: 100% bucket 75: 10% Sorting block of length 24 for bucket 62 (Using difference cover) bucket 64: 100% bucket 74: 20% bucket 69: 60% Getting block 80 of 202 bucket 65: 90% bucket 72: 40% Sorting block time: 00:00:00 bucket 67: 80% bucket 68: 80% bucket 66: 90% bucket 73: 30% Entering block accumulator loop for bucket 78: Reserving size (36) for bucket 79 bucket 70: 60% bucket 71: 50% Sorting block of length 20 for bucket 63 (Using difference cover) bucket 75: 20% Sorting block of length 24 for bucket 64 (Using difference cover) bucket 74: 30% bucket 69: 70% Reserving size (36) for bucket 80 bucket 65: 100% Returning block of 29 for bucket 55 bucket 72: 50% bucket 67: 90% bucket 68: 90% bucket 76: 10% bucket 66: 100% bucket 73: 40% Calculating Z arrays for bucket 79 bucket 70: 70% bucket 71: 60% bucket 77: 10% Getting block 81 of 202 bucket 75: 30% bucket 74: 40% bucket 69: 80% Calculating Z arrays for bucket 80 Sorting block of length 22 for bucket 65 (Using difference cover) bucket 72: 60% bucket 67: 100% bucket 68: 100% bucket 76: 20% Sorting block of length 27 for bucket 66 (Using difference cover) bucket 73: 50% Getting block 82 of 202 bucket 78: 10% bucket 70: 80% Entering block accumulator loop for bucket 79: bucket 71: 70% bucket 77: 20% Reserving size (36) for bucket 81 bucket 75: 40% bucket 74: 50% bucket 69: 90% Entering block accumulator loop for bucket 80: bucket 72: 70% Sorting block of length 14 for bucket 67 (Using difference cover) Sorting block of length 26 for bucket 68 (Using difference cover) bucket 76: 30% bucket 73: 60% Reserving size (36) for bucket 82 bucket 78: 20% bucket 70: 90% bucket 71: 80% bucket 77: 30% Calculating Z arrays for bucket 81 bucket 75: 50% bucket 74: 60% bucket 69: 100% bucket 72: 80% Getting block 83 of 202 bucket 76: 40% bucket 73: 70% Calculating Z arrays for bucket 82 bucket 78: 30% bucket 70: 100% bucket 79: 10% bucket 71: 90% bucket 77: 40% Entering block accumulator loop for bucket 81: bucket 75: 60% bucket 74: 70% Sorting block of length 27 for bucket 69 (Using difference cover) bucket 80: 10% bucket 72: 90% Reserving size (36) for bucket 83 bucket 76: 50% bucket 73: 80% Entering block accumulator loop for bucket 82: bucket 78: 40% Sorting block of length 20 for bucket 70 (Using difference cover) bucket 79: 20% bucket 71: 100% bucket 77: 50% bucket 75: 70% bucket 74: 80% bucket 80: 20% bucket 72: 100% Calculating Z arrays for bucket 83 bucket 76: 60% bucket 73: 90% bucket 78: 50% bucket 79: 30% Sorting block of length 34 for bucket 71 (Using difference cover) bucket 77: 60% bucket 81: 10% bucket 75: 80% bucket 74: 90% bucket 80: 30% Sorting block of length 27 for bucket 72 (Using difference cover) bucket 76: 70% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 83: bucket 73: 100% bucket 82: 10% bucket 78: 60% bucket 79: 40% bucket 77: 70% bucket 81: 20% bucket 75: 90% bucket 74: 100% bucket 80: 40% Returning block of 29 for bucket 57 bucket 76: 80% Sorting block of length 28 for bucket 73 (Using difference cover) bucket 82: 20% bucket 78: 70% bucket 79: 50% bucket 77: 80% bucket 81: 30% Sorting block of length 30 for bucket 74 (Using difference cover) bucket 75: 100% bucket 80: 50% bucket 76: 90% bucket 83: 10% bucket 82: 30% bucket 78: 80% bucket 79: 60% bucket 77: 90% Sorting block time: 00:00:00 bucket 81: 40% Sorting block of length 32 for bucket 75 (Using difference cover) bucket 80: 60% bucket 76: 100% bucket 83: 20% bucket 82: 40% bucket 78: 90% bucket 79: 70% Returning block of 32 for bucket 58 bucket 77: 100% bucket 81: 50% bucket 80: 70% Sorting block of length 35 for bucket 76 (Using difference cover) bucket 83: 30% bucket 82: 50% bucket 78: 100% bucket 79: 80% Getting block 84 of 202 Sorting block of length 26 for bucket 77 (Using difference cover) bucket 81: 60% bucket 80: 80% bucket 83: 40% bucket 82: 60% Sorting block of length 35 for bucket 78 (Using difference cover) bucket 79: 90% Reserving size (36) for bucket 84 bucket 81: 70% bucket 80: 90% bucket 83: 50% bucket 82: 70% bucket 79: 100% Calculating Z arrays for bucket 84 bucket 81: 80% bucket 80: 100% bucket 83: 60% bucket 82: 80% Sorting block of length 34 for bucket 79 (Using difference cover) Sorting block of length 30 for bucket 80 (Using difference cover) bucket 81: 90% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 84: bucket 83: 70% bucket 82: 90% Returning block of 36 for bucket 59 bucket 81: 100% bucket 83: 80% Getting block 85 of 202 bucket 82: 100% Sorting block of length 21 for bucket 81 (Using difference cover) bucket 84: 10% bucket 83: 90% Reserving size (36) for bucket 85 Sorting block of length 17 for bucket 82 (Using difference cover) bucket 84: 20% bucket 83: 100% Calculating Z arrays for bucket 85 bucket 84: 30% Sorting block of length 19 for bucket 83 (Using difference cover) bucket 84: 40% Entering block accumulator loop for bucket 85: bucket 84: 50% bucket 84: 60% bucket 85: 10% bucket 84: 70% Getting block 86 of 202 bucket 85: 20% bucket 84: 80% Reserving size (36) for bucket 86 bucket 85: 30% bucket 84: 90% Calculating Z arrays for bucket 86 bucket 85: 40% bucket 84: 100% bucket 85: 50% Sorting block of length 34 for bucket 84 (Using difference cover) Entering block accumulator loop for bucket 86: bucket 85: 60% bucket 85: 70% bucket 86: 10% bucket 85: 80% Sorting block time: 00:00:00 bucket 86: 20% Returning block of 21 for bucket 61 bucket 85: 90% bucket 86: 30% bucket 85: 100% bucket 86: 40% Sorting block of length 33 for bucket 85 (Using difference cover) bucket 86: 50% bucket 86: 60% bucket 86: 70% bucket 86: 80% bucket 86: 90% bucket 86: 100% Sorting block of length 33 for bucket 86 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25 for bucket 62 Getting block 87 of 202 Reserving size (36) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 87: 10% bucket 87: 20% bucket 87: 30% bucket 87: 40% bucket 87: 50% bucket 87: 60% bucket 87: 70% Getting block 88 of 202 bucket 87: 80% Reserving size (36) for bucket 88 bucket 87: 90% Calculating Z arrays for bucket 88 bucket 87: 100% Sorting block of length 7 for bucket 87 (Using difference cover) Entering block accumulator loop for bucket 88: bucket 88: 10% bucket 88: 20% bucket 88: 30% bucket 88: 40% bucket 88: 50% bucket 88: 60% bucket 88: 70% bucket 88: 80% bucket 88: 90% bucket 88: 100% Sorting block of length 35 for bucket 88 (Using difference cover) Sorting block time: 00:00:00 Returning block of 32 for bucket 60 Getting block 89 of 202 Reserving size (36) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 89: 10% bucket 89: 20% bucket 89: 30% bucket 89: 40% bucket 89: 50% bucket 89: 60% bucket 89: 70% bucket 89: 80% bucket 89: 90% bucket 89: 100% Sorting block of length 30 for bucket 89 (Using difference cover) Sorting block time: 00:00:00 Returning block of 28 for bucket 66 Sorting block time: 00:00:00 Returning block of 21 for bucket 63 Sorting block time: 00:00:00 Returning block of 25 for bucket 64 Getting block 90 of 202 Reserving size (36) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 90: 10% Getting block 91 of 202 Reserving size (36) for bucket 91 Calculating Z arrays for bucket 91 bucket 90: 20% Entering block accumulator loop for bucket 91: bucket 90: 30% Sorting block time: 00:00:00 bucket 91: 10% Returning block of 15 for bucket 67 Sorting block time: 00:00:00 bucket 90: 40% bucket 91: 20% Returning block of 21 for bucket 70 Sorting block time: 00:00:00 bucket 90: 50% Sorting block time: 00:00:00 bucket 91: 30% Returning block of 28 for bucket 69 Returning block of 23 for bucket 65 bucket 90: 60% Sorting block time: 00:00:00 bucket 91: 40% Returning block of 27 for bucket 68 Sorting block time: 00:00:00 bucket 90: 70% bucket 91: 50% Returning block of 29 for bucket 73 bucket 90: 80% bucket 91: 60% bucket 90: 90% Getting block 92 of 202 bucket 91: 70% bucket 90: 100% Reserving size (36) for bucket 92 bucket 91: 80% Sorting block of length 35 for bucket 90 (Using difference cover) Calculating Z arrays for bucket 92 bucket 91: 90% Getting block 93 of 202 bucket 91: 100% Reserving size (36) for bucket 93 Entering block accumulator loop for bucket 92: Sorting block of length 24 for bucket 91 (Using difference cover) Calculating Z arrays for bucket 93 Getting block 94 of 202 bucket 92: 10% Entering block accumulator loop for bucket 93: Reserving size (36) for bucket 94 bucket 92: 20% Calculating Z arrays for bucket 94 bucket 93: 10% bucket 92: 30% bucket 93: 20% bucket 92: 40% bucket 93: 30% Entering block accumulator loop for bucket 94: bucket 92: 50% bucket 93: 40% bucket 92: 60% bucket 93: 50% bucket 94: 10% bucket 92: 70% bucket 93: 60% bucket 94: 20% bucket 92: 80% bucket 93: 70% bucket 94: 30% bucket 92: 90% bucket 93: 80% bucket 94: 40% Getting block 95 of 202 bucket 92: 100% bucket 93: 90% bucket 94: 50% Reserving size (36) for bucket 95 Sorting block of length 23 for bucket 92 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 93: 100% Sorting block time: 00:00:00 bucket 94: 60% Calculating Z arrays for bucket 95 Returning block of 28 for bucket 72 Returning block of 35 for bucket 71 Sorting block of length 31 for bucket 93 (Using difference cover) Returning block of 31 for bucket 74 bucket 94: 70% Entering block accumulator loop for bucket 95: Getting block 96 of 202 Sorting block time: 00:00:00 bucket 94: 80% Reserving size (36) for bucket 96 Getting block 97 of 202 Returning block of 20 for bucket 83 bucket 94: 90% bucket 95: 10% Calculating Z arrays for bucket 96 Reserving size (36) for bucket 97 bucket 94: 100% bucket 95: 20% Calculating Z arrays for bucket 97 Getting block 98 of 202 Sorting block of length 34 for bucket 94 Sorting block time: 00:00:00 (Using difference cover) Entering block accumulator loop for bucket 96: bucket 95: 30% Reserving size (36) for bucket 98 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 97: Sorting block time: 00:00:00 Returning block of 27 for bucket 77 Sorting block time: 00:00:00 bucket 95: 40% Calculating Z arrays for bucket 98 Returning block of 35 for bucket 79 Sorting block time: 00:00:00 Returning block of 33 for bucket 75 Sorting block time: 00:00:00 Returning block of 36 for bucket 78 Sorting block time: 00:00:00 bucket 96: 10% bucket 95: 50% Entering block accumulator loop for bucket 98: Returning block of 31 for bucket 80 bucket 97: 10% Getting block 99 of 202 Returning block of 22 for bucket 81 Sorting block time: 00:00:00 Returning block of 36 for bucket 76 bucket 96: 20% bucket 95: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 97: 20% Sorting block time: 00:00:00 Reserving size (36) for bucket 99 Sorting block time: 00:00:00 Returning block of 18 for bucket 82 Returning block of 34 for bucket 86 bucket 96: 30% Returning block of 35 for bucket 84 bucket 95: 70% bucket 98: 10% Returning block of 36 for bucket 88 bucket 97: 30% Calculating Z arrays for bucket 99 Returning block of 34 for bucket 85 bucket 96: 40% bucket 95: 80% bucket 98: 20% Getting block 100 of 202 bucket 97: 40% Entering block accumulator loop for bucket 99: Sorting block time: 00:00:00 bucket 96: 50% bucket 95: 90% bucket 98: 30% Reserving size (36) for bucket 100 Getting block 101 of 202 bucket 97: 50% Returning block of 8 for bucket 87 bucket 96: 60% bucket 95: 100% Calculating Z arrays for bucket 100 bucket 98: 40% Reserving size (36) for bucket 101 bucket 97: 60% bucket 99: 10% Getting block 102 of 202 Sorting block of length 30 for bucket 95 (Using difference cover) bucket 96: 70% Entering block accumulator loop for bucket 100: bucket 98: 50% Calculating Z arrays for bucket 101 bucket 97: 70% bucket 99: 20% Reserving size (36) for bucket 102 bucket 96: 80% bucket 98: 60% Getting block 103 of 202 bucket 97: 80% Entering block accumulator loop for bucket 101: bucket 99: 30% Calculating Z arrays for bucket 102 bucket 100: 10% bucket 96: 90% bucket 98: 70% Sorting block time: 00:00:00 Reserving size (36) for bucket 103 bucket 97: 90% bucket 99: 40% Getting block 104 of 202 bucket 100: 20% Entering block accumulator loop for bucket 102: bucket 96: 100% Returning block of 31 for bucket 89 bucket 98: 80% Calculating Z arrays for bucket 103 bucket 97: 100% bucket 101: 10% bucket 99: 50% Reserving size (36) for bucket 104 bucket 100: 30% Sorting block of length 11 for bucket 96 (Using difference cover) bucket 98: 90% Sorting block of length 32 for bucket 97 (Using difference cover) Entering block accumulator loop for bucket 103: bucket 101: 20% bucket 99: 60% Calculating Z arrays for bucket 104 bucket 100: 40% bucket 102: 10% Getting block 105 of 202 bucket 98: 100% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 101: 30% bucket 99: 70% bucket 100: 50% Entering block accumulator loop for bucket 104: bucket 102: 20% Sorting block time: 00:00:00 Reserving size (36) for bucket 105 Returning block of 35 for bucket 94 Sorting block of length 35 for bucket 98 (Using difference cover) Getting block 106 of 202 Getting block 107 of 202 Returning block of 32 for bucket 93 bucket 103: 10% bucket 101: 40% bucket 99: 80% bucket 100: 60% Returning block of 25 for bucket 91 bucket 102: 30% Calculating Z arrays for bucket 105 Sorting block time: 00:00:00 Reserving size (36) for bucket 106 Reserving size (36) for bucket 107 bucket 103: 20% bucket 101: 50% Getting block 108 of 202 bucket 99: 90% bucket 100: 70% bucket 104: 10% bucket 102: 40% Getting block 109 of 202 Returning block of 36 for bucket 90 Entering block accumulator loop for bucket 105: Calculating Z arrays for bucket 106 Calculating Z arrays for bucket 107 bucket 103: 30% bucket 101: 60% Reserving size (36) for bucket 108 Getting block 110 of 202 bucket 99: 100% bucket 100: 80% Sorting block time: 00:00:00 bucket 104: 20% bucket 102: 50% Reserving size (36) for bucket 109 Entering block accumulator loop for bucket 106: bucket 103: 40% Getting block 111 of 202 Entering block accumulator loop for bucket 107: bucket 101: 70% Calculating Z arrays for bucket 108 Reserving size (36) for bucket 110 Sorting block of length 32 for bucket 99 (Using difference cover) Returning block of 24 for bucket 92 bucket 100: 90% bucket 104: 30% bucket 102: 60% Calculating Z arrays for bucket 109 Getting block 112 of 202 bucket 105: 10% Sorting block time: 00:00:00 bucket 103: 50% Reserving size (36) for bucket 111 bucket 101: 80% Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 108: bucket 100: 100% bucket 104: 40% bucket 102: 70% Entering block accumulator loop for bucket 109: Reserving size (36) for bucket 112 Returning block of 31 for bucket 95 bucket 105: 20% bucket 103: 60% Sorting block time: 00:00:00 Calculating Z arrays for bucket 111 bucket 107: 10% Sorting block time: 00:00:00 bucket 101: 90% Sorting block time: 00:00:00 bucket 106: 10% Sorting block time: 00:00:00 Getting block 113 of 202 Entering block accumulator loop for bucket 110: Sorting block of length 18 for bucket 100 (Using difference cover) bucket 104: 50% Getting block 114 of 202 bucket 102: 80% Calculating Z arrays for bucket 112 Getting block 115 of 202 bucket 105: 30% Returning block of 12 for bucket 96 bucket 103: 70% Returning block of 33 for bucket 97 Entering block accumulator loop for bucket 111: bucket 107: 20% bucket 101: 100% Returning block of 36 for bucket 98 Returning block of 33 for bucket 99 bucket 106: 20% Sorting block time: 00:00:00 bucket 108: 10% Reserving size (36) for bucket 113 bucket 104: 60% Reserving size (36) for bucket 114 Getting block 116 of 202 bucket 102: 90% bucket 109: 10% Reserving size (36) for bucket 115 Entering block accumulator loop for bucket 112: bucket 105: 40% bucket 103: 80% Getting block 117 of 202 bucket 107: 30% Sorting block of length 19 for bucket 101 (Using difference cover) Getting block 118 of 202 Returning block of 19 for bucket 100 bucket 106: 30% bucket 108: 20% Calculating Z arrays for bucket 113 bucket 110: 10% bucket 104: 70% Calculating Z arrays for bucket 114 Getting block 119 of 202 Reserving size (36) for bucket 116 bucket 102: 100% bucket 109: 20% Calculating Z arrays for bucket 115 bucket 105: 50% bucket 103: 90% bucket 111: 10% Reserving size (36) for bucket 117 bucket 107: 40% Sorting block time: 00:00:00 Reserving size (36) for bucket 118 bucket 106: 40% bucket 108: 30% bucket 110: 20% Entering block accumulator loop for bucket 113: bucket 104: 80% Reserving size (36) for bucket 119 Entering block accumulator loop for bucket 114: Calculating Z arrays for bucket 116 Sorting block of length 29 for bucket 102 (Using difference cover) bucket 109: 30% bucket 112: 10% bucket 105: 60% Entering block accumulator loop for bucket 115: bucket 103: 100% Getting block 120 of 202 bucket 111: 20% Calculating Z arrays for bucket 117 Returning block of 20 for bucket 101 bucket 107: 50% Calculating Z arrays for bucket 118 bucket 106: 50% bucket 108: 40% bucket 110: 30% Getting block 121 of 202 bucket 104: 90% Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 116: bucket 109: 40% bucket 112: 20% bucket 105: 70% Sorting block of length 34 for bucket 103 (Using difference cover) Reserving size (36) for bucket 120 bucket 111: 30% Sorting block time: 00:00:00 Getting block 122 of 202 Entering block accumulator loop for bucket 117: bucket 107: 60% bucket 106: 60% Entering block accumulator loop for bucket 118: bucket 108: 50% Getting block 123 of 202 bucket 110: 40% bucket 113: 10% Reserving size (36) for bucket 121 bucket 104: 100% Getting block 124 of 202 bucket 114: 10% Entering block accumulator loop for bucket 119: bucket 109: 50% bucket 112: 30% bucket 105: 80% bucket 115: 10% Calculating Z arrays for bucket 120 Sorting block time: 00:00:00 Getting block 125 of 202 Returning block of 30 for bucket 102 bucket 111: 40% Reserving size (36) for bucket 122 bucket 107: 70% bucket 106: 70% bucket 108: 60% Reserving size (36) for bucket 123 bucket 110: 50% Getting block 126 of 202 bucket 113: 20% Calculating Z arrays for bucket 121 Sorting block of length 30 for bucket 104 (Using difference cover) Reserving size (36) for bucket 124 bucket 114: 20% bucket 116: 10% bucket 109: 60% bucket 112: 40% bucket 105: 90% Returning block of 35 for bucket 103 bucket 115: 20% Reserving size (36) for bucket 125 Entering block accumulator loop for bucket 120: bucket 111: 50% Calculating Z arrays for bucket 122 bucket 117: 10% bucket 107: 80% bucket 106: 80% bucket 118: 10% Getting block 127 of 202 bucket 108: 70% Calculating Z arrays for bucket 123 bucket 110: 60% Reserving size (36) for bucket 126 Sorting block time: 00:00:00 bucket 113: 30% Entering block accumulator loop for bucket 121: Calculating Z arrays for bucket 124 Getting block 128 of 202 bucket 114: 30% bucket 116: 20% bucket 119: 10% bucket 109: 70% bucket 112: 50% bucket 105: 100% bucket 115: 30% Calculating Z arrays for bucket 125 bucket 111: 60% Entering block accumulator loop for bucket 122: bucket 117: 20% bucket 107: 90% bucket 106: 90% bucket 118: 20% Reserving size (36) for bucket 127 bucket 108: 80% Entering block accumulator loop for bucket 123: bucket 110: 70% Calculating Z arrays for bucket 126 Returning block of 31 for bucket 104 bucket 113: 40% Reserving size (36) for bucket 128 Entering block accumulator loop for bucket 124: bucket 114: 40% bucket 116: 30% Getting block 129 of 202 bucket 119: 20% bucket 109: 80% bucket 112: 60% Sorting block of length 22 for bucket 105 (Using difference cover) bucket 115: 40% bucket 120: 10% bucket 111: 70% Entering block accumulator loop for bucket 125: bucket 117: 30% bucket 107: 100% bucket 106: 100% bucket 118: 30% Calculating Z arrays for bucket 127 bucket 108: 90% bucket 110: 80% Getting block 130 of 202 Entering block accumulator loop for bucket 126: bucket 113: 50% bucket 121: 10% Calculating Z arrays for bucket 128 bucket 114: 50% bucket 116: 40% Reserving size (36) for bucket 129 bucket 119: 30% bucket 109: 90% bucket 112: 70% bucket 115: 50% bucket 120: 20% bucket 111: 80% bucket 122: 10% bucket 117: 40% Sorting block time: 00:00:00 Sorting block of length 9 for bucket 107 (Using difference cover) Sorting block of length 31 for bucket 106 (Using difference cover) bucket 118: 40% bucket 108: 100% bucket 123: 10% Entering block accumulator loop for bucket 127: bucket 110: 90% Reserving size (36) for bucket 130 bucket 113: 60% bucket 121: 20% bucket 124: 10% bucket 114: 60% Entering block accumulator loop for bucket 128: bucket 116: 50% Calculating Z arrays for bucket 129 bucket 119: 40% bucket 109: 100% bucket 112: 80% bucket 115: 60% bucket 120: 30% bucket 111: 90% bucket 125: 10% bucket 122: 20% Returning block of 23 for bucket 105 bucket 117: 50% Getting block 131 of 202 bucket 118: 50% Sorting block of length 32 for bucket 108 (Using difference cover) bucket 123: 20% bucket 110: 100% Calculating Z arrays for bucket 130 bucket 126: 10% bucket 113: 70% bucket 121: 30% bucket 124: 20% bucket 114: 70% Sorting block time: 00:00:00 bucket 116: 60% bucket 119: 50% Entering block accumulator loop for bucket 129: Sorting block of length 7 for bucket 109 (Using difference cover) bucket 112: 90% bucket 115: 70% bucket 120: 40% bucket 111: 100% bucket 125: 20% bucket 122: 30% bucket 117: 60% Reserving size (36) for bucket 131 bucket 118: 60% bucket 123: 30% Sorting block of length 31 for bucket 110 (Using difference cover) bucket 127: 10% Entering block accumulator loop for bucket 130: bucket 126: 20% bucket 113: 80% bucket 121: 40% bucket 124: 30% Sorting block time: 00:00:00 Returning block of 10 for bucket 107 bucket 114: 80% bucket 128: 10% bucket 116: 70% bucket 119: 60% bucket 112: 100% bucket 115: 80% bucket 120: 50% Sorting block of length 34 for bucket 111 (Using difference cover) bucket 125: 30% bucket 122: 40% bucket 117: 70% Calculating Z arrays for bucket 131 bucket 118: 70% bucket 123: 40% bucket 127: 20% bucket 126: 30% bucket 113: 90% bucket 121: 50% Returning block of 32 for bucket 106 bucket 124: 40% bucket 114: 90% bucket 128: 20% bucket 116: 80% Getting block 132 of 202 bucket 119: 70% bucket 129: 10% Sorting block of length 33 for bucket 112 (Using difference cover) bucket 115: 90% bucket 120: 60% bucket 125: 40% bucket 122: 50% bucket 117: 80% Entering block accumulator loop for bucket 131: bucket 118: 80% bucket 123: 50% bucket 127: 30% bucket 130: 10% bucket 126: 40% bucket 113: 100% bucket 121: 60% bucket 124: 50% bucket 114: 100% bucket 128: 30% bucket 116: 90% Sorting block time: 00:00:00 Reserving size (36) for bucket 132 bucket 119: 80% bucket 129: 20% bucket 115: 100% bucket 120: 70% bucket 125: 50% bucket 122: 60% bucket 117: 90% bucket 118: 90% bucket 123: 60% bucket 127: 40% Getting block 133 of 202 bucket 130: 20% bucket 126: 50% Sorting block of length 15 for bucket 113 (Using difference cover) bucket 121: 70% bucket 124: 60% Sorting block of length 34 for bucket 114 (Using difference cover) Sorting block time: 00:00:00 bucket 128: 40% Returning block of 33 for bucket 108 bucket 116: 100% Calculating Z arrays for bucket 132 bucket 119: 90% bucket 129: 30% Sorting block of length 18 for bucket 115 (Using difference cover) bucket 120: 80% bucket 125: 60% bucket 131: 10% bucket 122: 70% bucket 117: 100% bucket 118: 100% bucket 123: 70% bucket 127: 50% Reserving size (36) for bucket 133 bucket 130: 30% bucket 126: 60% Sorting block time: 00:00:00 Getting block 134 of 202 bucket 121: 80% bucket 124: 70% Returning block of 32 for bucket 110 bucket 128: 50% Sorting block of length 33 for bucket 116 (Using difference cover) bucket 119: 100% Entering block accumulator loop for bucket 132: bucket 129: 40% bucket 120: 90% bucket 125: 70% bucket 131: 20% bucket 122: 80% Sorting block time: 00:00:00 Sorting block of length 33 for bucket 117 (Using difference cover) Sorting block of length 22 for bucket 118 bucket 123: 80% bucket 127: 60% (Using difference cover) Calculating Z arrays for bucket 133 bucket 130: 40% Returning block of 8 for bucket 109 bucket 126: 70% Reserving size (36) for bucket 134 bucket 121: 90% bucket 124: 80% bucket 128: 60% Sorting block of length 31 for bucket 119 Sorting block time: 00:00:00 (Using difference cover) bucket 129: 50% bucket 120: 100% bucket 125: 80% bucket 131: 30% Returning block of 35 for bucket 111 bucket 122: 90% bucket 123: 90% bucket 127: 70% bucket 130: 50% Entering block accumulator loop for bucket 133: bucket 126: 80% Calculating Z arrays for bucket 134 bucket 121: 100% bucket 124: 90% bucket 128: 70% Returning block of 34 for bucket 112 bucket 132: 10% bucket 129: 60% Sorting block of length 25 for bucket 120 (Using difference cover) bucket 125: 90% bucket 131: 40% Getting block 135 of 202 Sorting block time: 00:00:00 bucket 122: 100% bucket 123: 100% Sorting block time: 00:00:00 Getting block 136 of 202 bucket 127: 80% bucket 130: 60% bucket 126: 90% Sorting block of length 12 for bucket 121 (Using difference cover) Entering block accumulator loop for bucket 134: bucket 124: 100% bucket 128: 80% bucket 132: 20% bucket 129: 70% bucket 125: 100% bucket 131: 50% Reserving size (36) for bucket 135 Returning block of 16 for bucket 113 Sorting block of length 27 for bucket 122 (Using difference cover) Sorting block of length 33 for bucket 123 (Using difference cover) Returning block of 19 for bucket 115 Reserving size (36) for bucket 136 bucket 127: 90% Getting block 137 of 202 bucket 130: 70% bucket 133: 10% bucket 126: 100% Sorting block of length 32 for bucket 124 (Using difference cover) bucket 128: 90% bucket 132: 30% bucket 129: 80% Sorting block of length 29 for bucket 125 (Using difference cover) bucket 131: 60% Calculating Z arrays for bucket 135 Getting block 138 of 202 Calculating Z arrays for bucket 136 bucket 127: 100% Reserving size (36) for bucket 137 bucket 130: 80% bucket 133: 20% Sorting block of length 22 for bucket 126 (Using difference cover) bucket 134: 10% bucket 128: 100% bucket 132: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 139 of 202 bucket 129: 90% bucket 131: 70% Reserving size (36) for bucket 138 Entering block accumulator loop for bucket 135: Sorting block of length 30 for bucket 127 (Using difference cover) Entering block accumulator loop for bucket 136: Calculating Z arrays for bucket 137 bucket 130: 90% bucket 133: 30% bucket 134: 20% Sorting block of length 16 for bucket 128 (Using difference cover) Returning block of 34 for bucket 117 Returning block of 34 for bucket 116 Returning block of 35 for bucket 114 bucket 132: 50% Reserving size (36) for bucket 139 bucket 129: 100% bucket 131: 80% Calculating Z arrays for bucket 138 Getting block 140 of 202 bucket 130: 100% Entering block accumulator loop for bucket 137: bucket 133: 40% bucket 134: 30% Getting block 141 of 202 bucket 132: 60% Calculating Z arrays for bucket 139 Sorting block of length 33 for bucket 129 (Using difference cover) bucket 131: 90% bucket 135: 10% Entering block accumulator loop for bucket 138: Reserving size (36) for bucket 140 Sorting block of length 35 for bucket 130 (Using difference cover) bucket 136: 10% bucket 133: 50% bucket 134: 40% Reserving size (36) for bucket 141 bucket 132: 70% Entering block accumulator loop for bucket 139: bucket 131: 100% bucket 135: 20% Calculating Z arrays for bucket 140 bucket 136: 20% bucket 137: 10% bucket 133: 60% bucket 134: 50% Calculating Z arrays for bucket 141 Getting block 142 of 202 bucket 132: 80% Sorting block of length 29 for bucket 131 (Using difference cover) bucket 138: 10% bucket 135: 30% bucket 136: 30% Entering block accumulator loop for bucket 140: bucket 137: 20% bucket 133: 70% bucket 134: 60% Reserving size (36) for bucket 142 Getting block 143 of 202 Entering block accumulator loop for bucket 141: bucket 132: 90% bucket 139: 10% bucket 138: 20% bucket 135: 40% bucket 136: 40% bucket 137: 30% bucket 133: 80% bucket 134: 70% Calculating Z arrays for bucket 142 Reserving size (36) for bucket 143 bucket 132: 100% bucket 139: 20% Getting block 144 of 202 bucket 138: 30% bucket 135: 50% bucket 136: 50% bucket 140: 10% bucket 137: 40% bucket 133: 90% bucket 134: 80% Calculating Z arrays for bucket 143 Sorting block of length 7 for bucket 132 (Using difference cover) bucket 141: 10% Entering block accumulator loop for bucket 142: bucket 139: 30% Reserving size (36) for bucket 144 bucket 138: 40% bucket 135: 60% bucket 136: 60% bucket 140: 20% bucket 137: 50% bucket 133: 100% bucket 134: 90% Entering block accumulator loop for bucket 143: bucket 141: 20% bucket 139: 40% Calculating Z arrays for bucket 144 bucket 138: 50% bucket 135: 70% bucket 136: 70% bucket 140: 30% bucket 137: 60% Sorting block of length 33 for bucket 133 (Using difference cover) bucket 134: 100% bucket 141: 30% bucket 142: 10% bucket 139: 50% bucket 138: 60% Entering block accumulator loop for bucket 144: bucket 135: 80% bucket 136: 80% bucket 140: 40% bucket 137: 70% Sorting block of length 18 for bucket 134 (Using difference cover) bucket 143: 10% bucket 141: 40% bucket 142: 20% bucket 139: 60% bucket 138: 70% bucket 135: 90% bucket 136: 90% bucket 140: 50% bucket 137: 80% bucket 143: 20% bucket 141: 50% bucket 142: 30% bucket 139: 70% bucket 138: 80% bucket 144: 10% bucket 135: 100% bucket 136: 100% bucket 140: 60% bucket 137: 90% bucket 143: 30% bucket 141: 60% bucket 142: 40% Sorting block time: 00:00:00 bucket 139: 80% bucket 138: 90% bucket 144: 20% Sorting block of length 21 for bucket 135 (Using difference cover) Sorting block of length 21 for bucket 136 (Using difference cover) Sorting block time: 00:00:00 bucket 140: 70% bucket 137: 100% bucket 143: 40% Sorting block time: 00:00:00 bucket 141: 70% Returning block of 26 for bucket 120 bucket 142: 50% bucket 139: 90% bucket 138: 100% bucket 144: 30% Returning block of 23 for bucket 118 bucket 140: 80% Sorting block of length 26 for bucket 137 (Using difference cover) Returning block of 32 for bucket 119 bucket 143: 50% bucket 141: 80% bucket 142: 60% bucket 139: 100% Sorting block of length 9 for bucket 138 (Using difference cover) bucket 144: 40% bucket 140: 90% bucket 143: 60% bucket 141: 90% bucket 142: 70% Sorting block of length 33 for bucket 139 (Using difference cover) bucket 144: 50% bucket 140: 100% bucket 143: 70% bucket 141: 100% bucket 142: 80% bucket 144: 60% Sorting block of length 30 for bucket 140 (Using difference cover) bucket 143: 80% Sorting block of length 32 for bucket 141 (Using difference cover) bucket 142: 90% bucket 144: 70% bucket 143: 90% bucket 142: 100% bucket 144: 80% bucket 143: 100% Sorting block of length 26 for bucket 142 (Using difference cover) bucket 144: 90% Sorting block of length 23 for bucket 143 (Using difference cover) bucket 144: 100% Sorting block time: 00:00:00 Returning block of 13 for bucket 121 Sorting block of length 29 for bucket 144 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 33 for bucket 124 Returning block of 23 for bucket 126 Getting block 145 of 202 Reserving size (36) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 145: 10% Getting block 146 of 202 Reserving size (36) for bucket 146 bucket 145: 20% Calculating Z arrays for bucket 146 bucket 145: 30% Entering block accumulator loop for bucket 146: bucket 145: 40% bucket 146: 10% bucket 145: 50% bucket 146: 20% bucket 145: 60% bucket 146: 30% bucket 145: 70% bucket 146: 40% bucket 145: 80% bucket 146: 50% bucket 145: 90% bucket 146: 60% bucket 145: 100% bucket 146: 70% Sorting block of length 23 for bucket 145 (Using difference cover) bucket 146: 80% bucket 146: 90% bucket 146: 100% Sorting block of length 14 for bucket 146 (Using difference cover) Getting block 147 of 202 Reserving size (36) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 147: 10% bucket 147: 20% Getting block 148 of 202 bucket 147: 30% Reserving size (36) for bucket 148 bucket 147: 40% Calculating Z arrays for bucket 148 bucket 147: 50% bucket 147: 60% Entering block accumulator loop for bucket 148: bucket 147: 70% Getting block 149 of 202 bucket 147: 80% bucket 148: 10% Reserving size (36) for bucket 149 bucket 147: 90% Calculating Z arrays for bucket 149 bucket 148: 20% bucket 147: 100% bucket 148: 30% Sorting block of length 31 for bucket 147 (Using difference cover) Entering block accumulator loop for bucket 149: bucket 148: 40% Getting block 150 of 202 bucket 148: 50% Sorting block time: 00:00:00 bucket 149: 10% Reserving size (36) for bucket 150 Returning block of 30 for bucket 125 bucket 148: 60% bucket 149: 20% Calculating Z arrays for bucket 150 bucket 148: 70% bucket 149: 30% bucket 148: 80% Entering block accumulator loop for bucket 150: bucket 149: 40% bucket 148: 90% bucket 149: 50% bucket 148: 100% bucket 150: 10% bucket 149: 60% Sorting block of length 33 for bucket 148 (Using difference cover) bucket 150: 20% bucket 149: 70% bucket 150: 30% bucket 149: 80% bucket 150: 40% bucket 149: 90% bucket 150: 50% Sorting block time: 00:00:00 bucket 149: 100% Returning block of 34 for bucket 123 bucket 150: 60% Sorting block of length 25 for bucket 149 (Using difference cover) Getting block 151 of 202 bucket 150: 70% Reserving size (36) for bucket 151 bucket 150: 80% Calculating Z arrays for bucket 151 bucket 150: 90% bucket 150: 100% Entering block accumulator loop for bucket 151: Sorting block of length 25 for bucket 150 (Using difference cover) bucket 151: 10% bucket 151: 20% bucket 151: 30% Getting block 152 of 202 bucket 151: 40% Reserving size (36) for bucket 152 bucket 151: 50% Calculating Z arrays for bucket 152 bucket 151: 60% bucket 151: 70% Entering block accumulator loop for bucket 152: bucket 151: 80% bucket 151: 90% bucket 152: 10% bucket 151: 100% Sorting block of length 24 for bucket 151 (Using difference cover) bucket 152: 20% bucket 152: 30% bucket 152: 40% bucket 152: 50% bucket 152: 60% bucket 152: 70% bucket 152: 80% bucket 152: 90% bucket 152: 100% Sorting block of length 20 for bucket 152 (Using difference cover) Sorting block time: 00:00:00 Returning block of 28 for bucket 122 Getting block 153 of 202 Reserving size (36) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 153: 10% bucket 153: 20% bucket 153: 30% Sorting block time: 00:00:00 Returning block of 34 for bucket 129 bucket 153: 40% bucket 153: 50% bucket 153: 60% bucket 153: 70% bucket 153: 80% bucket 153: 90% bucket 153: 100% Sorting block of length 24 for bucket 153 (Using difference cover) Getting block 154 of 202 Reserving size (36) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 154: 10% bucket 154: 20% bucket 154: 30% bucket 154: 40% Sorting block time: 00:00:00 Returning block of 17 for bucket 128 bucket 154: 50% bucket 154: 60% bucket 154: 70% bucket 154: 80% bucket 154: 90% bucket 154: 100% Sorting block of length 18 for bucket 154 (Using difference cover) Getting block 155 of 202 Reserving size (36) for bucket 155 Calculating Z arrays for bucket 155 Sorting block time: 00:00:00 Returning block of 30 for bucket 131 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 155: Returning block of 36 for bucket 130 bucket 155: 10% bucket 155: 20% bucket 155: 30% bucket 155: 40% bucket 155: 50% bucket 155: 60% bucket 155: 70% bucket 155: 80% bucket 155: 90% bucket 155: 100% Sorting block of length 29 for bucket 155 (Using difference cover) Getting block 156 of 202 Reserving size (36) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 156: 10% bucket 156: 20% Getting block 157 of 202 bucket 156: 30% Sorting block time: 00:00:00 Reserving size (36) for bucket 157 Returning block of 31 for bucket 127 bucket 156: 40% Calculating Z arrays for bucket 157 bucket 156: 50% bucket 156: 60% Entering block accumulator loop for bucket 157: bucket 156: 70% bucket 156: 80% bucket 157: 10% bucket 156: 90% bucket 157: 20% bucket 156: 100% bucket 157: 30% Sorting block of length 33 for bucket 156 (Using difference cover) bucket 157: 40% bucket 157: 50% bucket 157: 60% bucket 157: 70% Getting block 158 of 202 bucket 157: 80% Reserving size (36) for bucket 158 Calculating Z arrays for bucket 158 bucket 157: 90% bucket 157: 100% Sorting block of length 27 for bucket 157 (Using difference cover) Entering block accumulator loop for bucket 158: bucket 158: 10% bucket 158: 20% bucket 158: 30% bucket 158: 40% bucket 158: 50% bucket 158: 60% Sorting block time: 00:00:00 Returning block of 22 for bucket 136 bucket 158: 70% bucket 158: 80% bucket 158: 90% bucket 158: 100% Sorting block of length 32 for bucket 158 (Using difference cover) Getting block 159 of 202 Reserving size (36) for bucket 159 Calculating Z arrays for bucket 159 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 22 for bucket 135 Returning block of 34 for bucket 133 Entering block accumulator loop for bucket 159: Sorting block time: 00:00:00 Returning block of 8 for bucket 132 bucket 159: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 159: 20% Returning block of 19 for bucket 134 Returning block of 15 for bucket 146 bucket 159: 30% bucket 159: 40% bucket 159: 50% bucket 159: 60% bucket 159: 70% bucket 159: 80% Getting block 160 of 202 bucket 159: 90% Reserving size (36) for bucket 160 bucket 159: 100% Calculating Z arrays for bucket 160 Sorting block of length 34 for bucket 159 (Using difference cover) Entering block accumulator loop for bucket 160: bucket 160: 10% Getting block 161 of 202 bucket 160: 20% Reserving size (36) for bucket 161 bucket 160: 30% Calculating Z arrays for bucket 161 bucket 160: 40% Sorting block time: 00:00:00 Returning block of 27 for bucket 142 Sorting block time: 00:00:00 bucket 160: 50% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 161: Sorting block time: 00:00:00 Returning block of 33 for bucket 141 Sorting block time: 00:00:00 Returning block of 10 for bucket 138 bucket 160: 60% Getting block 162 of 202 Returning block of 27 for bucket 137 Returning block of 31 for bucket 140 bucket 160: 70% bucket 161: 10% Reserving size (36) for bucket 162 Getting block 163 of 202 bucket 160: 80% Calculating Z arrays for bucket 162 bucket 161: 20% Reserving size (36) for bucket 163 bucket 160: 90% bucket 161: 30% Calculating Z arrays for bucket 163 Getting block 164 of 202 Entering block accumulator loop for bucket 162: bucket 160: 100% bucket 161: 40% Sorting block time: 00:00:00 Reserving size (36) for bucket 164 Entering block accumulator loop for bucket 163: Sorting block time: 00:00:00 Sorting block of length 23 for bucket 160 (Using difference cover) Getting block 165 of 202 Returning block of 24 for bucket 143 bucket 161: 50% Calculating Z arrays for bucket 164 Returning block of 34 for bucket 139 bucket 162: 10% Reserving size (36) for bucket 165 Sorting block time: 00:00:00 bucket 161: 60% bucket 163: 10% Entering block accumulator loop for bucket 164: bucket 162: 20% Calculating Z arrays for bucket 165 Returning block of 24 for bucket 145 bucket 161: 70% Sorting block time: 00:00:00 bucket 163: 20% Getting block 166 of 202 bucket 162: 30% Entering block accumulator loop for bucket 165: Returning block of 30 for bucket 144 bucket 161: 80% bucket 163: 30% bucket 164: 10% Reserving size (36) for bucket 166 bucket 162: 40% bucket 161: 90% bucket 163: 40% bucket 164: 20% Calculating Z arrays for bucket 166 bucket 165: 10% bucket 162: 50% bucket 161: 100% bucket 163: 50% bucket 164: 30% bucket 165: 20% Entering block accumulator loop for bucket 166: Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 162: 60% Sorting block time: 00:00:00 Sorting block of length 28 for bucket 161 Sorting block time: 00:00:00 (Using difference cover) bucket 163: 60% bucket 164: 40% bucket 165: 30% Returning block of 32 for bucket 147 Returning block of 26 for bucket 149 Returning block of 34 for bucket 148 Returning block of 25 for bucket 151 bucket 162: 70% Returning block of 26 for bucket 150 bucket 163: 70% Getting block 167 of 202 bucket 164: 50% bucket 165: 40% Sorting block time: 00:00:00 bucket 166: 10% bucket 162: 80% Getting block 168 of 202 bucket 163: 80% Reserving size (36) for bucket 167 bucket 164: 60% Returning block of 21 for bucket 152 bucket 165: 50% Sorting block time: 00:00:00 bucket 166: 20% bucket 162: 90% Sorting block time: 00:00:00 Reserving size (36) for bucket 168 Sorting block time: 00:00:00 Getting block 169 of 202 bucket 163: 90% Calculating Z arrays for bucket 167 bucket 164: 70% Returning block of 30 for bucket 155 bucket 165: 60% bucket 166: 30% Returning block of 25 for bucket 153 bucket 162: 100% Calculating Z arrays for bucket 168 Returning block of 19 for bucket 154 Reserving size (36) for bucket 169 bucket 163: 100% Getting block 170 of 202 bucket 164: 80% Entering block accumulator loop for bucket 167: Sorting block time: 00:00:00 bucket 165: 70% bucket 166: 40% Sorting block of length 27 for bucket 162 (Using difference cover) Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 168: Sorting block of length 29 for bucket 163 (Using difference cover) Reserving size (36) for bucket 170 bucket 164: 90% Getting block 171 of 202 Returning block of 33 for bucket 158 bucket 165: 80% bucket 166: 50% Entering block accumulator loop for bucket 169: Calculating Z arrays for bucket 170 Getting block 172 of 202 bucket 164: 100% bucket 167: 10% Reserving size (36) for bucket 171 bucket 165: 90% bucket 166: 60% bucket 168: 10% Reserving size (36) for bucket 172 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 173 of 202 Sorting block of length 31 for bucket 164 (Using difference cover) Sorting block time: 00:00:00 Entering block accumulator loop for bucket 170: Calculating Z arrays for bucket 171 bucket 167: 20% Getting block 174 of 202 bucket 165: 100% bucket 166: 70% bucket 169: 10% bucket 168: 20% Calculating Z arrays for bucket 172 Returning block of 35 for bucket 159 Returning block of 34 for bucket 156 Reserving size (36) for bucket 173 Returning block of 28 for bucket 157 bucket 167: 30% Reserving size (36) for bucket 174 Entering block accumulator loop for bucket 171: Sorting block of length 17 for bucket 165 (Using difference cover) Getting block 175 of 202 bucket 166: 80% bucket 169: 20% Sorting block time: 00:00:00 bucket 168: 30% Entering block accumulator loop for bucket 172: Calculating Z arrays for bucket 173 Getting block 176 of 202 bucket 170: 10% Calculating Z arrays for bucket 174 bucket 167: 40% Reserving size (36) for bucket 175 bucket 166: 90% Returning block of 24 for bucket 160 bucket 169: 30% bucket 168: 40% Getting block 177 of 202 Reserving size (36) for bucket 176 Entering block accumulator loop for bucket 173: bucket 170: 20% bucket 167: 50% bucket 171: 10% Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 174: bucket 166: 100% Sorting block time: 00:00:00 bucket 169: 40% Sorting block time: 00:00:00 bucket 168: 50% bucket 172: 10% Reserving size (36) for bucket 177 Getting block 178 of 202 Calculating Z arrays for bucket 176 bucket 170: 30% bucket 167: 60% bucket 171: 20% Entering block accumulator loop for bucket 175: Returning block of 29 for bucket 161 Sorting block of length 33 for bucket 166 (Using difference cover) Getting block 179 of 202 Returning block of 28 for bucket 162 bucket 169: 50% bucket 168: 60% bucket 172: 20% Calculating Z arrays for bucket 177 Reserving size (36) for bucket 178 bucket 173: 10% bucket 170: 40% Entering block accumulator loop for bucket 176: bucket 167: 70% bucket 171: 30% bucket 174: 10% Reserving size (36) for bucket 179 Getting block 180 of 202 bucket 169: 60% bucket 168: 70% bucket 172: 30% Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 177: bucket 173: 20% bucket 170: 50% bucket 167: 80% bucket 171: 40% bucket 174: 20% bucket 175: 10% Calculating Z arrays for bucket 179 Reserving size (36) for bucket 180 bucket 169: 70% bucket 168: 80% bucket 172: 40% Entering block accumulator loop for bucket 178: bucket 173: 30% bucket 176: 10% bucket 170: 60% Getting block 181 of 202 bucket 167: 90% bucket 171: 50% bucket 174: 30% bucket 175: 20% Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 179: bucket 169: 80% bucket 168: 90% bucket 177: 10% bucket 172: 50% bucket 173: 40% bucket 176: 20% Getting block 182 of 202 bucket 170: 70% Reserving size (36) for bucket 181 bucket 167: 100% bucket 171: 60% bucket 174: 40% Sorting block time: 00:00:00 bucket 175: 30% Entering block accumulator loop for bucket 180: bucket 169: 90% bucket 178: 10% bucket 168: 100% bucket 177: 20% Getting block 183 of 202 bucket 172: 60% bucket 173: 50% bucket 176: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (36) for bucket 182 bucket 170: 80% Calculating Z arrays for bucket 181 Sorting block of length 32 for bucket 167 (Using difference cover) bucket 171: 70% Returning block of 30 for bucket 163 Sorting block time: 00:00:00 bucket 174: 50% Getting block 184 of 202 bucket 175: 40% bucket 179: 10% bucket 169: 100% bucket 178: 20% Sorting block of length 33 for bucket 168 (Using difference cover) bucket 177: 30% Reserving size (36) for bucket 183 bucket 172: 70% bucket 173: 60% Getting block 185 of 202 Returning block of 32 for bucket 164 Returning block of 18 for bucket 165 bucket 176: 40% Calculating Z arrays for bucket 182 bucket 170: 90% Entering block accumulator loop for bucket 181: bucket 171: 80% Returning block of 34 for bucket 166 bucket 174: 60% Reserving size (36) for bucket 184 Getting block 186 of 202 bucket 175: 50% bucket 179: 20% bucket 180: 10% Sorting block of length 13 for bucket 169 (Using difference cover) bucket 178: 30% bucket 177: 40% Calculating Z arrays for bucket 183 bucket 172: 80% bucket 173: 70% Reserving size (36) for bucket 185 bucket 176: 50% bucket 170: 100% Entering block accumulator loop for bucket 182: bucket 171: 90% bucket 174: 70% Calculating Z arrays for bucket 184 Reserving size (36) for bucket 186 bucket 175: 60% bucket 179: 30% bucket 180: 20% bucket 178: 40% bucket 177: 50% Getting block 187 of 202 bucket 172: 90% Entering block accumulator loop for bucket 183: bucket 173: 80% Calculating Z arrays for bucket 185 bucket 176: 60% Sorting block of length 31 for bucket 170 (Using difference cover) Sorting block time: 00:00:00 Getting block 188 of 202 bucket 181: 10% bucket 171: 100% bucket 174: 80% Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 184: bucket 175: 70% bucket 179: 40% bucket 180: 30% bucket 178: 50% Sorting block time: 00:00:00 bucket 177: 60% Reserving size (36) for bucket 187 bucket 172: 100% bucket 173: 90% bucket 176: 70% Entering block accumulator loop for bucket 185: bucket 182: 10% Returning block of 33 for bucket 167 Reserving size (36) for bucket 188 bucket 181: 20% Sorting block of length 28 for bucket 171 (Using difference cover) bucket 174: 90% Entering block accumulator loop for bucket 186: Getting block 189 of 202 bucket 175: 80% bucket 179: 50% bucket 180: 40% Returning block of 34 for bucket 168 bucket 178: 60% bucket 177: 70% Calculating Z arrays for bucket 187 Sorting block time: 00:00:00 Sorting block of length 16 for bucket 172 (Using difference cover) bucket 183: 10% bucket 173: 100% bucket 176: 80% Getting block 190 of 202 bucket 182: 20% Getting block 191 of 202 Calculating Z arrays for bucket 188 bucket 181: 30% Getting block 192 of 202 bucket 174: 100% bucket 184: 10% Reserving size (36) for bucket 189 bucket 175: 90% bucket 179: 60% bucket 180: 50% Getting block 193 of 202 bucket 178: 70% bucket 177: 80% Returning block of 14 for bucket 169 Entering block accumulator loop for bucket 187: Sorting block time: 00:00:00 bucket 183: 20% Sorting block of length 19 for bucket 173 (Using difference cover) bucket 176: 90% bucket 185: 10% Reserving size (36) for bucket 190 bucket 182: 30% Reserving size (36) for bucket 191 bucket 181: 40% Reserving size (36) for bucket 192 Entering block accumulator loop for bucket 188: Sorting block of length 31 for bucket 174 (Using difference cover) bucket 184: 20% bucket 186: 10% Calculating Z arrays for bucket 189 bucket 175: 100% bucket 179: 70% bucket 180: 60% Reserving size (36) for bucket 193 bucket 178: 80% bucket 177: 90% Returning block of 32 for bucket 170 bucket 183: 30% Getting block 194 of 202 bucket 176: 100% bucket 185: 20% Calculating Z arrays for bucket 190 bucket 182: 40% Calculating Z arrays for bucket 191 bucket 181: 50% Calculating Z arrays for bucket 192 bucket 184: 30% bucket 186: 20% Sorting block of length 14 for bucket 175 (Using difference cover) Entering block accumulator loop for bucket 189: bucket 179: 80% Getting block 195 of 202 bucket 180: 70% Calculating Z arrays for bucket 193 bucket 178: 90% bucket 177: 100% bucket 187: 10% bucket 183: 40% Reserving size (36) for bucket 194 Sorting block of length 27 for bucket 176 (Using difference cover) bucket 185: 30% bucket 182: 50% Entering block accumulator loop for bucket 190: bucket 181: 60% Entering block accumulator loop for bucket 191: Getting block 196 of 202 bucket 188: 10% bucket 184: 40% Entering block accumulator loop for bucket 192: Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 186: 30% bucket 179: 90% Reserving size (36) for bucket 195 bucket 180: 80% bucket 178: 100% Sorting block of length 35 for bucket 177 (Using difference cover) Entering block accumulator loop for bucket 193: bucket 187: 20% Calculating Z arrays for bucket 194 bucket 183: 50% bucket 185: 40% bucket 182: 60% bucket 181: 70% Reserving size (36) for bucket 196 bucket 188: 20% bucket 184: 50% Returning block of 29 for bucket 171 Returning block of 17 for bucket 172 bucket 186: 40% bucket 189: 10% Sorting block time: 00:00:00 bucket 179: 100% Calculating Z arrays for bucket 195 Getting block 197 of 202 bucket 180: 90% Sorting block of length 27 for bucket 178 (Using difference cover) bucket 187: 30% bucket 183: 60% Entering block accumulator loop for bucket 194: bucket 185: 50% bucket 182: 70% bucket 190: 10% bucket 181: 80% bucket 191: 10% Calculating Z arrays for bucket 196 bucket 188: 30% bucket 184: 60% bucket 192: 10% Returning block of 20 for bucket 173 bucket 186: 50% bucket 189: 20% Sorting block of length 24 for bucket 179 (Using difference cover) Reserving size (36) for bucket 197 Entering block accumulator loop for bucket 195: bucket 180: 100% bucket 193: 10% bucket 187: 40% bucket 183: 70% bucket 185: 60% bucket 182: 80% bucket 190: 20% bucket 181: 90% bucket 191: 20% bucket 188: 40% Entering block accumulator loop for bucket 196: bucket 184: 70% bucket 192: 20% bucket 186: 60% bucket 189: 30% Calculating Z arrays for bucket 197 Sorting block of length 14 for bucket 180 (Using difference cover) Sorting block time: 00:00:00 bucket 193: 20% bucket 187: 50% bucket 183: 80% bucket 194: 10% bucket 185: 70% Sorting block time: 00:00:00 bucket 182: 90% bucket 190: 30% Getting block 198 of 202 bucket 181: 100% bucket 191: 30% bucket 188: 50% bucket 184: 80% Sorting block time: 00:00:00 bucket 192: 30% bucket 186: 70% bucket 189: 40% Getting block 199 of 202 bucket 195: 10% Entering block accumulator loop for bucket 197: Returning block of 32 for bucket 174 bucket 193: 30% bucket 187: 60% bucket 183: 90% bucket 194: 20% Returning block of 28 for bucket 176 bucket 185: 80% bucket 182: 100% bucket 190: 40% Reserving size (36) for bucket 198 Sorting block of length 23 for bucket 181 (Using difference cover) Getting block 200 of 202 bucket 191: 40% bucket 188: 60% bucket 196: 10% Returning block of 15 for bucket 175 bucket 184: 90% bucket 192: 40% bucket 186: 80% bucket 189: 50% Reserving size (36) for bucket 199 bucket 195: 20% bucket 193: 40% bucket 187: 70% bucket 183: 100% bucket 194: 30% bucket 185: 90% Sorting block of length 18 for bucket 182 (Using difference cover) bucket 190: 50% Calculating Z arrays for bucket 198 Reserving size (36) for bucket 200 bucket 191: 50% bucket 188: 70% bucket 196: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 184: 100% bucket 192: 50% bucket 186: 90% bucket 189: 60% Calculating Z arrays for bucket 199 bucket 195: 30% bucket 197: 10% bucket 193: 50% bucket 187: 80% Sorting block of length 32 for bucket 183 (Using difference cover) bucket 194: 40% bucket 185: 100% bucket 190: 60% Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 198: bucket 191: 60% bucket 188: 80% Getting block 201 of 202 Returning block of 36 for bucket 177 Sorting block time: 00:00:00 Returning block of 28 for bucket 178 bucket 196: 30% Sorting block of length 29 for bucket 184 (Using difference cover) bucket 192: 60% bucket 186: 100% bucket 189: 70% bucket 195: 40% Entering block accumulator loop for bucket 199: bucket 197: 20% bucket 193: 60% bucket 187: 90% bucket 194: 50% Sorting block of length 32 for bucket 185 (Using difference cover) bucket 190: 70% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 200: bucket 191: 70% bucket 188: 90% Reserving size (36) for bucket 201 Returning block of 25 for bucket 179 bucket 196: 40% Getting block 202 of 202 bucket 192: 70% Sorting block of length 6 for bucket 186 (Using difference cover) bucket 189: 80% bucket 195: 50% bucket 197: 30% bucket 193: 70% bucket 187: 100% bucket 194: 60% Returning block of 15 for bucket 180 bucket 190: 80% bucket 198: 10% bucket 191: 80% bucket 188: 100% Calculating Z arrays for bucket 201 bucket 196: 50% Reserving size (36) for bucket 202 bucket 192: 80% bucket 189: 90% bucket 195: 60% bucket 199: 10% Sorting block time: 00:00:00 bucket 197: 40% bucket 193: 80% Sorting block of length 30 for bucket 187 (Using difference cover) bucket 194: 70% bucket 190: 90% bucket 200: 10% bucket 198: 20% bucket 191: 90% Sorting block of length 33 for bucket 188 (Using difference cover) bucket 196: 60% Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 201: bucket 192: 90% bucket 189: 100% bucket 195: 70% Returning block of 19 for bucket 182 bucket 199: 20% bucket 197: 50% bucket 193: 90% bucket 194: 80% Sorting block time: 00:00:00 bucket 190: 100% bucket 200: 20% bucket 198: 30% bucket 191: 100% bucket 196: 70% Entering block accumulator loop for bucket 202: bucket 192: 100% Sorting block of length 25 for bucket 189 (Using difference cover) bucket 195: 80% bucket 199: 30% bucket 197: 60% bucket 193: 100% Returning block of 24 for bucket 181 bucket 194: 90% Sorting block of length 19 for bucket 190 (Using difference cover) bucket 200: 30% bucket 198: 40% Sorting block of length 35 for bucket 191 (Using difference cover) bucket 196: 80% bucket 201: 10% Sorting block of length 34 for bucket 192 (Using difference cover) bucket 195: 90% bucket 199: 40% bucket 197: 70% Sorting block of length 14 for bucket 193 (Using difference cover) bucket 194: 100% bucket 200: 40% bucket 198: 50% bucket 196: 90% bucket 202: 10% bucket 201: 20% bucket 195: 100% bucket 199: 50% bucket 197: 80% Sorting block of length 33 for bucket 194 (Using difference cover) bucket 200: 50% bucket 198: 60% Sorting block time: 00:00:00 bucket 196: 100% bucket 202: 20% bucket 201: 30% Sorting block of length 35 for bucket 195 (Using difference cover) bucket 199: 60% Sorting block time: 00:00:00 bucket 197: 90% bucket 200: 60% Returning block of 33 for bucket 183 bucket 198: 70% Sorting block of length 19 for bucket 196 (Using difference cover) bucket 202: 30% bucket 201: 40% Returning block of 7 for bucket 186 bucket 199: 70% bucket 197: 100% bucket 200: 70% bucket 198: 80% bucket 202: 40% bucket 201: 50% bucket 199: 80% Sorting block of length 18 for bucket 197 (Using difference cover) bucket 200: 80% bucket 198: 90% bucket 202: 50% bucket 201: 60% bucket 199: 90% bucket 200: 90% bucket 198: 100% bucket 202: 60% bucket 201: 70% bucket 199: 100% bucket 200: 100% Sorting block of length 32 for bucket 198 (Using difference cover) bucket 202: 70% bucket 201: 80% Sorting block of length 26 for bucket 199 (Using difference cover) Sorting block of length 29 for bucket 200 (Using difference cover) bucket 202: 80% bucket 201: 90% bucket 202: 90% bucket 201: 100% bucket 202: 100% Sorting block of length 22 for bucket 201 (Using difference cover) Sorting block of length 21 for bucket 202 (Using difference cover) Sorting block time: 00:00:00 Returning block of 30 for bucket 184 Sorting block time: 00:00:00 Returning block of 34 for bucket 188 Sorting block time: 00:00:00 Returning block of 33 for bucket 185 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 19 for bucket 197 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 26 for bucket 189 Returning block of 31 for bucket 187 Returning block of 36 for bucket 191 Returning block of 35 for bucket 192 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 15 for bucket 193 Returning block of 34 for bucket 194 Sorting block time: 00:00:00 Returning block of 30 for bucket 200 Returning block of 36 for bucket 195 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 33 for bucket 198 Returning block of 27 for bucket 199 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 22 for bucket 202 Sorting block time: 00:00:00 Returning block of 23 for bucket 201 Returning block of 20 for bucket 190 Sorting block time: 00:00:00 Returning block of 20 for bucket 196 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1291 fchr[G]: 1291 fchr[T]: 2545 fchr[$]: 5386 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4196346 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 1352 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 5386 bwtLen: 5387 sz: 1347 bwtSz: 1347 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 337 offsSz: 1348 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 29 numLines: 29 ebwtTotLen: 1856 ebwtTotSz: 1856 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:00 Preparing indexing of GA converted genome in /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/GA_conversion/ Child process: Starting to index G->A converted genome with the following command: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2-build -f genome_mfa.GA_conversion.fa BS_GA --threads 28 Settings: Output files: "BS_GA.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 112 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: genome_mfa.GA_conversion.fa Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:00 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: 48 Using parameters --bmax 36 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 36 --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 308 sample suffixes Generating random suffixes QSorting 308 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 302 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 36, merged 144; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 20, merged 15; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 9, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 5; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 26.0704 (target: 35) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 2 of 199 Getting block 3 of 199 Getting block 1 of 199 Reserving size (36) for bucket 2 Getting block 4 of 199 Reserving size (36) for bucket 3 Reserving size (36) for bucket 1 Getting block 5 of 199 Getting block 6 of 199 Getting block 7 of 199 Getting block 8 of 199 Getting block 9 of 199 Getting block 10 of 199 Getting block 11 of 199 Getting block 12 of 199 Calculating Z arrays for bucket 2 Reserving size (36) for bucket 4 Getting block 13 of 199 Getting block 14 of 199 Getting block 15 of 199 Getting block 16 of 199 Getting block 17 of 199 Calculating Z arrays for bucket 3 Getting block 18 of 199 Getting block 19 of 199 Getting block 20 of 199 Getting block 21 of 199 Getting block 22 of 199 Calculating Z arrays for bucket 1 Reserving size (36) for bucket 5 Reserving size (36) for bucket 6 Getting block 23 of 199 Reserving size (36) for bucket 7 Reserving size (36) for bucket 8 Reserving size (36) for bucket 9 Reserving size (36) for bucket 10 Reserving size (36) for bucket 11 Reserving size (36) for bucket 12 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 2: Reserving size (36) for bucket 13 Reserving size (36) for bucket 14 Reserving size (36) for bucket 15 Reserving size (36) for bucket 16 Reserving size (36) for bucket 17 Entering block accumulator loop for bucket 3: Reserving size (36) for bucket 18 Reserving size (36) for bucket 19 Reserving size (36) for bucket 20 Reserving size (36) for bucket 21 Reserving size (36) for bucket 22 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 6 Reserving size (36) for bucket 23 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 9 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 11 Calculating Z arrays for bucket 12 Calculating Z arrays for bucket 13 Entering block accumulator loop for bucket 4: 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 Getting block 24 of 199 Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 23 Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 10: bucket 2: 10% Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 15: bucket 3: 10% Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 17: Reserving size (36) for bucket 24 Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 19: bucket 1: 10% Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 23: bucket 2: 20% bucket 4: 10% Getting block 25 of 199 bucket 3: 20% Calculating Z arrays for bucket 24 bucket 1: 20% bucket 5: 10% bucket 6: 10% bucket 7: 10% bucket 9: 10% bucket 8: 10% bucket 10: 10% bucket 2: 30% bucket 11: 10% bucket 4: 20% bucket 12: 10% bucket 13: 10% bucket 14: 10% bucket 15: 10% Reserving size (36) for bucket 25 bucket 3: 30% bucket 16: 10% bucket 17: 10% bucket 18: 10% bucket 19: 10% bucket 1: 30% bucket 20: 10% bucket 21: 10% bucket 22: 10% bucket 5: 20% bucket 23: 10% Entering block accumulator loop for bucket 24: bucket 6: 20% bucket 7: 20% bucket 9: 20% bucket 8: 20% bucket 10: 20% bucket 2: 40% bucket 11: 20% bucket 4: 30% bucket 12: 20% bucket 13: 20% bucket 14: 20% bucket 15: 20% Calculating Z arrays for bucket 25 bucket 3: 40% bucket 16: 20% bucket 17: 20% bucket 18: 20% bucket 19: 20% bucket 1: 40% bucket 20: 20% bucket 21: 20% bucket 22: 20% bucket 5: 30% bucket 23: 20% bucket 6: 30% bucket 7: 30% bucket 9: 30% bucket 8: 30% bucket 10: 30% bucket 2: 50% bucket 11: 30% bucket 4: 40% bucket 12: 30% bucket 13: 30% Getting block 26 of 199 bucket 14: 30% bucket 15: 30% bucket 3: 50% bucket 16: 30% bucket 17: 30% Entering block accumulator loop for bucket 25: bucket 18: 30% bucket 19: 30% bucket 1: 50% bucket 20: 30% bucket 21: 30% bucket 22: 30% bucket 5: 40% bucket 23: 30% bucket 24: 10% bucket 6: 40% bucket 7: 40% bucket 9: 40% bucket 8: 40% bucket 10: 40% bucket 2: 60% bucket 11: 40% bucket 4: 50% bucket 12: 40% bucket 13: 40% Reserving size (36) for bucket 26 bucket 14: 40% bucket 15: 40% bucket 3: 60% bucket 16: 40% bucket 17: 40% bucket 18: 40% bucket 19: 40% bucket 1: 60% bucket 20: 40% bucket 21: 40% bucket 22: 40% bucket 5: 50% bucket 23: 40% bucket 24: 20% bucket 6: 50% bucket 7: 50% bucket 9: 50% bucket 8: 50% bucket 10: 50% bucket 2: 70% bucket 11: 50% bucket 4: 60% bucket 12: 50% bucket 13: 50% Calculating Z arrays for bucket 26 bucket 14: 50% bucket 15: 50% bucket 3: 70% bucket 16: 50% bucket 17: 50% bucket 25: 10% bucket 18: 50% bucket 19: 50% bucket 1: 70% bucket 20: 50% bucket 21: 50% bucket 22: 50% bucket 5: 60% bucket 23: 50% bucket 24: 30% bucket 6: 60% Getting block 27 of 199 bucket 7: 60% bucket 9: 60% bucket 8: 60% bucket 10: 60% bucket 2: 80% bucket 11: 60% bucket 4: 70% bucket 12: 60% bucket 13: 60% bucket 14: 60% bucket 15: 60% bucket 3: 80% Entering block accumulator loop for bucket 26: bucket 16: 60% bucket 17: 60% bucket 25: 20% bucket 18: 60% bucket 19: 60% bucket 1: 80% bucket 20: 60% bucket 21: 60% bucket 22: 60% bucket 5: 70% bucket 23: 60% bucket 24: 40% bucket 6: 70% Reserving size (36) for bucket 27 bucket 7: 70% bucket 9: 70% bucket 8: 70% bucket 10: 70% bucket 2: 90% bucket 11: 70% bucket 4: 80% bucket 12: 70% bucket 13: 70% bucket 14: 70% bucket 15: 70% bucket 3: 90% bucket 16: 70% bucket 17: 70% bucket 25: 30% bucket 18: 70% bucket 19: 70% bucket 1: 90% bucket 20: 70% bucket 21: 70% bucket 22: 70% bucket 5: 80% bucket 23: 70% bucket 24: 50% bucket 6: 80% Calculating Z arrays for bucket 27 bucket 7: 80% bucket 9: 80% bucket 8: 80% bucket 10: 80% bucket 2: 100% bucket 11: 80% bucket 4: 90% bucket 12: 80% bucket 13: 80% bucket 14: 80% bucket 15: 80% bucket 3: 100% bucket 26: 10% bucket 16: 80% bucket 17: 80% bucket 25: 40% bucket 18: 80% bucket 19: 80% bucket 1: 100% bucket 20: 80% bucket 21: 80% bucket 22: 80% bucket 5: 90% bucket 23: 80% bucket 24: 60% bucket 6: 90% bucket 7: 90% bucket 9: 90% Entering block accumulator loop for bucket 27: bucket 8: 90% bucket 10: 90% Sorting block of length 33 for bucket 2 bucket 11: 90% (Using difference cover) bucket 4: 100% bucket 12: 90% bucket 13: 90% bucket 14: 90% Sorting block of length 29 for bucket 3 (Using difference cover) bucket 15: 90% bucket 26: 20% bucket 16: 90% bucket 17: 90% bucket 25: 50% bucket 18: 90% bucket 19: 90% Sorting block of length 23 for bucket 1 (Using difference cover) bucket 20: 90% bucket 21: 90% bucket 22: 90% bucket 5: 100% bucket 23: 90% bucket 24: 70% bucket 6: 100% bucket 7: 100% bucket 9: 100% bucket 8: 100% bucket 10: 100% bucket 11: 100% Sorting block of length 32 for bucket 4 (Using difference cover) bucket 12: 100% bucket 13: 100% bucket 14: 100% bucket 15: 100% bucket 26: 30% bucket 16: 100% bucket 17: 100% bucket 25: 60% bucket 18: 100% bucket 19: 100% bucket 20: 100% bucket 21: 100% bucket 22: 100% Sorting block of length 14 for bucket 5 (Using difference cover) bucket 23: 100% bucket 24: 80% Sorting block of length 33 for bucket 6 (Using difference cover) Sorting block of length 9 for bucket 7 (Using difference cover) Sorting block of length 32 for bucket 9 (Using difference cover) Sorting block of length 28 for bucket 8 (Using difference cover) bucket 27: 10% Sorting block of length 25 for bucket 10 (Using difference cover) Sorting block of length 34 for bucket 11 (Using difference cover) Sorting block of length 31 for bucket 12 (Using difference cover) Sorting block of length 34 for bucket 13 (Using difference cover) Sorting block of length 22 for bucket 14 (Using difference cover) Sorting block of length 17 for bucket 15 (Using difference cover) bucket 26: 40% Sorting block of length 32 for bucket 16 (Using difference cover) Sorting block of length 35 for bucket 17 (Using difference cover) bucket 25: 70% Sorting block of length 35 for bucket 18 (Using difference cover) Sorting block of length 32 for bucket 19 (Using difference cover) Sorting block of length 24 for bucket 20 (Using difference cover) Sorting block of length 27 for bucket 21 (Using difference cover) Sorting block of length 13 for bucket 22 (Using difference cover) Sorting block of length 35 for bucket 23 (Using difference cover) bucket 24: 90% bucket 27: 20% bucket 26: 50% bucket 25: 80% bucket 24: 100% bucket 27: 30% bucket 26: 60% bucket 25: 90% Sorting block of length 20 for bucket 24 (Using difference cover) bucket 27: 40% bucket 26: 70% bucket 25: 100% bucket 27: 50% bucket 26: 80% Sorting block of length 34 for bucket 25 (Using difference cover) bucket 27: 60% bucket 26: 90% bucket 27: 70% bucket 26: 100% bucket 27: 80% Sorting block of length 15 for bucket 26 (Using difference cover) bucket 27: 90% bucket 27: 100% Sorting block of length 33 for bucket 27 (Using difference cover) Sorting block time: 00:00:00 Returning block of 34 for bucket 2 Getting block 28 of 199 Reserving size (36) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 28: 10% bucket 28: 20% bucket 28: 30% bucket 28: 40% bucket 28: 50% bucket 28: 60% bucket 28: 70% bucket 28: 80% bucket 28: 90% bucket 28: 100% Sorting block of length 35 for bucket 28 (Using difference cover) Sorting block time: 00:00:00 Returning block of 30 for bucket 3 Getting block 29 of 199 Reserving size (36) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 29: 10% bucket 29: 20% bucket 29: 30% bucket 29: 40% bucket 29: 50% bucket 29: 60% bucket 29: 70% bucket 29: 80% bucket 29: 90% bucket 29: 100% Sorting block of length 11 for bucket 29 (Using difference cover) Sorting block time: 00:00:00 Returning block of 24 for bucket 1 Getting block 30 of 199 Reserving size (36) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 30: 10% bucket 30: 20% bucket 30: 30% bucket 30: 40% bucket 30: 50% bucket 30: 60% bucket 30: 70% bucket 30: 80% bucket 30: 90% bucket 30: 100% Sorting block of length 30 for bucket 30 (Using difference cover) Sorting block time: 00:00:00 Returning block of 33 for bucket 4 Sorting block time: 00:00:00 Returning block of 15 for bucket 5 Getting block 31 of 199 Reserving size (36) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: bucket 31: 10% bucket 31: 20% bucket 31: 30% bucket 31: 40% Getting block 32 of 199 bucket 31: 50% Reserving size (36) for bucket 32 bucket 31: 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 Calculating Z arrays for bucket 32 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 28 for bucket 21 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 36 for bucket 18 Sorting block time: 00:00:00 Returning block of 36 for bucket 17 Sorting block time: 00:00:00 Returning block of 25 for bucket 20 Returning block of 33 for bucket 16 bucket 31: 70% Returning block of 29 for bucket 8 Returning block of 16 for bucket 26 Returning block of 35 for bucket 11 Returning block of 32 for bucket 12 Returning block of 33 for bucket 9 Returning block of 33 for bucket 19 Returning block of 14 for bucket 22 Entering block accumulator loop for bucket 32: Returning block of 34 for bucket 27 Sorting block time: 00:00:00 Returning block of 34 for bucket 6 bucket 31: 80% Returning block of 35 for bucket 13 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 33 of 199 Sorting block time: 00:00:00 bucket 31: 90% Sorting block time: 00:00:00 bucket 32: 10% Returning block of 18 for bucket 15 Getting block 34 of 199 Returning block of 23 for bucket 14 Returning block of 10 for bucket 7 Reserving size (36) for bucket 33 Returning block of 26 for bucket 10 Returning block of 36 for bucket 23 bucket 31: 100% bucket 32: 20% Reserving size (36) for bucket 34 Calculating Z arrays for bucket 33 Sorting block of length 16 for bucket 31 (Using difference cover) Getting block 35 of 199 bucket 32: 30% Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 33: Reserving size (36) for bucket 35 bucket 32: 40% Getting block 36 of 199 Sorting block time: 00:00:00 Calculating Z arrays for bucket 35 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 34: Sorting block time: 00:00:00 bucket 32: 50% Reserving size (36) for bucket 36 Sorting block time: 00:00:00 Returning block of 35 for bucket 25 bucket 33: 10% Returning block of 36 for bucket 28 Returning block of 21 for bucket 24 Entering block accumulator loop for bucket 35: Getting block 37 of 199 bucket 32: 60% Calculating Z arrays for bucket 36 Returning block of 12 for bucket 29 bucket 33: 20% bucket 34: 10% Reserving size (36) for bucket 37 bucket 32: 70% Getting block 38 of 199 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 36: bucket 33: 30% Sorting block time: 00:00:00 bucket 34: 20% bucket 35: 10% Calculating Z arrays for bucket 37 bucket 32: 80% Reserving size (36) for bucket 38 Returning block of 31 for bucket 30 Returning block of 17 for bucket 31 bucket 33: 40% bucket 34: 30% bucket 35: 20% bucket 32: 90% Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 37: Getting block 39 of 199 bucket 36: 10% bucket 33: 50% bucket 34: 40% bucket 35: 30% bucket 32: 100% Reserving size (36) for bucket 39 Entering block accumulator loop for bucket 38: bucket 36: 20% bucket 33: 60% bucket 34: 50% bucket 35: 40% Sorting block of length 24 for bucket 32 (Using difference cover) bucket 37: 10% Calculating Z arrays for bucket 39 bucket 36: 30% bucket 33: 70% bucket 34: 60% bucket 35: 50% bucket 37: 20% bucket 38: 10% bucket 36: 40% bucket 33: 80% Entering block accumulator loop for bucket 39: bucket 34: 70% bucket 35: 60% Getting block 40 of 199 bucket 37: 30% bucket 38: 20% bucket 36: 50% bucket 33: 90% bucket 34: 80% bucket 35: 70% Reserving size (36) for bucket 40 bucket 37: 40% bucket 38: 30% bucket 36: 60% bucket 33: 100% bucket 39: 10% bucket 34: 90% Sorting block time: 00:00:00 bucket 35: 80% Calculating Z arrays for bucket 40 Getting block 41 of 199 bucket 37: 50% bucket 38: 40% Sorting block of length 32 for bucket 33 (Using difference cover) bucket 36: 70% bucket 39: 20% Returning block of 25 for bucket 32 bucket 34: 100% bucket 35: 90% Reserving size (36) for bucket 41 Entering block accumulator loop for bucket 40: bucket 37: 60% bucket 38: 50% bucket 36: 80% bucket 39: 30% Sorting block of length 16 for bucket 34 (Using difference cover) Getting block 42 of 199 bucket 35: 100% Calculating Z arrays for bucket 41 bucket 37: 70% bucket 38: 60% Getting block 43 of 199 bucket 36: 90% bucket 39: 40% Reserving size (36) for bucket 42 Sorting block of length 32 for bucket 35 (Using difference cover) bucket 40: 10% bucket 37: 80% Getting block 44 of 199 Entering block accumulator loop for bucket 41: bucket 38: 70% Reserving size (36) for bucket 43 bucket 36: 100% bucket 39: 50% Calculating Z arrays for bucket 42 bucket 40: 20% bucket 37: 90% Reserving size (36) for bucket 44 bucket 38: 80% Sorting block time: 00:00:00 Calculating Z arrays for bucket 43 Getting block 45 of 199 Sorting block of length 34 for bucket 36 (Using difference cover) bucket 39: 60% Entering block accumulator loop for bucket 42: bucket 40: 30% bucket 37: 100% Calculating Z arrays for bucket 44 bucket 41: 10% Returning block of 33 for bucket 33 bucket 38: 90% Entering block accumulator loop for bucket 43: Reserving size (36) for bucket 45 Getting block 46 of 199 bucket 39: 70% bucket 40: 40% Sorting block of length 3 for bucket 37 (Using difference cover) bucket 41: 20% Entering block accumulator loop for bucket 44: Sorting block time: 00:00:00 bucket 38: 100% Calculating Z arrays for bucket 45 Reserving size (36) for bucket 46 bucket 39: 80% bucket 42: 10% bucket 40: 50% bucket 41: 30% Getting block 47 of 199 Returning block of 17 for bucket 34 bucket 43: 10% Sorting block of length 32 for bucket 38 (Using difference cover) Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 45: bucket 39: 90% bucket 42: 20% bucket 40: 60% bucket 41: 40% bucket 44: 10% Reserving size (36) for bucket 47 bucket 43: 20% Getting block 48 of 199 bucket 39: 100% Entering block accumulator loop for bucket 46: bucket 42: 30% Sorting block time: 00:00:00 bucket 40: 70% bucket 41: 50% bucket 44: 20% Calculating Z arrays for bucket 47 Sorting block time: 00:00:00 bucket 43: 30% Reserving size (36) for bucket 48 Getting block 49 of 199 bucket 45: 10% Sorting block of length 28 for bucket 39 (Using difference cover) Returning block of 33 for bucket 35 bucket 42: 40% bucket 40: 80% bucket 41: 60% Returning block of 4 for bucket 37 bucket 44: 30% Getting block 50 of 199 bucket 43: 40% Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 47: Reserving size (36) for bucket 49 bucket 45: 20% bucket 46: 10% bucket 42: 50% bucket 40: 90% bucket 41: 70% Sorting block time: 00:00:00 bucket 44: 40% Reserving size (36) for bucket 50 bucket 43: 50% Getting block 51 of 199 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 48: bucket 45: 30% bucket 46: 20% bucket 42: 60% bucket 40: 100% Getting block 52 of 199 Returning block of 35 for bucket 36 bucket 41: 80% bucket 44: 50% Calculating Z arrays for bucket 50 bucket 43: 60% bucket 47: 10% Sorting block time: 00:00:00 Reserving size (36) for bucket 51 Entering block accumulator loop for bucket 49: bucket 45: 40% Sorting block time: 00:00:00 bucket 46: 30% bucket 42: 70% Sorting block of length 14 for bucket 40 (Using difference cover) Reserving size (36) for bucket 52 bucket 41: 90% bucket 44: 60% bucket 43: 70% Entering block accumulator loop for bucket 50: Returning block of 33 for bucket 38 bucket 47: 20% Calculating Z arrays for bucket 51 bucket 48: 10% Returning block of 29 for bucket 39 bucket 45: 50% bucket 46: 40% bucket 42: 80% Calculating Z arrays for bucket 52 bucket 41: 100% bucket 44: 70% bucket 43: 80% Getting block 53 of 199 bucket 47: 30% bucket 48: 20% Entering block accumulator loop for bucket 51: Sorting block time: 00:00:00 bucket 49: 10% bucket 45: 60% bucket 46: 50% bucket 42: 90% Sorting block of length 21 for bucket 41 (Using difference cover) Getting block 54 of 199 Entering block accumulator loop for bucket 52: bucket 44: 80% bucket 43: 90% bucket 50: 10% Reserving size (36) for bucket 53 Getting block 55 of 199 bucket 47: 40% bucket 48: 30% Returning block of 15 for bucket 40 bucket 49: 20% bucket 45: 70% bucket 46: 60% bucket 42: 100% Reserving size (36) for bucket 54 bucket 44: 90% bucket 43: 100% bucket 50: 20% Calculating Z arrays for bucket 53 Reserving size (36) for bucket 55 Getting block 56 of 199 bucket 47: 50% bucket 48: 40% Sorting block time: 00:00:00 bucket 51: 10% bucket 49: 30% bucket 45: 80% Getting block 57 of 199 Sorting block of length 21 for bucket 42 (Using difference cover) bucket 46: 70% Calculating Z arrays for bucket 54 bucket 52: 10% bucket 44: 100% Sorting block of length 23 for bucket 43 (Using difference cover) bucket 50: 30% Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 53: Reserving size (36) for bucket 56 bucket 47: 60% Returning block of 22 for bucket 41 bucket 48: 50% bucket 51: 20% Getting block 58 of 199 bucket 49: 40% bucket 45: 90% Reserving size (36) for bucket 57 bucket 46: 80% bucket 52: 20% Sorting block of length 13 for bucket 44 (Using difference cover) Entering block accumulator loop for bucket 54: Getting block 59 of 199 bucket 50: 40% Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 55: bucket 47: 70% bucket 48: 60% bucket 51: 30% Reserving size (36) for bucket 58 Getting block 60 of 199 bucket 49: 50% bucket 45: 100% Calculating Z arrays for bucket 57 bucket 46: 90% bucket 52: 30% Reserving size (36) for bucket 59 Getting block 61 of 199 bucket 50: 50% bucket 53: 10% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 56: bucket 47: 80% bucket 48: 70% Calculating Z arrays for bucket 58 bucket 51: 40% Reserving size (36) for bucket 60 bucket 49: 60% Sorting block of length 35 for bucket 45 (Using difference cover) Getting block 62 of 199 bucket 46: 100% Entering block accumulator loop for bucket 57: bucket 52: 40% Calculating Z arrays for bucket 59 bucket 54: 10% Reserving size (36) for bucket 61 bucket 50: 60% Returning block of 22 for bucket 42 Getting block 63 of 199 bucket 53: 20% bucket 55: 10% Sorting block time: 00:00:00 bucket 47: 90% bucket 48: 80% bucket 51: 50% Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 58: bucket 49: 70% Reserving size (36) for bucket 62 Sorting block of length 23 for bucket 46 (Using difference cover) bucket 52: 50% Getting block 64 of 199 bucket 54: 20% Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 59: bucket 50: 70% Reserving size (36) for bucket 63 Sorting block time: 00:00:00 bucket 53: 30% Returning block of 24 for bucket 43 bucket 55: 20% bucket 56: 10% bucket 47: 100% bucket 48: 90% bucket 51: 60% Entering block accumulator loop for bucket 60: Getting block 65 of 199 bucket 49: 80% Calculating Z arrays for bucket 62 bucket 57: 10% Getting block 66 of 199 bucket 52: 60% Reserving size (36) for bucket 64 bucket 54: 30% Entering block accumulator loop for bucket 61: bucket 50: 80% Sorting block time: 00:00:00 Calculating Z arrays for bucket 63 Returning block of 14 for bucket 44 Getting block 67 of 199 Sorting block time: 00:00:00 bucket 53: 40% bucket 55: 30% bucket 56: 20% Sorting block of length 22 for bucket 47 (Using difference cover) bucket 48: 100% bucket 58: 10% bucket 51: 70% Reserving size (36) for bucket 65 bucket 49: 90% bucket 57: 20% Reserving size (36) for bucket 66 Entering block accumulator loop for bucket 62: Getting block 68 of 199 bucket 52: 70% Calculating Z arrays for bucket 64 bucket 54: 40% bucket 59: 10% Returning block of 36 for bucket 45 bucket 50: 90% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 63: Reserving size (36) for bucket 67 Returning block of 24 for bucket 46 Getting block 69 of 199 bucket 53: 50% bucket 55: 40% bucket 56: 30% Sorting block of length 18 for bucket 48 (Using difference cover) bucket 58: 20% bucket 51: 80% bucket 60: 10% Calculating Z arrays for bucket 65 bucket 49: 100% bucket 57: 30% Calculating Z arrays for bucket 66 Reserving size (36) for bucket 68 bucket 52: 80% bucket 61: 10% Entering block accumulator loop for bucket 64: bucket 54: 50% Sorting block time: 00:00:00 bucket 59: 20% Returning block of 23 for bucket 47 bucket 50: 100% Calculating Z arrays for bucket 67 Reserving size (36) for bucket 69 Getting block 70 of 199 bucket 53: 60% bucket 55: 50% bucket 56: 40% bucket 58: 30% bucket 51: 90% bucket 60: 20% Sorting block of length 34 for bucket 49 (Using difference cover) Entering block accumulator loop for bucket 65: Getting block 71 of 199 Entering block accumulator loop for bucket 66: bucket 62: 10% Calculating Z arrays for bucket 68 bucket 57: 40% bucket 52: 90% bucket 61: 20% Returning block of 19 for bucket 48 bucket 54: 60% bucket 59: 30% Sorting block of length 19 for bucket 50 (Using difference cover) bucket 63: 10% Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 67: Reserving size (36) for bucket 70 bucket 53: 70% bucket 55: 60% bucket 56: 50% bucket 58: 40% bucket 51: 100% bucket 60: 30% Getting block 72 of 199 Reserving size (36) for bucket 71 Getting block 73 of 199 Entering block accumulator loop for bucket 68: bucket 57: 50% bucket 52: 100% bucket 61: 30% bucket 64: 10% bucket 62: 20% bucket 54: 70% bucket 59: 40% bucket 63: 20% Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 69: bucket 53: 80% bucket 55: 70% Sorting block time: 00:00:00 bucket 56: 60% Sorting block of length 29 for bucket 51 (Using difference cover) bucket 58: 50% bucket 60: 40% Sorting block time: 00:00:00 bucket 65: 10% Reserving size (36) for bucket 72 Calculating Z arrays for bucket 71 Getting block 74 of 199 bucket 66: 10% Reserving size (36) for bucket 73 bucket 57: 60% Sorting block of length 22 for bucket 52 bucket 61: 40% (Using difference cover) bucket 64: 20% bucket 62: 30% bucket 54: 80% bucket 59: 50% bucket 63: 30% bucket 67: 10% Entering block accumulator loop for bucket 70: bucket 53: 90% Returning block of 35 for bucket 49 bucket 55: 80% bucket 56: 70% bucket 58: 60% Returning block of 20 for bucket 50 bucket 60: 50% bucket 65: 20% Calculating Z arrays for bucket 72 Reserving size (36) for bucket 74 Entering block accumulator loop for bucket 71: bucket 66: 20% Calculating Z arrays for bucket 73 Getting block 75 of 199 bucket 68: 10% bucket 57: 70% bucket 61: 50% Sorting block time: 00:00:00 bucket 64: 30% bucket 62: 40% bucket 54: 90% bucket 59: 60% bucket 63: 40% bucket 67: 20% Sorting block time: 00:00:00 bucket 69: 10% bucket 53: 100% bucket 55: 90% bucket 56: 80% bucket 58: 70% bucket 60: 60% bucket 65: 30% Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 72: bucket 66: 30% Reserving size (36) for bucket 75 Entering block accumulator loop for bucket 73: bucket 68: 20% bucket 57: 80% Returning block of 30 for bucket 51 bucket 61: 60% bucket 64: 40% bucket 62: 50% bucket 54: 100% bucket 59: 70% bucket 63: 50% Returning block of 23 for bucket 52 bucket 67: 30% bucket 70: 10% bucket 69: 20% Sorting block of length 30 for bucket 53 (Using difference cover) bucket 55: 100% bucket 56: 90% bucket 58: 80% bucket 60: 70% bucket 65: 40% bucket 71: 10% Entering block accumulator loop for bucket 74: bucket 66: 40% Calculating Z arrays for bucket 75 bucket 68: 30% bucket 57: 90% bucket 61: 70% bucket 64: 50% Getting block 76 of 199 bucket 62: 60% Sorting block of length 35 for bucket 54 (Using difference cover) bucket 59: 80% bucket 63: 60% bucket 67: 40% bucket 70: 20% bucket 69: 30% Sorting block of length 25 for bucket 55 (Using difference cover) bucket 56: 100% bucket 58: 90% bucket 60: 80% bucket 65: 50% Getting block 77 of 199 bucket 71: 20% bucket 72: 10% bucket 66: 50% bucket 73: 10% bucket 68: 40% Entering block accumulator loop for bucket 75: bucket 57: 100% bucket 61: 80% bucket 64: 60% Reserving size (36) for bucket 76 bucket 62: 70% bucket 59: 90% bucket 63: 70% bucket 67: 50% bucket 70: 30% bucket 69: 40% Sorting block of length 34 for bucket 56 (Using difference cover) Getting block 78 of 199 Sorting block time: 00:00:00 bucket 58: 100% bucket 60: 90% bucket 65: 60% Reserving size (36) for bucket 77 bucket 71: 30% bucket 74: 10% bucket 72: 20% bucket 66: 60% bucket 73: 20% bucket 68: 50% Sorting block of length 28 for bucket 57 (Using difference cover) bucket 61: 90% Getting block 79 of 199 bucket 64: 70% Calculating Z arrays for bucket 76 bucket 62: 80% bucket 59: 100% bucket 63: 80% bucket 67: 60% bucket 70: 40% bucket 69: 50% Reserving size (36) for bucket 78 Returning block of 31 for bucket 53 Sorting block of length 32 for bucket 58 (Using difference cover) bucket 60: 100% Sorting block time: 00:00:00 bucket 65: 70% Calculating Z arrays for bucket 77 bucket 71: 40% bucket 74: 20% bucket 72: 30% bucket 66: 70% bucket 73: 30% bucket 68: 60% bucket 75: 10% bucket 61: 100% Reserving size (36) for bucket 79 bucket 64: 80% bucket 62: 90% Sorting block of length 18 for bucket 59 (Using difference cover) Entering block accumulator loop for bucket 76: bucket 63: 90% bucket 67: 70% bucket 70: 50% bucket 69: 60% Calculating Z arrays for bucket 78 Sorting block of length 17 for bucket 60 (Using difference cover) Returning block of 36 for bucket 54 bucket 65: 80% bucket 71: 50% Entering block accumulator loop for bucket 77: bucket 74: 30% bucket 72: 40% bucket 66: 80% bucket 73: 40% bucket 68: 70% Sorting block of length 34 for bucket 61 (Using difference cover) bucket 75: 20% Calculating Z arrays for bucket 79 bucket 64: 90% bucket 62: 100% bucket 63: 100% bucket 67: 80% bucket 70: 60% bucket 69: 70% Entering block accumulator loop for bucket 78: bucket 65: 90% bucket 71: 60% bucket 74: 40% bucket 72: 50% bucket 66: 90% bucket 73: 50% bucket 68: 80% bucket 75: 30% Getting block 80 of 199 Sorting block of length 31 for bucket 62 (Using difference cover) bucket 64: 100% Entering block accumulator loop for bucket 79: bucket 76: 10% Sorting block of length 5 for bucket 63 (Using difference cover) bucket 67: 90% bucket 70: 70% bucket 69: 80% bucket 65: 100% bucket 71: 70% bucket 77: 10% bucket 74: 50% bucket 72: 60% bucket 66: 100% bucket 73: 60% bucket 68: 90% bucket 75: 40% Reserving size (36) for bucket 80 Sorting block of length 31 for bucket 64 (Using difference cover) bucket 76: 20% bucket 67: 100% bucket 70: 80% bucket 69: 90% bucket 78: 10% Sorting block of length 22 for bucket 65 (Using difference cover) bucket 71: 80% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 77: 20% bucket 74: 60% bucket 72: 70% Sorting block of length 28 for bucket 66 (Using difference cover) Getting block 81 of 199 bucket 73: 70% bucket 68: 100% bucket 75: 50% Calculating Z arrays for bucket 80 bucket 79: 10% bucket 76: 30% Sorting block of length 30 for bucket 67 (Using difference cover) bucket 70: 90% bucket 69: 100% bucket 78: 20% Returning block of 35 for bucket 56 Returning block of 26 for bucket 55 bucket 71: 90% bucket 77: 30% bucket 74: 70% bucket 72: 80% Reserving size (36) for bucket 81 bucket 73: 80% Sorting block of length 15 for bucket 68 (Using difference cover) bucket 75: 60% bucket 79: 20% Entering block accumulator loop for bucket 80: bucket 76: 40% bucket 70: 100% Sorting block of length 25 for bucket 69 (Using difference cover) bucket 78: 30% bucket 71: 100% bucket 77: 40% bucket 74: 80% bucket 72: 90% Calculating Z arrays for bucket 81 bucket 73: 90% bucket 75: 70% bucket 79: 30% bucket 76: 50% Sorting block of length 21 for bucket 70 (Using difference cover) Sorting block of length 35 for bucket 71 (Using difference cover) bucket 78: 40% bucket 77: 50% bucket 74: 90% bucket 72: 100% bucket 73: 100% Entering block accumulator loop for bucket 81: bucket 75: 80% bucket 79: 40% bucket 80: 10% bucket 76: 60% bucket 78: 50% Getting block 82 of 199 bucket 77: 60% Sorting block of length 33 for bucket 72 (Using difference cover) bucket 74: 100% Sorting block of length 30 for bucket 73 (Using difference cover) bucket 75: 90% bucket 79: 50% bucket 80: 20% bucket 76: 70% bucket 78: 60% Reserving size (36) for bucket 82 bucket 77: 70% Sorting block of length 35 for bucket 74 (Using difference cover) Getting block 83 of 199 bucket 81: 10% bucket 75: 100% bucket 79: 60% bucket 80: 30% bucket 76: 80% Calculating Z arrays for bucket 82 bucket 78: 70% bucket 77: 80% Reserving size (36) for bucket 83 Sorting block of length 35 for bucket 75 (Using difference cover) bucket 81: 20% Sorting block time: 00:00:00 bucket 79: 70% bucket 80: 40% bucket 76: 90% bucket 78: 80% Entering block accumulator loop for bucket 82: bucket 77: 90% Calculating Z arrays for bucket 83 Returning block of 29 for bucket 57 bucket 81: 30% bucket 79: 80% bucket 80: 50% bucket 76: 100% bucket 78: 90% bucket 77: 100% Entering block accumulator loop for bucket 83: bucket 81: 40% bucket 79: 90% bucket 80: 60% Sorting block of length 33 for bucket 76 (Using difference cover) bucket 78: 100% Sorting block of length 23 for bucket 77 (Using difference cover) bucket 82: 10% bucket 81: 50% bucket 79: 100% bucket 80: 70% Sorting block of length 19 for bucket 78 (Using difference cover) bucket 82: 20% bucket 83: 10% bucket 81: 60% Sorting block of length 30 for bucket 79 (Using difference cover) bucket 80: 80% bucket 82: 30% bucket 83: 20% bucket 81: 70% bucket 80: 90% bucket 82: 40% bucket 83: 30% bucket 81: 80% bucket 80: 100% bucket 82: 50% bucket 83: 40% bucket 81: 90% Sorting block of length 29 for bucket 80 (Using difference cover) bucket 82: 60% bucket 83: 50% bucket 81: 100% Sorting block time: 00:00:00 bucket 82: 70% bucket 83: 60% Sorting block of length 26 for bucket 81 (Using difference cover) Returning block of 6 for bucket 63 bucket 82: 80% bucket 83: 70% Getting block 84 of 199 bucket 82: 90% bucket 83: 80% Reserving size (36) for bucket 84 bucket 82: 100% bucket 83: 90% Calculating Z arrays for bucket 84 Sorting block of length 17 for bucket 82 (Using difference cover) bucket 83: 100% Entering block accumulator loop for bucket 84: Sorting block of length 31 for bucket 83 (Using difference cover) bucket 84: 10% bucket 84: 20% bucket 84: 30% Getting block 85 of 199 bucket 84: 40% Reserving size (36) for bucket 85 Calculating Z arrays for bucket 85 bucket 84: 50% bucket 84: 60% Entering block accumulator loop for bucket 85: bucket 84: 70% Sorting block time: 00:00:00 Returning block of 33 for bucket 58 bucket 84: 80% bucket 85: 10% bucket 84: 90% bucket 85: 20% bucket 84: 100% Sorting block of length 30 for bucket 84 (Using difference cover) bucket 85: 30% bucket 85: 40% bucket 85: 50% bucket 85: 60% bucket 85: 70% bucket 85: 80% bucket 85: 90% bucket 85: 100% Sorting block of length 23 for bucket 85 (Using difference cover) Sorting block time: 00:00:00 Returning block of 18 for bucket 60 Getting block 86 of 199 Reserving size (36) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 86: 10% bucket 86: 20% bucket 86: 30% Getting block 87 of 199 bucket 86: 40% Reserving size (36) for bucket 87 Calculating Z arrays for bucket 87 bucket 86: 50% bucket 86: 60% Entering block accumulator loop for bucket 87: bucket 86: 70% bucket 86: 80% bucket 87: 10% bucket 86: 90% bucket 87: 20% bucket 86: 100% bucket 87: 30% Sorting block of length 35 for bucket 86 (Using difference cover) bucket 87: 40% bucket 87: 50% bucket 87: 60% bucket 87: 70% bucket 87: 80% bucket 87: 90% bucket 87: 100% Sorting block of length 30 for bucket 87 (Using difference cover) Sorting block time: 00:00:00 Returning block of 35 for bucket 61 Getting block 88 of 199 Reserving size (36) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 88: 10% bucket 88: 20% bucket 88: 30% bucket 88: 40% bucket 88: 50% bucket 88: 60% bucket 88: 70% bucket 88: 80% bucket 88: 90% bucket 88: 100% Sorting block of length 28 for bucket 88 (Using difference cover) Sorting block time: 00:00:00 Returning block of 19 for bucket 59 Getting block 89 of 199 Reserving size (36) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 89: 10% bucket 89: 20% bucket 89: 30% bucket 89: 40% bucket 89: 50% bucket 89: 60% bucket 89: 70% bucket 89: 80% bucket 89: 90% bucket 89: 100% Sorting block of length 17 for bucket 89 (Using difference cover) Sorting block time: 00:00:00 Returning block of 32 for bucket 64 Sorting block time: 00:00:00 Returning block of 32 for bucket 62 Getting block 90 of 199 Reserving size (36) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 90: 10% bucket 90: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 23 for bucket 65 Returning block of 16 for bucket 68 bucket 90: 30% Getting block 91 of 199 bucket 90: 40% Reserving size (36) for bucket 91 bucket 90: 50% Calculating Z arrays for bucket 91 bucket 90: 60% bucket 90: 70% Entering block accumulator loop for bucket 91: bucket 90: 80% bucket 91: 10% bucket 90: 90% bucket 91: 20% bucket 90: 100% Sorting block of length 35 for bucket 90 (Using difference cover) bucket 91: 30% bucket 91: 40% bucket 91: 50% bucket 91: 60% Getting block 92 of 199 bucket 91: 70% Reserving size (36) for bucket 92 Calculating Z arrays for bucket 92 bucket 91: 80% bucket 91: 90% Entering block accumulator loop for bucket 92: bucket 91: 100% Sorting block of length 24 for bucket 91 (Using difference cover) bucket 92: 10% Getting block 93 of 199 bucket 92: 20% Reserving size (36) for bucket 93 bucket 92: 30% Calculating Z arrays for bucket 93 bucket 92: 40% bucket 92: 50% Entering block accumulator loop for bucket 93: bucket 92: 60% bucket 92: 70% bucket 93: 10% bucket 92: 80% bucket 93: 20% bucket 92: 90% bucket 93: 30% Sorting block time: 00:00:00 bucket 92: 100% 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 31 for bucket 67 bucket 93: 40% Returning block of 34 for bucket 72 Sorting block time: 00:00:00 Sorting block of length 23 for bucket 92 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 31 for bucket 73 Returning block of 29 for bucket 66 Returning block of 36 for bucket 75 bucket 93: 50% Returning block of 26 for bucket 69 Returning block of 36 for bucket 71 Returning block of 36 for bucket 74 bucket 93: 60% bucket 93: 70% bucket 93: 80% bucket 93: 90% bucket 93: 100% Sorting block of length 34 for bucket 93 (Using difference cover) Sorting block time: 00:00:00 Returning block of 20 for bucket 78 Sorting block time: 00:00:00 Returning block of 18 for bucket 82 Getting block 94 of 199 Reserving size (36) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: Sorting block time: 00:00:00 Returning block of 34 for bucket 76 Sorting block time: 00:00:00 bucket 94: 10% Returning block of 22 for bucket 70 Sorting block time: 00:00:00 bucket 94: 20% Getting block 95 of 199 Returning block of 27 for bucket 81 bucket 94: 30% Reserving size (36) for bucket 95 bucket 94: 40% Calculating Z arrays for bucket 95 bucket 94: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 94: 60% Sorting block time: 00:00:00 Returning block of 24 for bucket 77 Sorting block time: 00:00:00 Returning block of 32 for bucket 83 Entering block accumulator loop for bucket 95: Returning block of 30 for bucket 80 bucket 94: 70% Returning block of 31 for bucket 79 bucket 94: 80% bucket 95: 10% bucket 94: 90% bucket 95: 20% bucket 94: 100% bucket 95: 30% Sorting block of length 10 for bucket 94 (Using difference cover) bucket 95: 40% Getting block 96 of 199 bucket 95: 50% Reserving size (36) for bucket 96 bucket 95: 60% Calculating Z arrays for bucket 96 bucket 95: 70% bucket 95: 80% Entering block accumulator loop for bucket 96: bucket 95: 90% bucket 95: 100% bucket 96: 10% Sorting block of length 32 for bucket 95 (Using difference cover) bucket 96: 20% Getting block 97 of 199 bucket 96: 30% Reserving size (36) for bucket 97 bucket 96: 40% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Calculating Z arrays for bucket 97 Sorting block time: 00:00:00 Returning block of 24 for bucket 85 Returning block of 31 for bucket 87 Returning block of 36 for bucket 86 bucket 96: 50% Returning block of 31 for bucket 84 Entering block accumulator loop for bucket 97: Getting block 98 of 199 bucket 96: 60% Reserving size (36) for bucket 98 Getting block 99 of 199 bucket 96: 70% bucket 97: 10% Calculating Z arrays for bucket 98 Reserving size (36) for bucket 99 bucket 96: 80% bucket 97: 20% Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 98: bucket 96: 90% bucket 97: 30% Getting block 100 of 199 Entering block accumulator loop for bucket 99: bucket 96: 100% bucket 97: 40% bucket 98: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (36) for bucket 100 Sorting block of length 29 for bucket 96 (Using difference cover) bucket 97: 50% Returning block of 18 for bucket 89 Returning block of 29 for bucket 88 bucket 98: 20% Calculating Z arrays for bucket 100 Getting block 101 of 199 bucket 99: 10% bucket 97: 60% bucket 98: 30% Reserving size (36) for bucket 101 Entering block accumulator loop for bucket 100: Getting block 102 of 199 bucket 99: 20% bucket 97: 70% bucket 98: 40% Calculating Z arrays for bucket 101 Reserving size (36) for bucket 102 bucket 99: 30% bucket 97: 80% bucket 98: 50% bucket 100: 10% Calculating Z arrays for bucket 102 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 101: Getting block 103 of 199 bucket 99: 40% bucket 97: 90% bucket 98: 60% bucket 100: 20% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 25 for bucket 91 Returning block of 36 for bucket 90 Entering block accumulator loop for bucket 102: Reserving size (36) for bucket 103 bucket 99: 50% bucket 97: 100% bucket 98: 70% Returning block of 24 for bucket 92 Returning block of 35 for bucket 93 bucket 100: 30% bucket 101: 10% Calculating Z arrays for bucket 103 bucket 99: 60% Sorting block of length 18 for bucket 97 (Using difference cover) bucket 98: 80% bucket 100: 40% bucket 101: 20% bucket 102: 10% bucket 99: 70% Entering block accumulator loop for bucket 103: Getting block 104 of 199 Sorting block time: 00:00:00 bucket 98: 90% bucket 100: 50% bucket 101: 30% Sorting block time: 00:00:00 bucket 102: 20% bucket 99: 80% Reserving size (36) for bucket 104 Returning block of 33 for bucket 95 bucket 98: 100% Getting block 105 of 199 Returning block of 11 for bucket 94 bucket 100: 60% bucket 101: 40% bucket 102: 30% bucket 99: 90% bucket 103: 10% Calculating Z arrays for bucket 104 Sorting block of length 32 for bucket 98 (Using difference cover) Reserving size (36) for bucket 105 bucket 100: 70% bucket 101: 50% bucket 102: 40% bucket 99: 100% bucket 103: 20% Sorting block time: 00:00:00 Getting block 106 of 199 Entering block accumulator loop for bucket 104: Calculating Z arrays for bucket 105 bucket 100: 80% bucket 101: 60% bucket 102: 50% Sorting block of length 35 for bucket 99 (Using difference cover) Returning block of 30 for bucket 96 bucket 103: 30% Reserving size (36) for bucket 106 Getting block 107 of 199 Entering block accumulator loop for bucket 105: bucket 100: 90% bucket 101: 70% bucket 102: 60% Getting block 108 of 199 bucket 103: 40% Calculating Z arrays for bucket 106 Reserving size (36) for bucket 107 bucket 104: 10% bucket 100: 100% bucket 101: 80% Getting block 109 of 199 Sorting block time: 00:00:00 bucket 102: 70% Reserving size (36) for bucket 108 bucket 103: 50% Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 106: bucket 105: 10% bucket 104: 20% Sorting block of length 6 for bucket 100 (Using difference cover) Returning block of 19 for bucket 97 bucket 101: 90% Reserving size (36) for bucket 109 bucket 102: 80% Calculating Z arrays for bucket 108 Getting block 110 of 199 bucket 103: 60% Entering block accumulator loop for bucket 107: bucket 105: 20% bucket 104: 30% bucket 101: 100% Calculating Z arrays for bucket 109 bucket 102: 90% Entering block accumulator loop for bucket 108: Sorting block time: 00:00:00 Reserving size (36) for bucket 110 bucket 103: 70% bucket 106: 10% bucket 105: 30% Getting block 111 of 199 bucket 104: 40% Sorting block of length 34 for bucket 101 (Using difference cover) Getting block 112 of 199 Entering block accumulator loop for bucket 109: bucket 102: 100% Returning block of 33 for bucket 98 Calculating Z arrays for bucket 110 bucket 103: 80% bucket 106: 20% bucket 107: 10% bucket 105: 40% Reserving size (36) for bucket 111 Getting block 113 of 199 bucket 104: 50% Reserving size (36) for bucket 112 Sorting block time: 00:00:00 Sorting block of length 8 for bucket 102 (Using difference cover) bucket 108: 10% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 110: bucket 103: 90% bucket 106: 30% bucket 107: 20% bucket 105: 50% Calculating Z arrays for bucket 111 Reserving size (36) for bucket 113 Getting block 114 of 199 bucket 104: 60% Calculating Z arrays for bucket 112 Returning block of 36 for bucket 99 bucket 109: 10% Getting block 115 of 199 Returning block of 7 for bucket 100 bucket 108: 20% bucket 103: 100% bucket 106: 40% bucket 107: 30% bucket 105: 60% Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 111: Reserving size (36) for bucket 114 Getting block 116 of 199 bucket 104: 70% Entering block accumulator loop for bucket 112: bucket 109: 20% Reserving size (36) for bucket 115 bucket 108: 30% bucket 110: 10% Sorting block of length 34 for bucket 103 (Using difference cover) bucket 106: 50% bucket 107: 40% bucket 105: 70% Entering block accumulator loop for bucket 113: Calculating Z arrays for bucket 114 Reserving size (36) for bucket 116 Getting block 117 of 199 bucket 104: 80% bucket 109: 30% Calculating Z arrays for bucket 115 bucket 108: 40% Sorting block time: 00:00:00 bucket 110: 20% bucket 106: 60% bucket 107: 50% Getting block 118 of 199 bucket 105: 80% bucket 111: 10% Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 114: Reserving size (36) for bucket 117 bucket 104: 90% bucket 112: 10% bucket 109: 40% Returning block of 35 for bucket 101 Entering block accumulator loop for bucket 115: bucket 108: 50% Sorting block time: 00:00:00 Getting block 119 of 199 bucket 110: 30% bucket 106: 70% Sorting block time: 00:00:00 bucket 107: 60% Reserving size (36) for bucket 118 bucket 105: 90% bucket 111: 20% bucket 113: 10% Entering block accumulator loop for bucket 116: Calculating Z arrays for bucket 117 bucket 104: 100% Getting block 120 of 199 bucket 112: 20% bucket 109: 50% Returning block of 9 for bucket 102 bucket 108: 60% Reserving size (36) for bucket 119 bucket 110: 40% Returning block of 35 for bucket 103 bucket 106: 80% Calculating Z arrays for bucket 118 bucket 107: 70% bucket 105: 100% bucket 111: 30% bucket 113: 20% bucket 114: 10% Getting block 121 of 199 Sorting block of length 20 for bucket 104 (Using difference cover) Entering block accumulator loop for bucket 117: Reserving size (36) for bucket 120 bucket 112: 30% bucket 109: 60% Sorting block time: 00:00:00 Getting block 122 of 199 bucket 115: 10% bucket 108: 70% Calculating Z arrays for bucket 119 bucket 110: 50% bucket 106: 90% Entering block accumulator loop for bucket 118: bucket 107: 80% Sorting block of length 27 for bucket 105 (Using difference cover) Getting block 123 of 199 bucket 111: 40% bucket 113: 30% bucket 114: 20% bucket 116: 10% Reserving size (36) for bucket 121 Calculating Z arrays for bucket 120 Getting block 124 of 199 bucket 112: 40% Sorting block time: 00:00:00 bucket 109: 70% Returning block of 21 for bucket 104 Reserving size (36) for bucket 122 bucket 115: 20% bucket 108: 80% Entering block accumulator loop for bucket 119: bucket 110: 60% Getting block 125 of 199 bucket 106: 100% bucket 107: 90% Reserving size (36) for bucket 123 bucket 111: 50% Getting block 126 of 199 bucket 113: 40% bucket 116: 20% bucket 114: 30% Calculating Z arrays for bucket 121 bucket 117: 10% Entering block accumulator loop for bucket 120: Reserving size (36) for bucket 124 Getting block 127 of 199 Returning block of 28 for bucket 105 bucket 112: 50% Getting block 128 of 199 Getting block 129 of 199 bucket 109: 80% Calculating Z arrays for bucket 122 bucket 115: 30% bucket 108: 90% bucket 110: 70% Reserving size (36) for bucket 125 Sorting block of length 25 for bucket 106 (Using difference cover) bucket 118: 10% bucket 107: 100% Calculating Z arrays for bucket 123 bucket 111: 60% Reserving size (36) for bucket 126 bucket 113: 50% bucket 116: 30% bucket 114: 40% Getting block 130 of 199 Entering block accumulator loop for bucket 121: bucket 117: 20% Calculating Z arrays for bucket 124 Reserving size (36) for bucket 127 bucket 112: 60% Reserving size (36) for bucket 128 Reserving size (36) for bucket 129 bucket 109: 90% Entering block accumulator loop for bucket 122: bucket 115: 40% bucket 108: 100% bucket 119: 10% bucket 110: 80% Calculating Z arrays for bucket 125 bucket 118: 20% Sorting block of length 25 for bucket 107 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 123: bucket 111: 70% Calculating Z arrays for bucket 126 Getting block 131 of 199 bucket 113: 60% bucket 116: 40% bucket 114: 50% Reserving size (36) for bucket 130 bucket 120: 10% bucket 117: 30% Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 124: bucket 112: 70% Calculating Z arrays for bucket 128 Calculating Z arrays for bucket 129 bucket 109: 100% Sorting block of length 24 for bucket 108 (Using difference cover) bucket 115: 50% bucket 119: 20% bucket 110: 90% bucket 118: 30% Entering block accumulator loop for bucket 125: Returning block of 26 for bucket 106 Returning block of 26 for bucket 107 bucket 111: 80% Entering block accumulator loop for bucket 126: Reserving size (36) for bucket 131 bucket 113: 70% bucket 116: 50% bucket 114: 60% Calculating Z arrays for bucket 130 bucket 121: 10% bucket 120: 20% bucket 117: 40% Getting block 132 of 199 Entering block accumulator loop for bucket 127: bucket 112: 80% Entering block accumulator loop for bucket 128: Sorting block time: 00:00:00 Sorting block of length 21 for bucket 109 (Using difference cover) Sorting block time: 00:00:00 bucket 122: 10% Entering block accumulator loop for bucket 129: bucket 115: 60% bucket 119: 30% bucket 110: 100% bucket 118: 40% bucket 123: 10% bucket 111: 90% Calculating Z arrays for bucket 131 bucket 113: 80% bucket 116: 60% bucket 114: 70% Entering block accumulator loop for bucket 130: bucket 121: 20% bucket 120: 30% bucket 117: 50% Reserving size (36) for bucket 132 bucket 124: 10% Returning block of 25 for bucket 108 bucket 112: 90% Returning block of 22 for bucket 109 bucket 122: 20% bucket 115: 70% bucket 119: 40% Sorting block of length 28 for bucket 110 (Using difference cover) bucket 118: 50% bucket 125: 10% bucket 123: 20% bucket 111: 100% bucket 126: 10% Entering block accumulator loop for bucket 131: bucket 113: 90% bucket 116: 70% bucket 114: 80% bucket 121: 30% bucket 120: 40% bucket 117: 60% Calculating Z arrays for bucket 132 bucket 127: 10% bucket 124: 20% Getting block 133 of 199 Getting block 134 of 199 bucket 112: 100% bucket 128: 10% bucket 122: 30% bucket 129: 10% bucket 115: 80% bucket 119: 50% bucket 118: 60% Sorting block time: 00:00:00 bucket 125: 20% bucket 123: 30% Sorting block of length 33 for bucket 111 (Using difference cover) bucket 126: 20% bucket 113: 100% bucket 116: 80% bucket 114: 90% bucket 130: 10% bucket 121: 40% bucket 120: 50% bucket 117: 70% Entering block accumulator loop for bucket 132: bucket 127: 20% Reserving size (36) for bucket 133 bucket 124: 30% Reserving size (36) for bucket 134 Sorting block of length 28 for bucket 112 (Using difference cover) bucket 128: 20% bucket 122: 40% bucket 129: 20% bucket 115: 90% bucket 119: 60% Sorting block time: 00:00:00 Returning block of 29 for bucket 110 bucket 118: 70% bucket 125: 30% bucket 123: 40% bucket 131: 10% bucket 126: 30% Sorting block of length 22 for bucket 113 (Using difference cover) bucket 116: 90% bucket 114: 100% bucket 130: 20% bucket 121: 50% Getting block 135 of 199 bucket 120: 60% bucket 117: 80% bucket 127: 30% Calculating Z arrays for bucket 133 bucket 124: 40% Calculating Z arrays for bucket 134 bucket 128: 30% Getting block 136 of 199 bucket 122: 50% bucket 129: 30% bucket 115: 100% Returning block of 34 for bucket 111 bucket 119: 70% bucket 118: 80% bucket 125: 40% bucket 123: 50% bucket 131: 20% bucket 126: 40% bucket 116: 100% Sorting block of length 15 for bucket 114 (Using difference cover) bucket 130: 30% bucket 121: 60% Reserving size (36) for bucket 135 bucket 120: 70% bucket 117: 90% Sorting block time: 00:00:00 bucket 132: 10% bucket 127: 40% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 133: bucket 124: 50% Entering block accumulator loop for bucket 134: bucket 128: 40% Reserving size (36) for bucket 136 bucket 122: 60% bucket 129: 40% Sorting block of length 35 for bucket 115 (Using difference cover) bucket 119: 80% bucket 118: 90% bucket 125: 50% bucket 123: 60% bucket 131: 30% bucket 126: 50% Sorting block of length 33 for bucket 116 (Using difference cover) bucket 130: 40% bucket 121: 70% Calculating Z arrays for bucket 135 Returning block of 29 for bucket 112 bucket 120: 80% bucket 117: 100% bucket 132: 20% Returning block of 23 for bucket 113 bucket 127: 50% bucket 124: 60% bucket 128: 50% Calculating Z arrays for bucket 136 Getting block 137 of 199 bucket 122: 70% bucket 129: 50% bucket 119: 90% bucket 118: 100% bucket 125: 60% bucket 123: 70% bucket 131: 40% bucket 126: 60% bucket 130: 50% bucket 121: 80% Entering block accumulator loop for bucket 135: bucket 120: 90% Sorting block of length 24 for bucket 117 (Using difference cover) bucket 132: 30% bucket 127: 60% bucket 133: 10% bucket 124: 70% bucket 134: 10% bucket 128: 60% Entering block accumulator loop for bucket 136: Reserving size (36) for bucket 137 bucket 122: 80% bucket 129: 60% bucket 119: 100% Sorting block of length 33 for bucket 118 (Using difference cover) bucket 125: 70% bucket 123: 80% bucket 131: 50% bucket 126: 70% Getting block 138 of 199 bucket 130: 60% bucket 121: 90% bucket 120: 100% bucket 132: 40% bucket 127: 70% bucket 133: 20% bucket 124: 80% bucket 134: 20% bucket 128: 70% Calculating Z arrays for bucket 137 bucket 122: 90% Sorting block of length 14 for bucket 119 (Using difference cover) bucket 129: 70% bucket 125: 80% bucket 123: 90% bucket 131: 60% bucket 126: 80% Reserving size (36) for bucket 138 bucket 130: 70% bucket 121: 100% Sorting block time: 00:00:00 bucket 135: 10% Sorting block of length 29 for bucket 120 (Using difference cover) bucket 132: 50% bucket 127: 80% bucket 133: 30% bucket 124: 90% bucket 134: 30% bucket 136: 10% bucket 128: 80% bucket 122: 100% Entering block accumulator loop for bucket 137: bucket 129: 80% bucket 125: 90% bucket 123: 100% bucket 131: 70% bucket 126: 90% Calculating Z arrays for bucket 138 Getting block 139 of 199 bucket 130: 80% Sorting block of length 28 for bucket 121 (Using difference cover) Returning block of 16 for bucket 114 bucket 135: 20% bucket 132: 60% Getting block 140 of 199 bucket 127: 90% bucket 133: 40% bucket 124: 100% bucket 134: 40% bucket 136: 20% bucket 128: 90% Sorting block time: 00:00:00 Sorting block of length 24 for bucket 122 (Using difference cover) bucket 129: 90% bucket 125: 100% Sorting block of length 14 for bucket 123 (Using difference cover) bucket 131: 80% bucket 126: 100% Reserving size (36) for bucket 139 Entering block accumulator loop for bucket 138: bucket 130: 90% bucket 135: 30% bucket 132: 70% Reserving size (36) for bucket 140 bucket 127: 100% bucket 133: 50% Sorting block of length 27 for bucket 124 (Using difference cover) bucket 134: 50% bucket 136: 30% Returning block of 36 for bucket 115 bucket 128: 100% bucket 137: 10% bucket 129: 100% Sorting block of length 15 for bucket 125 (Using difference cover) Sorting block time: 00:00:00 bucket 131: 90% Sorting block of length 30 for bucket 126 (Using difference cover) Calculating Z arrays for bucket 139 bucket 130: 100% bucket 135: 40% bucket 132: 80% Calculating Z arrays for bucket 140 Sorting block of length 26 for bucket 127 (Using difference cover) bucket 133: 60% bucket 134: 60% bucket 136: 40% Sorting block of length 23 for bucket 128 (Using difference cover) bucket 137: 20% Sorting block of length 32 for bucket 129 (Using difference cover) Returning block of 34 for bucket 116 bucket 131: 100% bucket 138: 10% Sorting block of length 25 for bucket 130 (Using difference cover) Entering block accumulator loop for bucket 139: bucket 135: 50% bucket 132: 90% Entering block accumulator loop for bucket 140: bucket 133: 70% bucket 134: 70% bucket 136: 50% bucket 137: 30% Sorting block of length 33 for bucket 131 (Using difference cover) bucket 138: 20% bucket 135: 60% bucket 132: 100% bucket 133: 80% bucket 134: 80% bucket 136: 60% Getting block 141 of 199 bucket 137: 40% bucket 138: 30% bucket 139: 10% bucket 135: 70% Sorting block of length 34 for bucket 132 (Using difference cover) Getting block 142 of 199 bucket 140: 10% bucket 133: 90% bucket 134: 90% bucket 136: 70% Reserving size (36) for bucket 141 bucket 138: 40% bucket 137: 50% bucket 139: 20% bucket 135: 80% Reserving size (36) for bucket 142 bucket 140: 20% bucket 133: 100% bucket 134: 100% bucket 136: 80% Calculating Z arrays for bucket 141 bucket 138: 50% bucket 137: 60% bucket 139: 30% bucket 135: 90% Calculating Z arrays for bucket 142 bucket 140: 30% Sorting block of length 33 for bucket 133 (Using difference cover) Sorting block of length 34 for bucket 134 (Using difference cover) bucket 136: 90% bucket 138: 60% Entering block accumulator loop for bucket 141: bucket 137: 70% bucket 139: 40% bucket 135: 100% Getting block 143 of 199 bucket 140: 40% Entering block accumulator loop for bucket 142: bucket 136: 100% bucket 138: 70% bucket 137: 80% bucket 139: 50% Sorting block of length 30 for bucket 135 (Using difference cover) Reserving size (36) for bucket 143 bucket 140: 50% Sorting block of length 35 for bucket 136 (Using difference cover) bucket 138: 80% bucket 141: 10% bucket 137: 90% bucket 139: 60% Calculating Z arrays for bucket 143 bucket 140: 60% bucket 142: 10% bucket 138: 90% bucket 141: 20% bucket 137: 100% bucket 139: 70% bucket 140: 70% Entering block accumulator loop for bucket 143: bucket 142: 20% bucket 138: 100% Sorting block of length 15 for bucket 137 (Using difference cover) bucket 141: 30% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 139: 80% bucket 140: 80% bucket 142: 30% Sorting block of length 30 for bucket 138 (Using difference cover) Returning block of 25 for bucket 117 Returning block of 15 for bucket 119 Returning block of 34 for bucket 118 bucket 141: 40% bucket 139: 90% bucket 140: 90% bucket 143: 10% bucket 142: 40% bucket 141: 50% bucket 139: 100% bucket 140: 100% bucket 143: 20% bucket 142: 50% bucket 141: 60% Sorting block of length 29 for bucket 139 (Using difference cover) Sorting block of length 19 for bucket 140 (Using difference cover) bucket 143: 30% bucket 142: 60% bucket 141: 70% bucket 143: 40% bucket 142: 70% bucket 141: 80% bucket 143: 50% bucket 142: 80% bucket 141: 90% bucket 143: 60% bucket 142: 90% bucket 141: 100% bucket 143: 70% bucket 142: 100% Sorting block of length 31 for bucket 141 (Using difference cover) Sorting block of length 32 for bucket 142 (Using difference cover) bucket 143: 80% Getting block 144 of 199 bucket 143: 90% Reserving size (36) for bucket 144 bucket 143: 100% Calculating Z arrays for bucket 144 Sorting block of length 16 for bucket 143 (Using difference cover) Getting block 145 of 199 Entering block accumulator loop for bucket 144: Reserving size (36) for bucket 145 Calculating Z arrays for bucket 145 bucket 144: 10% bucket 144: 20% Entering block accumulator loop for bucket 145: bucket 144: 30% bucket 144: 40% bucket 145: 10% bucket 144: 50% Getting block 146 of 199 bucket 145: 20% bucket 144: 60% Reserving size (36) for bucket 146 bucket 145: 30% bucket 144: 70% Calculating Z arrays for bucket 146 bucket 145: 40% bucket 144: 80% bucket 145: 50% Entering block accumulator loop for bucket 146: bucket 144: 90% bucket 145: 60% bucket 144: 100% bucket 145: 70% Sorting block of length 23 for bucket 144 (Using difference cover) bucket 146: 10% bucket 145: 80% bucket 146: 20% bucket 145: 90% bucket 146: 30% bucket 145: 100% Sorting block of length 24 for bucket 145 (Using difference cover) bucket 146: 40% bucket 146: 50% bucket 146: 60% bucket 146: 70% bucket 146: 80% bucket 146: 90% bucket 146: 100% Sorting block of length 32 for bucket 146 (Using difference cover) Sorting block time: 00:00:00 Returning block of 29 for bucket 121 Sorting block time: 00:00:00 Returning block of 30 for bucket 120 Getting block 147 of 199 Reserving size (36) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 147: 10% bucket 147: 20% bucket 147: 30% bucket 147: 40% Sorting block time: 00:00:00 Getting block 148 of 199 Returning block of 25 for bucket 122 bucket 147: 50% Reserving size (36) for bucket 148 bucket 147: 60% Calculating Z arrays for bucket 148 bucket 147: 70% bucket 147: 80% Entering block accumulator loop for bucket 148: bucket 147: 90% bucket 147: 100% bucket 148: 10% Sorting block of length 24 for bucket 147 (Using difference cover) bucket 148: 20% bucket 148: 30% bucket 148: 40% bucket 148: 50% bucket 148: 60% bucket 148: 70% bucket 148: 80% bucket 148: 90% bucket 148: 100% Sorting block of length 29 for bucket 148 (Using difference cover) Getting block 149 of 199 Reserving size (36) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: bucket 149: 10% bucket 149: 20% bucket 149: 30% bucket 149: 40% bucket 149: 50% Sorting block time: 00:00:00 Returning block of 15 for bucket 123 bucket 149: 60% bucket 149: 70% bucket 149: 80% bucket 149: 90% bucket 149: 100% Sorting block of length 35 for bucket 149 (Using difference cover) Getting block 150 of 199 Reserving size (36) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 150: 10% bucket 150: 20% bucket 150: 30% bucket 150: 40% bucket 150: 50% bucket 150: 60% bucket 150: 70% bucket 150: 80% bucket 150: 90% bucket 150: 100% Sorting block of length 33 for bucket 150 (Using difference cover) Sorting block time: 00:00:00 Returning block of 26 for bucket 130 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 33 for bucket 129 Returning block of 28 for bucket 124 Sorting block time: 00:00:00 Returning block of 27 for bucket 127 Sorting block time: 00:00:00 Returning block of 31 for bucket 126 Sorting block time: 00:00:00 Returning block of 24 for bucket 128 Sorting block time: 00:00:00 Returning block of 16 for bucket 125 Sorting block time: 00:00:00 Returning block of 34 for bucket 131 Sorting block time: 00:00:00 Getting block 151 of 199 Returning block of 34 for bucket 133 Reserving size (36) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: Getting block 152 of 199 bucket 151: 10% Reserving size (36) for bucket 152 bucket 151: 20% Calculating Z arrays for bucket 152 bucket 151: 30% bucket 151: 40% Entering block accumulator loop for bucket 152: bucket 151: 50% bucket 151: 60% bucket 152: 10% bucket 151: 70% bucket 152: 20% bucket 151: 80% bucket 152: 30% bucket 151: 90% bucket 152: 40% bucket 151: 100% Sorting block of length 32 for bucket 151 (Using difference cover) bucket 152: 50% bucket 152: 60% bucket 152: 70% bucket 152: 80% bucket 152: 90% bucket 152: 100% Sorting block of length 35 for bucket 152 (Using difference cover) Getting block 153 of 199 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 35 for bucket 132 Reserving size (36) for bucket 153 Returning block of 20 for bucket 140 Sorting block time: 00:00:00 Calculating Z arrays for bucket 153 Sorting block time: 00:00:00 Returning block of 33 for bucket 142 Sorting block time: 00:00:00 Returning block of 31 for bucket 135 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 153: Sorting block time: 00:00:00 Returning block of 32 for bucket 141 Getting block 154 of 199 Returning block of 30 for bucket 139 Returning block of 35 for bucket 134 Reserving size (36) for bucket 154 bucket 153: 10% Calculating Z arrays for bucket 154 bucket 153: 20% Getting block 155 of 199 bucket 153: 30% Reserving size (36) for bucket 155 Entering block accumulator loop for bucket 154: bucket 153: 40% Calculating Z arrays for bucket 155 bucket 153: 50% bucket 154: 10% bucket 153: 60% Entering block accumulator loop for bucket 155: bucket 154: 20% bucket 153: 70% Getting block 156 of 199 bucket 154: 30% bucket 153: 80% Sorting block time: 00:00:00 bucket 155: 10% Reserving size (36) for bucket 156 Sorting block time: 00:00:00 bucket 154: 40% Sorting block time: 00:00:00 Returning block of 36 for bucket 136 Sorting block time: 00:00:00 bucket 153: 90% bucket 155: 20% Calculating Z arrays for bucket 156 Returning block of 25 for bucket 145 Returning block of 31 for bucket 138 bucket 154: 50% Returning block of 16 for bucket 137 bucket 153: 100% bucket 155: 30% Getting block 157 of 199 Entering block accumulator loop for bucket 156: bucket 154: 60% Sorting block of length 17 for bucket 153 (Using difference cover) bucket 155: 40% Reserving size (36) for bucket 157 Getting block 158 of 199 bucket 154: 70% bucket 155: 50% Calculating Z arrays for bucket 157 Reserving size (36) for bucket 158 Getting block 159 of 199 bucket 156: 10% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 154: 80% bucket 155: 60% Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 157: Reserving size (36) for bucket 159 Returning block of 17 for bucket 143 Returning block of 33 for bucket 146 Returning block of 24 for bucket 144 bucket 156: 20% Getting block 160 of 199 bucket 154: 90% bucket 155: 70% Entering block accumulator loop for bucket 158: Calculating Z arrays for bucket 159 bucket 156: 30% Reserving size (36) for bucket 160 bucket 154: 100% bucket 155: 80% bucket 157: 10% Getting block 161 of 199 Entering block accumulator loop for bucket 159: bucket 156: 40% Calculating Z arrays for bucket 160 Sorting block of length 34 for bucket 154 Sorting block time: 00:00:00 (Using difference cover) bucket 155: 90% Sorting block time: 00:00:00 bucket 158: 10% Sorting block time: 00:00:00 bucket 157: 20% Reserving size (36) for bucket 161 bucket 156: 50% Entering block accumulator loop for bucket 160: Returning block of 34 for bucket 150 Returning block of 36 for bucket 149 bucket 155: 100% Returning block of 25 for bucket 147 bucket 158: 20% bucket 157: 30% Calculating Z arrays for bucket 161 bucket 159: 10% bucket 156: 60% Sorting block of length 21 for bucket 155 (Using difference cover) Getting block 162 of 199 bucket 158: 30% bucket 157: 40% bucket 159: 20% Entering block accumulator loop for bucket 161: Sorting block time: 00:00:00 bucket 156: 70% bucket 160: 10% Reserving size (36) for bucket 162 Sorting block time: 00:00:00 bucket 158: 40% Getting block 163 of 199 bucket 157: 50% bucket 159: 30% Returning block of 30 for bucket 148 bucket 156: 80% Returning block of 33 for bucket 151 bucket 160: 20% Calculating Z arrays for bucket 162 bucket 158: 50% Reserving size (36) for bucket 163 bucket 157: 60% bucket 161: 10% bucket 159: 40% bucket 156: 90% Getting block 164 of 199 bucket 160: 30% Entering block accumulator loop for bucket 162: bucket 158: 60% Calculating Z arrays for bucket 163 Sorting block time: 00:00:00 bucket 157: 70% bucket 161: 20% Getting block 165 of 199 bucket 159: 50% bucket 156: 100% Reserving size (36) for bucket 164 bucket 160: 40% bucket 158: 70% Returning block of 36 for bucket 152 bucket 157: 80% Entering block accumulator loop for bucket 163: bucket 161: 30% Reserving size (36) for bucket 165 bucket 159: 60% Sorting block of length 23 for bucket 156 (Using difference cover) Sorting block time: 00:00:00 Calculating Z arrays for bucket 164 Getting block 166 of 199 bucket 162: 10% Sorting block time: 00:00:00 bucket 160: 50% bucket 158: 80% bucket 157: 90% bucket 161: 40% Calculating Z arrays for bucket 165 Getting block 167 of 199 bucket 159: 70% Returning block of 18 for bucket 153 Reserving size (36) for bucket 166 Entering block accumulator loop for bucket 164: Returning block of 35 for bucket 154 bucket 162: 20% bucket 160: 60% bucket 158: 90% Getting block 168 of 199 bucket 157: 100% bucket 163: 10% bucket 161: 50% Reserving size (36) for bucket 167 Entering block accumulator loop for bucket 165: bucket 159: 80% Calculating Z arrays for bucket 166 bucket 162: 30% bucket 160: 70% bucket 158: 100% Reserving size (36) for bucket 168 Sorting block time: 00:00:00 Sorting block of length 31 for bucket 157 (Using difference cover) bucket 163: 20% Sorting block time: 00:00:00 Getting block 169 of 199 bucket 161: 60% Calculating Z arrays for bucket 167 bucket 159: 90% Getting block 170 of 199 bucket 164: 10% bucket 162: 40% Entering block accumulator loop for bucket 166: bucket 160: 80% Sorting block of length 7 for bucket 158 (Using difference cover) Returning block of 22 for bucket 155 Calculating Z arrays for bucket 168 Returning block of 24 for bucket 156 bucket 163: 30% Reserving size (36) for bucket 169 bucket 161: 70% bucket 165: 10% bucket 159: 100% Entering block accumulator loop for bucket 167: Reserving size (36) for bucket 170 bucket 164: 20% Getting block 171 of 199 bucket 162: 50% bucket 160: 90% Entering block accumulator loop for bucket 168: bucket 163: 40% Calculating Z arrays for bucket 169 Getting block 172 of 199 bucket 161: 80% bucket 165: 20% Sorting block of length 29 for bucket 159 (Using difference cover) Calculating Z arrays for bucket 170 bucket 164: 30% Reserving size (36) for bucket 171 bucket 162: 60% bucket 166: 10% Getting block 173 of 199 bucket 160: 100% Sorting block time: 00:00:00 bucket 163: 50% Reserving size (36) for bucket 172 Entering block accumulator loop for bucket 169: bucket 161: 90% bucket 165: 30% Getting block 174 of 199 bucket 167: 10% bucket 164: 40% Entering block accumulator loop for bucket 170: Calculating Z arrays for bucket 171 bucket 162: 70% bucket 166: 20% Reserving size (36) for bucket 173 Sorting block of length 25 for bucket 160 (Using difference cover) Returning block of 32 for bucket 157 bucket 168: 10% Getting block 175 of 199 bucket 163: 60% Calculating Z arrays for bucket 172 bucket 161: 100% bucket 165: 40% Reserving size (36) for bucket 174 bucket 167: 20% bucket 164: 50% Sorting block time: 00:00:00 bucket 162: 80% Getting block 176 of 199 Entering block accumulator loop for bucket 171: bucket 166: 30% Calculating Z arrays for bucket 173 bucket 168: 20% Reserving size (36) for bucket 175 bucket 163: 70% bucket 169: 10% Sorting block time: 00:00:00 Sorting block of length 17 for bucket 161 (Using difference cover) Entering block accumulator loop for bucket 172: bucket 165: 50% Calculating Z arrays for bucket 174 bucket 167: 30% Returning block of 8 for bucket 158 bucket 164: 60% bucket 170: 10% bucket 162: 90% Reserving size (36) for bucket 176 bucket 166: 40% bucket 168: 30% Entering block accumulator loop for bucket 173: Calculating Z arrays for bucket 175 bucket 163: 80% Returning block of 30 for bucket 159 bucket 169: 20% bucket 165: 60% Getting block 177 of 199 Getting block 178 of 199 Entering block accumulator loop for bucket 174: bucket 167: 40% bucket 164: 70% bucket 170: 20% Getting block 179 of 199 bucket 162: 100% Calculating Z arrays for bucket 176 bucket 171: 10% bucket 166: 50% bucket 168: 40% bucket 163: 90% Entering block accumulator loop for bucket 175: Getting block 180 of 199 Sorting block time: 00:00:00 bucket 172: 10% bucket 169: 30% Sorting block time: 00:00:00 bucket 165: 70% Reserving size (36) for bucket 177 Reserving size (36) for bucket 178 Getting block 181 of 199 bucket 167: 50% bucket 164: 80% bucket 170: 30% Reserving size (36) for bucket 179 Sorting block of length 26 for bucket 162 (Using difference cover) Entering block accumulator loop for bucket 176: bucket 171: 20% bucket 166: 60% bucket 168: 50% bucket 173: 10% bucket 163: 100% Reserving size (36) for bucket 180 Returning block of 26 for bucket 160 bucket 172: 20% Returning block of 18 for bucket 161 bucket 169: 40% bucket 165: 80% Calculating Z arrays for bucket 177 Getting block 182 of 199 Calculating Z arrays for bucket 178 bucket 174: 10% Reserving size (36) for bucket 181 bucket 167: 60% bucket 164: 90% bucket 170: 40% Sorting block time: 00:00:00 Calculating Z arrays for bucket 179 bucket 171: 30% bucket 166: 70% bucket 168: 60% bucket 173: 20% Sorting block of length 33 for bucket 163 (Using difference cover) Getting block 183 of 199 bucket 175: 10% Calculating Z arrays for bucket 180 bucket 172: 30% bucket 169: 50% bucket 165: 90% Reserving size (36) for bucket 182 Entering block accumulator loop for bucket 177: Entering block accumulator loop for bucket 178: bucket 174: 20% Calculating Z arrays for bucket 181 Getting block 184 of 199 bucket 167: 70% bucket 164: 100% Returning block of 27 for bucket 162 bucket 170: 50% bucket 176: 10% Entering block accumulator loop for bucket 179: bucket 171: 40% Getting block 185 of 199 bucket 166: 80% bucket 168: 70% bucket 173: 30% Sorting block time: 00:00:00 Reserving size (36) for bucket 183 bucket 175: 20% bucket 172: 40% Entering block accumulator loop for bucket 180: bucket 169: 60% bucket 165: 100% Calculating Z arrays for bucket 182 bucket 174: 30% Reserving size (36) for bucket 184 Getting block 186 of 199 Entering block accumulator loop for bucket 181: bucket 167: 80% Sorting block of length 28 for bucket 164 (Using difference cover) bucket 170: 60% bucket 176: 20% bucket 171: 50% Reserving size (36) for bucket 185 bucket 166: 90% bucket 168: 80% Returning block of 34 for bucket 163 bucket 173: 40% Calculating Z arrays for bucket 183 Getting block 187 of 199 bucket 175: 30% bucket 172: 50% bucket 169: 70% Sorting block of length 31 for bucket 165 (Using difference cover) Getting block 188 of 199 bucket 178: 10% bucket 177: 10% Entering block accumulator loop for bucket 182: bucket 174: 40% Calculating Z arrays for bucket 184 Reserving size (36) for bucket 186 bucket 167: 90% bucket 170: 70% bucket 176: 30% bucket 179: 10% bucket 171: 60% Calculating Z arrays for bucket 185 bucket 166: 100% bucket 168: 90% bucket 173: 50% Reserving size (36) for bucket 187 Entering block accumulator loop for bucket 183: Getting block 189 of 199 bucket 175: 40% bucket 172: 60% bucket 180: 10% bucket 169: 80% Reserving size (36) for bucket 188 bucket 178: 20% bucket 177: 20% bucket 174: 50% Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 184: Sorting block time: 00:00:00 bucket 181: 10% bucket 167: 100% bucket 170: 80% bucket 176: 40% Sorting block time: 00:00:00 bucket 179: 20% bucket 171: 70% Sorting block of length 23 for bucket 166 (Using difference cover) Entering block accumulator loop for bucket 185: bucket 168: 100% bucket 173: 60% Calculating Z arrays for bucket 187 Reserving size (36) for bucket 189 bucket 175: 50% bucket 172: 70% bucket 180: 20% bucket 169: 90% Calculating Z arrays for bucket 188 bucket 178: 30% bucket 177: 30% bucket 182: 10% bucket 174: 60% Returning block of 29 for bucket 164 Entering block accumulator loop for bucket 186: bucket 181: 20% Sorting block of length 30 for bucket 167 (Using difference cover) Getting block 190 of 199 bucket 170: 90% Returning block of 32 for bucket 165 bucket 176: 50% bucket 179: 30% bucket 171: 80% Sorting block of length 24 for bucket 168 (Using difference cover) bucket 173: 70% bucket 183: 10% Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 187: bucket 175: 60% bucket 172: 80% bucket 180: 30% bucket 169: 100% Entering block accumulator loop for bucket 188: bucket 178: 40% bucket 177: 40% bucket 182: 20% bucket 174: 70% bucket 184: 10% bucket 181: 30% Reserving size (36) for bucket 190 bucket 170: 100% bucket 176: 60% Sorting block time: 00:00:00 bucket 179: 40% bucket 171: 90% bucket 185: 10% bucket 173: 80% bucket 183: 20% Entering block accumulator loop for bucket 189: bucket 175: 70% bucket 172: 90% bucket 180: 40% Sorting block of length 32 for bucket 169 (Using difference cover) bucket 178: 50% bucket 177: 50% bucket 182: 30% bucket 174: 80% bucket 184: 20% bucket 186: 10% bucket 181: 40% Calculating Z arrays for bucket 190 Sorting block of length 9 for bucket 170 (Using difference cover) Returning block of 24 for bucket 166 bucket 176: 70% bucket 179: 50% Sorting block time: 00:00:00 bucket 171: 100% bucket 185: 20% bucket 173: 90% bucket 183: 30% bucket 187: 10% bucket 175: 80% bucket 172: 100% bucket 180: 50% Getting block 191 of 199 bucket 188: 10% bucket 178: 60% bucket 177: 60% bucket 182: 40% bucket 174: 90% bucket 184: 30% bucket 186: 20% bucket 181: 50% Entering block accumulator loop for bucket 190: bucket 176: 80% Returning block of 31 for bucket 167 bucket 179: 60% Sorting block of length 34 for bucket 171 (Using difference cover) bucket 185: 30% Getting block 192 of 199 bucket 173: 100% bucket 183: 40% bucket 189: 10% bucket 187: 20% bucket 175: 90% Sorting block of length 28 for bucket 172 (Using difference cover) bucket 180: 60% Reserving size (36) for bucket 191 bucket 188: 20% bucket 178: 70% bucket 177: 70% bucket 182: 50% bucket 174: 100% bucket 184: 40% bucket 186: 30% bucket 181: 60% Sorting block time: 00:00:00 bucket 176: 90% bucket 179: 70% bucket 185: 40% Reserving size (36) for bucket 192 Sorting block of length 35 for bucket 173 bucket 183: 50% (Using difference cover) bucket 189: 20% Sorting block time: 00:00:00 bucket 187: 30% bucket 175: 100% bucket 180: 70% Calculating Z arrays for bucket 191 bucket 188: 30% bucket 178: 80% bucket 177: 80% bucket 182: 60% Sorting block of length 21 for bucket 174 (Using difference cover) Getting block 193 of 199 bucket 184: 50% bucket 186: 40% Returning block of 25 for bucket 168 bucket 181: 70% bucket 190: 10% bucket 176: 100% bucket 179: 80% bucket 185: 50% Calculating Z arrays for bucket 192 bucket 183: 60% Returning block of 10 for bucket 170 bucket 189: 30% bucket 187: 40% Sorting block of length 30 for bucket 175 (Using difference cover) bucket 180: 80% Entering block accumulator loop for bucket 191: bucket 188: 40% bucket 178: 90% bucket 177: 90% bucket 182: 70% Reserving size (36) for bucket 193 bucket 184: 60% Getting block 194 of 199 bucket 186: 50% bucket 181: 80% bucket 190: 20% Sorting block of length 34 for bucket 176 Sorting block time: 00:00:00 (Using difference cover) bucket 179: 90% bucket 185: 60% bucket 183: 70% Entering block accumulator loop for bucket 192: bucket 189: 40% bucket 187: 50% bucket 180: 90% bucket 188: 50% bucket 178: 100% bucket 177: 100% bucket 182: 80% Calculating Z arrays for bucket 193 bucket 184: 70% Reserving size (36) for bucket 194 bucket 186: 60% bucket 181: 90% bucket 190: 30% Returning block of 33 for bucket 169 bucket 179: 100% bucket 185: 70% bucket 183: 80% bucket 189: 50% bucket 187: 60% bucket 180: 100% bucket 191: 10% bucket 188: 60% Sorting block of length 29 for bucket 178 (Using difference cover) Sorting block of length 26 for bucket 177 (Using difference cover) bucket 182: 90% Getting block 195 of 199 Entering block accumulator loop for bucket 193: bucket 184: 80% Calculating Z arrays for bucket 194 bucket 186: 70% bucket 181: 100% bucket 190: 40% Sorting block of length 30 for bucket 179 (Using difference cover) bucket 185: 80% bucket 183: 90% bucket 192: 10% bucket 189: 60% bucket 187: 70% Sorting block of length 18 for bucket 180 (Using difference cover) bucket 191: 20% bucket 188: 70% Getting block 196 of 199 bucket 182: 100% Reserving size (36) for bucket 195 bucket 184: 90% Entering block accumulator loop for bucket 194: bucket 186: 80% Sorting block of length 23 for bucket 181 (Using difference cover) bucket 190: 50% bucket 185: 90% bucket 183: 100% bucket 192: 20% bucket 189: 70% bucket 187: 80% bucket 191: 30% bucket 188: 80% Reserving size (36) for bucket 196 Sorting block of length 35 for bucket 182 (Using difference cover) Calculating Z arrays for bucket 195 bucket 193: 10% bucket 184: 100% bucket 186: 90% Getting block 197 of 199 bucket 190: 60% bucket 185: 100% Sorting block of length 31 for bucket 183 bucket 192: 30% (Using difference cover) bucket 189: 80% bucket 187: 90% bucket 191: 40% bucket 188: 90% Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 195: bucket 193: 20% Sorting block of length 28 for bucket 184 (Using difference cover) bucket 194: 10% bucket 186: 100% Reserving size (36) for bucket 197 bucket 190: 70% Sorting block of length 28 for bucket 185 (Using difference cover) bucket 192: 40% bucket 189: 90% bucket 187: 100% bucket 191: 50% bucket 188: 100% Entering block accumulator loop for bucket 196: bucket 193: 30% bucket 194: 20% Sorting block of length 22 for bucket 186 (Using difference cover) Calculating Z arrays for bucket 197 bucket 190: 80% bucket 192: 50% Sorting block time: 00:00:00 bucket 189: 100% Sorting block time: 00:00:00 Sorting block of length 21 for bucket 187 (Using difference cover) bucket 191: 60% Sorting block of length 35 for bucket 188 (Using difference cover) bucket 195: 10% bucket 193: 40% bucket 194: 30% bucket 190: 90% Entering block accumulator loop for bucket 197: Returning block of 35 for bucket 171 bucket 192: 60% Sorting block of length 19 for bucket 189 (Using difference cover) Returning block of 29 for bucket 172 bucket 191: 70% bucket 195: 20% bucket 196: 10% bucket 193: 50% bucket 194: 40% bucket 190: 100% bucket 192: 70% bucket 191: 80% bucket 195: 30% bucket 196: 20% bucket 193: 60% bucket 194: 50% Sorting block of length 21 for bucket 190 (Using difference cover) bucket 197: 10% bucket 192: 80% bucket 191: 90% bucket 195: 40% bucket 196: 30% bucket 193: 70% bucket 194: 60% bucket 197: 20% bucket 192: 90% bucket 191: 100% bucket 195: 50% bucket 196: 40% bucket 193: 80% bucket 194: 70% bucket 197: 30% bucket 192: 100% Sorting block of length 17 for bucket 191 (Using difference cover) Getting block 198 of 199 bucket 195: 60% bucket 196: 50% bucket 193: 90% bucket 194: 80% bucket 197: 40% Sorting block of length 32 for bucket 192 (Using difference cover) Reserving size (36) for bucket 198 bucket 195: 70% bucket 196: 60% bucket 193: 100% bucket 194: 90% bucket 197: 50% Calculating Z arrays for bucket 198 bucket 195: 80% Getting block 199 of 199 bucket 196: 70% Sorting block of length 27 for bucket 193 (Using difference cover) bucket 194: 100% bucket 197: 60% bucket 195: 90% Entering block accumulator loop for bucket 198: Reserving size (36) for bucket 199 bucket 196: 80% Sorting block of length 27 for bucket 194 (Using difference cover) bucket 197: 70% bucket 195: 100% Calculating Z arrays for bucket 199 bucket 196: 90% bucket 197: 80% Sorting block of length 18 for bucket 195 (Using difference cover) bucket 198: 10% Entering block accumulator loop for bucket 199: bucket 196: 100% bucket 197: 90% bucket 198: 20% Sorting block of length 34 for bucket 196 (Using difference cover) bucket 197: 100% bucket 199: 10% bucket 198: 30% Sorting block of length 8 for bucket 197 (Using difference cover) bucket 199: 20% bucket 198: 40% bucket 199: 30% bucket 198: 50% bucket 199: 40% bucket 198: 60% bucket 199: 50% bucket 198: 70% bucket 199: 60% bucket 198: 80% bucket 199: 70% bucket 198: 90% bucket 199: 80% bucket 198: 100% bucket 199: 90% Sorting block of length 35 for bucket 198 (Using difference cover) bucket 199: 100% Sorting block of length 12 for bucket 199 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 31 for bucket 175 Returning block of 36 for bucket 173 Sorting block time: 00:00:00 Returning block of 22 for bucket 174 Sorting block time: 00:00:00 Returning block of 35 for bucket 176 Sorting block time: 00:00:00 Returning block of 27 for bucket 177 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 30 for bucket 178 Returning block of 19 for bucket 180 Sorting block time: 00:00:00 Returning block of 24 for bucket 181 Sorting block time: 00:00:00 Returning block of 36 for bucket 188 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 23 for bucket 186 Sorting block time: 00:00:00 Returning block of 29 for bucket 184 Sorting block time: 00:00:00 Returning block of 29 for bucket 185 Sorting block time: 00:00:00 Returning block of 20 for bucket 189 Returning block of 32 for bucket 183 Returning block of 36 for bucket 182 Returning block of 22 for bucket 187 Sorting block time: 00:00:00 Returning block of 31 for bucket 179 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 19 for bucket 195 Sorting block time: 00:00:00 Returning block of 13 for bucket 199 Returning block of 28 for bucket 194 Sorting block time: 00:00:00 Returning block of 22 for bucket 190 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 36 for bucket 198 Returning block of 28 for bucket 193 Returning block of 35 for bucket 196 Returning block of 33 for bucket 192 Sorting block time: 00:00:00 Returning block of 9 for bucket 197 Sorting block time: 00:00:00 Returning block of 18 for bucket 191 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2545 fchr[G]: 3702 fchr[T]: 3702 fchr[$]: 5386 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4196346 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 1352 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 5386 bwtLen: 5387 sz: 1347 bwtSz: 1347 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 337 offsSz: 1348 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 29 numLines: 29 ebwtTotLen: 1856 ebwtTotSz: 1856 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:00 Reading reference sizes Time reading reference sizes: 00:00:00 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: 48 Using parameters --bmax 36 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 36 --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 308 sample suffixes Generating random suffixes QSorting 308 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 302 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 39, merged 137; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 17, merged 19; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 11, merged 9; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 4, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 2; iterating... Avg bucket size: 25.5369 (target: 35) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 203 Reserving size (36) for bucket 1 Getting block 2 of 203 Getting block 3 of 203 Getting block 4 of 203 Getting block 5 of 203 Getting block 6 of 203 Getting block 7 of 203 Getting block 8 of 203 Getting block 9 of 203 Getting block 10 of 203 Getting block 11 of 203 Getting block 12 of 203 Getting block 13 of 203 Getting block 14 of 203 Getting block 15 of 203 Getting block 16 of 203 Calculating Z arrays for bucket 1 Getting block 17 of 203 Reserving size (36) for bucket 2 Getting block 18 of 203 Reserving size (36) for bucket 3 Reserving size (36) for bucket 4 Reserving size (36) for bucket 5 Reserving size (36) for bucket 6 Reserving size (36) for bucket 7 Reserving size (36) for bucket 8 Reserving size (36) for bucket 9 Reserving size (36) for bucket 10 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 Getting block 25 of 203 Getting block 26 of 203 Getting block 27 of 203 Reserving size (36) for bucket 11 Reserving size (36) for bucket 12 Reserving size (36) for bucket 13 Reserving size (36) for bucket 14 Reserving size (36) for bucket 15 Reserving size (36) for bucket 16 Entering block accumulator loop for bucket 1: Reserving size (36) for bucket 17 Calculating Z arrays for bucket 2 Reserving size (36) for bucket 18 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 9 Calculating Z arrays for bucket 10 Reserving size (36) for bucket 19 Reserving size (36) for bucket 20 Reserving size (36) for bucket 21 Reserving size (36) for bucket 22 Reserving size (36) for bucket 23 Reserving size (36) for bucket 24 Reserving size (36) for bucket 25 Reserving size (36) for bucket 26 Reserving size (36) for bucket 27 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 Entering block accumulator loop for bucket 2: Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 9: Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 20 Entering block accumulator loop for bucket 10: Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 25 Calculating Z arrays for bucket 26 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 14: bucket 1: 10% Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 27: bucket 1: 20% bucket 2: 10% bucket 3: 10% bucket 4: 10% bucket 5: 10% bucket 6: 10% bucket 7: 10% bucket 8: 10% bucket 9: 10% bucket 10: 10% bucket 11: 10% bucket 12: 10% bucket 13: 10% bucket 14: 10% bucket 1: 30% bucket 15: 10% bucket 16: 10% bucket 17: 10% bucket 2: 20% bucket 3: 20% bucket 18: 10% bucket 4: 20% bucket 5: 20% bucket 6: 20% bucket 7: 20% bucket 19: 10% bucket 8: 20% bucket 9: 20% bucket 10: 20% bucket 20: 10% bucket 21: 10% bucket 22: 10% bucket 23: 10% bucket 24: 10% bucket 25: 10% bucket 26: 10% bucket 27: 10% bucket 11: 20% bucket 12: 20% bucket 13: 20% bucket 14: 20% bucket 1: 40% bucket 15: 20% bucket 16: 20% bucket 17: 20% bucket 2: 30% bucket 3: 30% bucket 18: 20% bucket 4: 30% bucket 5: 30% bucket 6: 30% bucket 7: 30% bucket 19: 20% bucket 8: 30% bucket 9: 30% bucket 10: 30% bucket 20: 20% bucket 21: 20% bucket 22: 20% bucket 23: 20% bucket 24: 20% bucket 25: 20% bucket 26: 20% bucket 27: 20% bucket 11: 30% bucket 12: 30% bucket 13: 30% bucket 14: 30% bucket 1: 50% bucket 15: 30% bucket 16: 30% bucket 17: 30% bucket 2: 40% bucket 3: 40% bucket 18: 30% bucket 4: 40% bucket 5: 40% bucket 6: 40% bucket 7: 40% bucket 19: 30% bucket 8: 40% bucket 9: 40% bucket 10: 40% bucket 20: 30% bucket 21: 30% bucket 22: 30% bucket 23: 30% bucket 24: 30% bucket 25: 30% bucket 26: 30% bucket 27: 30% bucket 11: 40% bucket 12: 40% bucket 13: 40% bucket 14: 40% bucket 1: 60% bucket 15: 40% bucket 16: 40% bucket 17: 40% bucket 2: 50% bucket 3: 50% bucket 18: 40% bucket 4: 50% bucket 5: 50% bucket 6: 50% bucket 7: 50% bucket 19: 40% bucket 8: 50% bucket 9: 50% bucket 10: 50% bucket 20: 40% bucket 21: 40% bucket 22: 40% bucket 23: 40% bucket 24: 40% bucket 25: 40% bucket 26: 40% bucket 27: 40% bucket 11: 50% bucket 12: 50% bucket 13: 50% bucket 14: 50% bucket 1: 70% bucket 15: 50% bucket 16: 50% bucket 17: 50% bucket 2: 60% bucket 3: 60% bucket 18: 50% bucket 4: 60% bucket 5: 60% bucket 6: 60% bucket 7: 60% bucket 19: 50% bucket 8: 60% bucket 9: 60% bucket 10: 60% bucket 20: 50% bucket 21: 50% bucket 22: 50% bucket 23: 50% bucket 24: 50% bucket 25: 50% bucket 26: 50% bucket 27: 50% bucket 11: 60% bucket 12: 60% bucket 13: 60% bucket 14: 60% bucket 1: 80% bucket 15: 60% bucket 16: 60% bucket 17: 60% bucket 2: 70% bucket 3: 70% bucket 18: 60% bucket 4: 70% bucket 5: 70% bucket 6: 70% bucket 7: 70% bucket 19: 60% bucket 8: 70% bucket 9: 70% bucket 10: 70% bucket 20: 60% bucket 21: 60% bucket 22: 60% bucket 23: 60% bucket 24: 60% bucket 25: 60% bucket 26: 60% bucket 27: 60% bucket 11: 70% bucket 12: 70% bucket 13: 70% bucket 14: 70% bucket 1: 90% bucket 15: 70% bucket 16: 70% bucket 17: 70% bucket 2: 80% bucket 3: 80% bucket 18: 70% bucket 4: 80% bucket 5: 80% bucket 6: 80% bucket 7: 80% bucket 19: 70% bucket 8: 80% bucket 9: 80% bucket 10: 80% bucket 20: 70% bucket 21: 70% bucket 22: 70% bucket 23: 70% bucket 24: 70% bucket 25: 70% bucket 26: 70% bucket 27: 70% bucket 11: 80% bucket 12: 80% bucket 13: 80% bucket 14: 80% bucket 1: 100% bucket 15: 80% bucket 16: 80% bucket 17: 80% bucket 2: 90% bucket 3: 90% bucket 18: 80% bucket 4: 90% bucket 5: 90% bucket 6: 90% bucket 7: 90% bucket 19: 80% bucket 8: 90% bucket 9: 90% bucket 10: 90% bucket 20: 80% bucket 21: 80% bucket 22: 80% bucket 23: 80% bucket 24: 80% bucket 25: 80% bucket 26: 80% bucket 27: 80% bucket 11: 90% bucket 12: 90% bucket 13: 90% bucket 14: 90% Sorting block of length 22 for bucket 1 (Using difference cover) bucket 15: 90% bucket 16: 90% bucket 17: 90% bucket 2: 100% bucket 3: 100% bucket 18: 90% bucket 4: 100% bucket 5: 100% bucket 6: 100% bucket 7: 100% bucket 19: 90% bucket 8: 100% bucket 9: 100% bucket 10: 100% bucket 20: 90% Sorting block time: 00:00:00 bucket 21: 90% bucket 22: 90% bucket 23: 90% bucket 24: 90% bucket 25: 90% bucket 26: 90% bucket 27: 90% bucket 11: 100% bucket 12: 100% bucket 13: 100% bucket 14: 100% bucket 15: 100% bucket 16: 100% bucket 17: 100% Sorting block of length 28 for bucket 2 (Using difference cover) Sorting block of length 28 for bucket 3 (Using difference cover) bucket 18: 100% Sorting block of length 29 for bucket 4 (Using difference cover) Sorting block of length 33 for bucket 5 (Using difference cover) Sorting block of length 33 for bucket 6 (Using difference cover) Sorting block of length 5 for bucket 7 (Using difference cover) bucket 19: 100% Sorting block of length 34 for bucket 8 (Using difference cover) Sorting block of length 15 for bucket 9 (Using difference cover) Sorting block of length 35 for bucket 10 (Using difference cover) bucket 20: 100% Returning block of 23 for bucket 1 bucket 21: 100% bucket 22: 100% bucket 23: 100% bucket 24: 100% bucket 25: 100% bucket 26: 100% bucket 27: 100% Sorting block of length 31 for bucket 11 (Using difference cover) Sorting block of length 32 for bucket 12 (Using difference cover) Sorting block of length 35 for bucket 13 (Using difference cover) Sorting block of length 23 for bucket 14 (Using difference cover) Sorting block of length 25 for bucket 15 (Using difference cover) Sorting block of length 32 for bucket 16 (Using difference cover) Sorting block of length 19 for bucket 17 (Using difference cover) Sorting block of length 35 for bucket 18 (Using difference cover) Returning block of 1 for bucket 19 Sorting block of length 9 for bucket 20 (Using difference cover) Sorting block of length 29 for bucket 21 (Using difference cover) Sorting block of length 12 for bucket 22 (Using difference cover) Sorting block of length 5 for bucket 23 (Using difference cover) Sorting block of length 34 for bucket 24 (Using difference cover) Sorting block of length 28 for bucket 25 (Using difference cover) Sorting block of length 16 for bucket 26 (Using difference cover) Sorting block of length 19 for bucket 27 (Using difference cover) Getting block 28 of 203 Reserving size (36) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: Getting block 29 of 203 bucket 28: 10% Reserving size (36) for bucket 29 bucket 28: 20% Calculating Z arrays for bucket 29 bucket 28: 30% bucket 28: 40% Entering block accumulator loop for bucket 29: bucket 28: 50% bucket 28: 60% bucket 29: 10% bucket 28: 70% bucket 29: 20% bucket 28: 80% bucket 29: 30% bucket 28: 90% bucket 29: 40% bucket 28: 100% bucket 29: 50% Sorting block of length 21 for bucket 28 (Using difference cover) bucket 29: 60% bucket 29: 70% bucket 29: 80% bucket 29: 90% bucket 29: 100% Sorting block of length 34 for bucket 29 (Using difference cover) Sorting block time: 00:00:00 Returning block of 6 for bucket 7 Getting block 30 of 203 Reserving size (36) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 30: 10% bucket 30: 20% bucket 30: 30% bucket 30: 40% bucket 30: 50% bucket 30: 60% bucket 30: 70% bucket 30: 80% bucket 30: 90% bucket 30: 100% Sorting block of length 35 for bucket 30 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 29 for bucket 2 Returning block of 16 for bucket 9 Sorting block time: 00:00:00 Returning block of 6 for bucket 23 Getting block 31 of 203 Reserving size (36) for bucket 31 Sorting block time: 00:00:00 Calculating Z arrays for bucket 31 Returning block of 30 for bucket 4 Entering block accumulator loop for bucket 31: bucket 31: 10% Sorting block time: 00:00:00 Returning block of 35 for bucket 8 Sorting block time: 00:00:00 bucket 31: 20% Sorting block time: 00:00:00 Returning block of 29 for bucket 3 Sorting block time: 00:00:00 Getting block 32 of 203 Returning block of 34 for bucket 5 bucket 31: 30% Returning block of 34 for bucket 6 Reserving size (36) for bucket 32 bucket 31: 40% Calculating Z arrays for bucket 32 Sorting block time: 00:00:00 Getting block 33 of 203 bucket 31: 50% Returning block of 13 for bucket 22 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Reserving size (36) for bucket 33 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 32: bucket 31: 60% Returning block of 36 for bucket 10 Returning block of 22 for bucket 28 Calculating Z arrays for bucket 33 Returning block of 33 for bucket 12 Getting block 34 of 203 bucket 31: 70% Entering block accumulator loop for bucket 33: bucket 32: 10% Reserving size (36) for bucket 34 bucket 31: 80% bucket 32: 20% Sorting block time: 00:00:00 Calculating Z arrays for bucket 34 Getting block 35 of 203 bucket 31: 90% bucket 33: 10% Sorting block time: 00:00:00 Returning block of 36 for bucket 13 bucket 32: 30% Entering block accumulator loop for bucket 34: Reserving size (36) for bucket 35 bucket 31: 100% Returning block of 36 for bucket 18 bucket 33: 20% bucket 32: 40% Calculating Z arrays for bucket 35 Sorting block of length 33 for bucket 31 (Using difference cover) Getting block 36 of 203 bucket 33: 30% bucket 32: 50% bucket 34: 10% Entering block accumulator loop for bucket 35: Sorting block time: 00:00:00 Reserving size (36) for bucket 36 bucket 33: 40% bucket 32: 60% bucket 34: 20% Sorting block time: 00:00:00 Returning block of 26 for bucket 15 Calculating Z arrays for bucket 36 bucket 33: 50% bucket 32: 70% Sorting block time: 00:00:00 Returning block of 10 for bucket 20 Sorting block time: 00:00:00 bucket 34: 30% Sorting block time: 00:00:00 bucket 35: 10% bucket 33: 60% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 36: Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 32 for bucket 11 bucket 32: 80% Returning block of 35 for bucket 29 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 35 for bucket 24 bucket 34: 40% Sorting block time: 00:00:00 Getting block 37 of 203 Sorting block time: 00:00:00 bucket 35: 20% Returning block of 24 for bucket 14 bucket 33: 70% Sorting block time: 00:00:00 Returning block of 33 for bucket 16 Returning block of 17 for bucket 26 Returning block of 30 for bucket 21 bucket 32: 90% Returning block of 20 for bucket 27 Returning block of 20 for bucket 17 Returning block of 36 for bucket 30 bucket 34: 50% Reserving size (36) for bucket 37 Returning block of 29 for bucket 25 bucket 35: 30% Returning block of 34 for bucket 31 bucket 33: 80% bucket 36: 10% Getting block 38 of 203 bucket 32: 100% bucket 34: 60% Calculating Z arrays for bucket 37 Getting block 39 of 203 bucket 35: 40% bucket 33: 90% bucket 36: 20% Reserving size (36) for bucket 38 Getting block 40 of 203 Sorting block of length 16 for bucket 32 (Using difference cover) bucket 34: 70% Getting block 41 of 203 Reserving size (36) for bucket 39 Entering block accumulator loop for bucket 37: bucket 35: 50% bucket 33: 100% bucket 36: 30% Calculating Z arrays for bucket 38 Reserving size (36) for bucket 40 Getting block 42 of 203 bucket 34: 80% Reserving size (36) for bucket 41 Calculating Z arrays for bucket 39 bucket 35: 60% Sorting block of length 27 for bucket 33 (Using difference cover) bucket 36: 40% Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 38: Reserving size (36) for bucket 42 bucket 34: 90% Calculating Z arrays for bucket 41 Getting block 43 of 203 bucket 37: 10% bucket 35: 70% Entering block accumulator loop for bucket 39: bucket 36: 50% Entering block accumulator loop for bucket 40: Calculating Z arrays for bucket 42 bucket 34: 100% Reserving size (36) for bucket 43 Entering block accumulator loop for bucket 41: bucket 37: 20% bucket 35: 80% Getting block 44 of 203 bucket 36: 60% bucket 38: 10% Sorting block of length 26 for bucket 34 (Using difference cover) Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 42: bucket 37: 30% bucket 35: 90% bucket 39: 10% Reserving size (36) for bucket 44 bucket 36: 70% bucket 38: 20% bucket 40: 10% Getting block 45 of 203 Sorting block time: 00:00:00 bucket 41: 10% Entering block accumulator loop for bucket 43: bucket 37: 40% bucket 35: 100% bucket 39: 20% Calculating Z arrays for bucket 44 bucket 36: 80% bucket 38: 30% Getting block 46 of 203 bucket 40: 20% Sorting block time: 00:00:00 bucket 42: 10% Reserving size (36) for bucket 45 Returning block of 17 for bucket 32 bucket 41: 20% bucket 37: 50% Sorting block of length 31 for bucket 35 (Using difference cover) bucket 39: 30% bucket 36: 90% Entering block accumulator loop for bucket 44: bucket 38: 40% Reserving size (36) for bucket 46 Getting block 47 of 203 Returning block of 28 for bucket 33 bucket 40: 30% bucket 42: 20% Calculating Z arrays for bucket 45 bucket 41: 30% bucket 43: 10% bucket 37: 60% Getting block 48 of 203 bucket 39: 40% bucket 36: 100% bucket 38: 50% Calculating Z arrays for bucket 46 Reserving size (36) for bucket 47 bucket 40: 40% bucket 42: 30% bucket 41: 40% Entering block accumulator loop for bucket 45: bucket 43: 20% bucket 37: 70% Reserving size (36) for bucket 48 bucket 39: 50% Sorting block of length 24 for bucket 36 (Using difference cover) bucket 44: 10% bucket 38: 60% Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 46: Sorting block time: 00:00:00 bucket 40: 50% bucket 42: 40% bucket 41: 50% bucket 43: 30% bucket 37: 80% Calculating Z arrays for bucket 48 Getting block 49 of 203 bucket 39: 60% bucket 44: 20% bucket 38: 70% Getting block 50 of 203 Returning block of 27 for bucket 34 Entering block accumulator loop for bucket 47: bucket 40: 60% bucket 42: 50% bucket 41: 60% bucket 45: 10% bucket 43: 40% bucket 37: 90% Reserving size (36) for bucket 49 Entering block accumulator loop for bucket 48: Getting block 51 of 203 bucket 39: 70% bucket 44: 30% bucket 38: 80% Reserving size (36) for bucket 50 Sorting block time: 00:00:00 bucket 46: 10% bucket 40: 70% Sorting block time: 00:00:00 bucket 42: 60% bucket 41: 70% bucket 45: 20% bucket 43: 50% bucket 37: 100% Calculating Z arrays for bucket 49 Reserving size (36) for bucket 51 Getting block 52 of 203 bucket 39: 80% bucket 44: 40% bucket 38: 90% Calculating Z arrays for bucket 50 Returning block of 32 for bucket 35 bucket 46: 20% bucket 47: 10% Getting block 53 of 203 Returning block of 25 for bucket 36 bucket 40: 80% bucket 42: 70% bucket 41: 80% bucket 45: 30% bucket 43: 60% Sorting block of length 26 for bucket 37 (Using difference cover) Calculating Z arrays for bucket 51 bucket 48: 10% Reserving size (36) for bucket 52 Entering block accumulator loop for bucket 49: Getting block 54 of 203 bucket 39: 90% bucket 44: 50% bucket 38: 100% Entering block accumulator loop for bucket 50: bucket 46: 30% bucket 47: 20% Reserving size (36) for bucket 53 bucket 40: 90% bucket 42: 80% bucket 41: 90% Getting block 55 of 203 bucket 45: 40% bucket 43: 70% bucket 48: 20% Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 51: Reserving size (36) for bucket 54 bucket 39: 100% bucket 44: 60% Sorting block of length 12 for bucket 38 (Using difference cover) Sorting block time: 00:00:00 bucket 46: 40% bucket 47: 30% Calculating Z arrays for bucket 53 bucket 40: 100% bucket 42: 90% bucket 41: 100% Reserving size (36) for bucket 55 bucket 45: 50% bucket 43: 80% bucket 48: 30% Getting block 56 of 203 Calculating Z arrays for bucket 54 bucket 49: 10% Entering block accumulator loop for bucket 52: Sorting block of length 28 for bucket 39 (Using difference cover) bucket 44: 70% Sorting block time: 00:00:00 Getting block 57 of 203 Returning block of 27 for bucket 37 bucket 50: 10% bucket 46: 50% bucket 47: 40% Sorting block of length 30 for bucket 40 (Using difference cover) Entering block accumulator loop for bucket 53: bucket 42: 100% Sorting block of length 25 for bucket 41 (Using difference cover) Calculating Z arrays for bucket 55 bucket 45: 60% bucket 43: 90% bucket 48: 40% bucket 51: 10% Reserving size (36) for bucket 56 Getting block 58 of 203 bucket 49: 20% Entering block accumulator loop for bucket 54: Returning block of 13 for bucket 38 bucket 44: 80% Reserving size (36) for bucket 57 bucket 50: 20% bucket 46: 60% bucket 47: 50% Sorting block of length 19 for bucket 42 Getting block 59 of 203 bucket 45: 70% (Using difference cover) Entering block accumulator loop for bucket 55: bucket 43: 100% bucket 48: 50% bucket 51: 20% Calculating Z arrays for bucket 56 Reserving size (36) for bucket 58 bucket 49: 30% bucket 52: 10% bucket 44: 90% Calculating Z arrays for bucket 57 Sorting block time: 00:00:00 Getting block 60 of 203 bucket 50: 30% bucket 46: 70% Getting block 61 of 203 bucket 47: 60% bucket 53: 10% Reserving size (36) for bucket 59 bucket 45: 80% Sorting block of length 29 for bucket 43 (Using difference cover) bucket 48: 60% bucket 51: 30% Calculating Z arrays for bucket 58 Getting block 62 of 203 Entering block accumulator loop for bucket 56: bucket 49: 40% bucket 54: 10% bucket 52: 20% bucket 44: 100% Returning block of 29 for bucket 39 Reserving size (36) for bucket 60 Entering block accumulator loop for bucket 57: bucket 50: 40% bucket 46: 80% Reserving size (36) for bucket 61 bucket 47: 70% bucket 53: 20% Calculating Z arrays for bucket 59 bucket 45: 90% bucket 55: 10% bucket 48: 70% bucket 51: 40% Reserving size (36) for bucket 62 Entering block accumulator loop for bucket 58: bucket 49: 50% bucket 54: 20% bucket 52: 30% Sorting block of length 17 for bucket 44 (Using difference cover) Getting block 63 of 203 Sorting block time: 00:00:00 Getting block 64 of 203 Calculating Z arrays for bucket 60 Sorting block time: 00:00:00 Getting block 65 of 203 bucket 50: 50% bucket 46: 90% Calculating Z arrays for bucket 61 bucket 47: 80% bucket 53: 30% bucket 45: 100% Entering block accumulator loop for bucket 59: bucket 55: 20% Sorting block time: 00:00:00 bucket 48: 80% bucket 51: 50% Calculating Z arrays for bucket 62 bucket 56: 10% bucket 49: 60% bucket 54: 30% bucket 52: 40% Reserving size (36) for bucket 63 Returning block of 26 for bucket 41 Reserving size (36) for bucket 64 Returning block of 31 for bucket 40 bucket 57: 10% Reserving size (36) for bucket 65 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 60: bucket 50: 60% bucket 46: 100% bucket 47: 90% Entering block accumulator loop for bucket 61: bucket 53: 40% Sorting block of length 27 for bucket 45 (Using difference cover) Getting block 66 of 203 Sorting block time: 00:00:00 Returning block of 20 for bucket 42 bucket 55: 30% bucket 48: 90% bucket 51: 60% bucket 58: 10% Entering block accumulator loop for bucket 62: bucket 56: 20% bucket 49: 70% bucket 54: 40% bucket 52: 50% Calculating Z arrays for bucket 63 Calculating Z arrays for bucket 64 bucket 57: 20% Calculating Z arrays for bucket 65 Returning block of 30 for bucket 43 bucket 50: 70% Sorting block of length 32 for bucket 46 (Using difference cover) bucket 47: 100% bucket 53: 50% bucket 59: 10% Reserving size (36) for bucket 66 Returning block of 18 for bucket 44 bucket 55: 40% bucket 48: 100% bucket 51: 70% bucket 58: 20% bucket 56: 30% bucket 49: 80% bucket 54: 50% bucket 52: 60% Entering block accumulator loop for bucket 63: Entering block accumulator loop for bucket 64: bucket 57: 30% Getting block 67 of 203 Entering block accumulator loop for bucket 65: bucket 60: 10% bucket 50: 80% Sorting block of length 24 for bucket 47 Sorting block time: 00:00:00 (Using difference cover) bucket 61: 10% bucket 53: 60% Sorting block time: 00:00:00 bucket 59: 20% Calculating Z arrays for bucket 66 bucket 55: 50% Sorting block of length 29 for bucket 48 (Using difference cover) Getting block 68 of 203 bucket 51: 80% bucket 58: 30% bucket 62: 10% bucket 56: 40% bucket 49: 90% bucket 54: 60% bucket 52: 70% bucket 57: 40% Reserving size (36) for bucket 67 bucket 60: 20% Returning block of 28 for bucket 45 bucket 50: 90% bucket 61: 20% Returning block of 33 for bucket 46 bucket 53: 70% bucket 59: 30% Entering block accumulator loop for bucket 66: bucket 55: 60% Reserving size (36) for bucket 68 bucket 51: 90% bucket 58: 40% bucket 62: 20% bucket 56: 50% bucket 49: 100% bucket 54: 70% Getting block 69 of 203 bucket 52: 80% bucket 64: 10% bucket 63: 10% bucket 57: 50% Calculating Z arrays for bucket 67 bucket 65: 10% Getting block 70 of 203 bucket 60: 30% bucket 50: 100% bucket 61: 30% bucket 53: 80% Sorting block time: 00:00:00 bucket 59: 40% bucket 55: 70% Calculating Z arrays for bucket 68 Sorting block time: 00:00:00 bucket 51: 100% Getting block 71 of 203 bucket 58: 50% bucket 62: 30% bucket 56: 60% Sorting block of length 16 for bucket 49 (Using difference cover) bucket 54: 80% Reserving size (36) for bucket 69 bucket 52: 90% bucket 64: 20% bucket 63: 20% bucket 57: 60% bucket 65: 20% Entering block accumulator loop for bucket 67: Reserving size (36) for bucket 70 bucket 60: 40% Sorting block of length 28 for bucket 50 (Using difference cover) bucket 61: 40% Returning block of 25 for bucket 47 bucket 53: 90% bucket 59: 50% bucket 66: 10% bucket 55: 80% Returning block of 30 for bucket 48 Sorting block of length 33 for bucket 51 (Using difference cover) Entering block accumulator loop for bucket 68: Reserving size (36) for bucket 71 bucket 58: 60% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 62: 40% bucket 56: 70% bucket 54: 90% Calculating Z arrays for bucket 69 Getting block 72 of 203 bucket 52: 100% bucket 64: 30% bucket 63: 30% bucket 57: 70% bucket 65: 30% Calculating Z arrays for bucket 70 bucket 60: 50% bucket 61: 50% bucket 53: 100% bucket 59: 60% bucket 66: 20% Getting block 73 of 203 bucket 55: 90% Sorting block time: 00:00:00 Calculating Z arrays for bucket 71 Returning block of 17 for bucket 49 Returning block of 29 for bucket 50 bucket 58: 70% bucket 62: 50% bucket 56: 80% bucket 54: 100% Reserving size (36) for bucket 72 Sorting block of length 21 for bucket 52 (Using difference cover) Entering block accumulator loop for bucket 69: bucket 64: 40% bucket 63: 40% bucket 57: 80% bucket 65: 40% bucket 67: 10% bucket 60: 60% Entering block accumulator loop for bucket 70: bucket 61: 60% Sorting block of length 14 for bucket 53 (Using difference cover) bucket 59: 70% bucket 66: 30% Reserving size (36) for bucket 73 Returning block of 34 for bucket 51 bucket 55: 100% bucket 68: 10% Entering block accumulator loop for bucket 71: bucket 58: 80% bucket 62: 60% bucket 56: 90% Sorting block of length 29 for bucket 54 (Using difference cover) Getting block 74 of 203 Calculating Z arrays for bucket 72 bucket 64: 50% bucket 63: 50% bucket 57: 90% bucket 65: 50% Getting block 75 of 203 bucket 67: 20% bucket 60: 70% bucket 61: 70% bucket 59: 80% bucket 66: 40% Calculating Z arrays for bucket 73 Sorting block of length 13 for bucket 55 (Using difference cover) bucket 68: 20% bucket 58: 90% bucket 62: 70% bucket 56: 100% Reserving size (36) for bucket 74 bucket 64: 60% bucket 69: 10% bucket 63: 60% Entering block accumulator loop for bucket 72: bucket 57: 100% bucket 65: 60% Reserving size (36) for bucket 75 Getting block 76 of 203 bucket 67: 30% bucket 60: 80% bucket 70: 10% bucket 61: 80% bucket 59: 90% bucket 66: 50% Getting block 77 of 203 Entering block accumulator loop for bucket 73: bucket 68: 30% bucket 71: 10% bucket 58: 100% bucket 62: 80% Sorting block of length 26 for bucket 56 (Using difference cover) Calculating Z arrays for bucket 74 bucket 64: 70% bucket 69: 20% bucket 63: 70% Sorting block of length 12 for bucket 57 (Using difference cover) bucket 65: 70% Calculating Z arrays for bucket 75 Getting block 78 of 203 Reserving size (36) for bucket 76 bucket 67: 40% bucket 60: 90% bucket 70: 20% bucket 61: 90% bucket 59: 100% bucket 66: 60% Reserving size (36) for bucket 77 Sorting block time: 00:00:00 bucket 68: 40% Sorting block of length 29 for bucket 58 (Using difference cover) bucket 71: 20% bucket 62: 90% bucket 64: 80% Entering block accumulator loop for bucket 74: bucket 69: 30% bucket 63: 80% bucket 72: 10% bucket 65: 80% Reserving size (36) for bucket 78 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 75: bucket 67: 50% bucket 60: 100% bucket 70: 30% bucket 61: 100% Sorting block of length 35 for bucket 59 (Using difference cover) bucket 66: 70% Calculating Z arrays for bucket 77 Returning block of 22 for bucket 52 bucket 73: 10% bucket 68: 50% bucket 71: 30% bucket 62: 100% bucket 64: 90% bucket 69: 40% bucket 63: 90% bucket 72: 20% bucket 65: 90% Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 76: bucket 67: 60% Sorting block of length 34 for bucket 60 (Using difference cover) bucket 70: 40% Sorting block of length 31 for bucket 61 (Using difference cover) bucket 66: 80% Entering block accumulator loop for bucket 77: bucket 73: 20% bucket 68: 60% bucket 71: 40% Sorting block of length 34 for bucket 62 (Using difference cover) bucket 64: 100% bucket 74: 10% bucket 69: 50% Sorting block time: 00:00:00 bucket 63: 100% bucket 72: 30% bucket 65: 100% bucket 75: 10% Entering block accumulator loop for bucket 78: bucket 67: 70% bucket 70: 50% bucket 66: 90% bucket 73: 30% bucket 68: 70% bucket 71: 50% Sorting block of length 14 for bucket 64 (Using difference cover) bucket 74: 20% Returning block of 15 for bucket 53 bucket 69: 60% Sorting block of length 28 for bucket 63 (Using difference cover) bucket 72: 40% Sorting block of length 32 for bucket 65 (Using difference cover) bucket 75: 20% bucket 76: 10% bucket 67: 80% bucket 70: 60% bucket 66: 100% bucket 77: 10% bucket 73: 40% bucket 68: 80% bucket 71: 60% bucket 74: 30% bucket 69: 70% bucket 72: 50% Sorting block time: 00:00:00 bucket 75: 30% bucket 76: 20% bucket 78: 10% bucket 67: 90% bucket 70: 70% Sorting block of length 29 for bucket 66 (Using difference cover) Getting block 79 of 203 bucket 77: 20% bucket 73: 50% bucket 68: 90% bucket 71: 70% bucket 74: 40% bucket 69: 80% Returning block of 30 for bucket 54 bucket 72: 60% Sorting block time: 00:00:00 bucket 75: 40% bucket 76: 30% bucket 78: 20% bucket 67: 100% bucket 70: 80% Reserving size (36) for bucket 79 bucket 77: 30% bucket 73: 60% bucket 68: 100% bucket 71: 80% bucket 74: 50% bucket 69: 90% Returning block of 13 for bucket 57 bucket 72: 70% Getting block 80 of 203 bucket 75: 50% bucket 76: 40% bucket 78: 30% Sorting block of length 26 for bucket 67 (Using difference cover) bucket 70: 90% Calculating Z arrays for bucket 79 bucket 77: 40% bucket 73: 70% Sorting block of length 25 for bucket 68 (Using difference cover) bucket 71: 90% bucket 74: 60% bucket 69: 100% bucket 72: 80% Reserving size (36) for bucket 80 bucket 75: 60% bucket 76: 50% bucket 78: 40% bucket 70: 100% bucket 77: 50% bucket 73: 80% Entering block accumulator loop for bucket 79: bucket 71: 100% bucket 74: 70% Sorting block of length 15 for bucket 69 Sorting block time: 00:00:00 (Using difference cover) bucket 72: 90% Calculating Z arrays for bucket 80 Getting block 81 of 203 bucket 75: 70% bucket 76: 60% bucket 78: 50% Sorting block of length 31 for bucket 70 (Using difference cover) bucket 77: 60% bucket 73: 90% Sorting block of length 29 for bucket 71 (Using difference cover) Returning block of 14 for bucket 55 bucket 74: 80% Getting block 82 of 203 bucket 72: 100% Reserving size (36) for bucket 81 Entering block accumulator loop for bucket 80: bucket 75: 80% bucket 76: 70% bucket 78: 60% bucket 77: 70% bucket 73: 100% bucket 79: 10% bucket 74: 90% Reserving size (36) for bucket 82 Sorting block of length 24 for bucket 72 (Using difference cover) Calculating Z arrays for bucket 81 bucket 75: 90% bucket 76: 80% bucket 78: 70% bucket 77: 80% Sorting block of length 17 for bucket 73 (Using difference cover) bucket 79: 20% bucket 74: 100% Calculating Z arrays for bucket 82 bucket 75: 100% bucket 80: 10% Entering block accumulator loop for bucket 81: bucket 76: 90% bucket 78: 80% bucket 77: 90% Sorting block of length 32 for bucket 74 (Using difference cover) bucket 79: 30% Sorting block of length 27 for bucket 75 (Using difference cover) bucket 80: 20% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 82: bucket 76: 100% bucket 78: 90% Getting block 83 of 203 bucket 77: 100% bucket 79: 40% Returning block of 27 for bucket 56 bucket 80: 30% Sorting block of length 17 for bucket 76 (Using difference cover) bucket 81: 10% bucket 78: 100% Reserving size (36) for bucket 83 Sorting block of length 34 for bucket 77 (Using difference cover) bucket 79: 50% bucket 80: 40% bucket 82: 10% Sorting block of length 30 for bucket 78 (Using difference cover) bucket 81: 20% Calculating Z arrays for bucket 83 bucket 79: 60% bucket 80: 50% bucket 82: 20% bucket 81: 30% bucket 79: 70% Entering block accumulator loop for bucket 83: bucket 80: 60% bucket 82: 30% bucket 81: 40% bucket 79: 80% bucket 80: 70% bucket 82: 40% bucket 81: 50% bucket 83: 10% bucket 79: 90% bucket 80: 80% bucket 82: 50% bucket 81: 60% bucket 83: 20% bucket 79: 100% bucket 80: 90% bucket 82: 60% Getting block 84 of 203 bucket 81: 70% bucket 83: 30% Sorting block of length 32 for bucket 79 (Using difference cover) bucket 80: 100% bucket 82: 70% Reserving size (36) for bucket 84 bucket 81: 80% bucket 83: 40% Sorting block of length 12 for bucket 80 (Using difference cover) bucket 82: 80% Calculating Z arrays for bucket 84 bucket 81: 90% bucket 83: 50% bucket 82: 90% bucket 81: 100% bucket 83: 60% Entering block accumulator loop for bucket 84: bucket 82: 100% Sorting block of length 27 for bucket 81 (Using difference cover) bucket 83: 70% Sorting block of length 29 for bucket 82 (Using difference cover) bucket 83: 80% bucket 84: 10% bucket 83: 90% bucket 84: 20% bucket 83: 100% Sorting block of length 35 for bucket 83 (Using difference cover) bucket 84: 30% bucket 84: 40% bucket 84: 50% bucket 84: 60% bucket 84: 70% bucket 84: 80% bucket 84: 90% bucket 84: 100% Sorting block of length 31 for bucket 84 (Using difference cover) Sorting block time: 00:00:00 Returning block of 30 for bucket 58 Getting block 85 of 203 Reserving size (36) for bucket 85 Sorting block time: 00:00:00 Calculating Z arrays for bucket 85 Returning block of 33 for bucket 65 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 36 for bucket 59 Sorting block time: 00:00:00 Entering block accumulator loop for bucket 85: Returning block of 35 for bucket 60 Returning block of 35 for bucket 62 bucket 85: 10% bucket 85: 20% bucket 85: 30% bucket 85: 40% bucket 85: 50% bucket 85: 60% bucket 85: 70% Sorting block time: 00:00:00 Getting block 86 of 203 Returning block of 32 for bucket 61 bucket 85: 80% Reserving size (36) for bucket 86 bucket 85: 90% Calculating Z arrays for bucket 86 bucket 85: 100% Sorting block of length 23 for bucket 85 (Using difference cover) Entering block accumulator loop for bucket 86: bucket 86: 10% bucket 86: 20% bucket 86: 30% bucket 86: 40% bucket 86: 50% bucket 86: 60% bucket 86: 70% bucket 86: 80% bucket 86: 90% Getting block 87 of 203 bucket 86: 100% Reserving size (36) for bucket 87 Sorting block of length 28 for bucket 86 (Using difference cover) Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: Getting block 88 of 203 bucket 87: 10% Reserving size (36) for bucket 88 Calculating Z arrays for bucket 88 bucket 87: 20% bucket 87: 30% Entering block accumulator loop for bucket 88: bucket 87: 40% bucket 87: 50% bucket 88: 10% bucket 87: 60% bucket 88: 20% bucket 87: 70% Getting block 89 of 203 bucket 88: 30% bucket 87: 80% Reserving size (36) for bucket 89 bucket 88: 40% Calculating Z arrays for bucket 89 bucket 87: 90% bucket 88: 50% bucket 87: 100% Entering block accumulator loop for bucket 89: bucket 88: 60% Sorting block of length 10 for bucket 87 (Using difference cover) bucket 88: 70% bucket 89: 10% Getting block 90 of 203 bucket 88: 80% bucket 89: 20% Reserving size (36) for bucket 90 bucket 88: 90% bucket 89: 30% Calculating Z arrays for bucket 90 bucket 88: 100% bucket 89: 40% Sorting block of length 29 for bucket 88 (Using difference cover) bucket 89: 50% Entering block accumulator loop for bucket 90: bucket 89: 60% bucket 89: 70% bucket 90: 10% bucket 89: 80% bucket 90: 20% bucket 89: 90% bucket 90: 30% bucket 89: 100% Sorting block of length 33 for bucket 89 (Using difference cover) bucket 90: 40% bucket 90: 50% bucket 90: 60% bucket 90: 70% bucket 90: 80% bucket 90: 90% bucket 90: 100% Sorting block of length 22 for bucket 90 (Using difference cover) Sorting block time: 00:00:00 Returning block of 15 for bucket 64 Sorting block time: 00:00:00 Returning block of 29 for bucket 63 Getting block 91 of 203 Reserving size (36) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 91: 10% bucket 91: 20% bucket 91: 30% Getting block 92 of 203 bucket 91: 40% Reserving size (36) for bucket 92 Calculating Z arrays for bucket 92 bucket 91: 50% bucket 91: 60% Entering block accumulator loop for bucket 92: bucket 91: 70% bucket 91: 80% bucket 92: 10% bucket 91: 90% bucket 92: 20% bucket 91: 100% Sorting block of length 34 for bucket 91 (Using difference cover) bucket 92: 30% bucket 92: 40% bucket 92: 50% bucket 92: 60% bucket 92: 70% bucket 92: 80% bucket 92: 90% bucket 92: 100% Sorting block of length 30 for bucket 92 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 18 for bucket 73 Returning block of 30 for bucket 66 Returning block of 26 for bucket 68 Sorting block time: 00:00:00 Returning block of 16 for bucket 69 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 27 for bucket 67 Returning block of 25 for bucket 72 Getting block 93 of 203 Reserving size (36) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 93: 10% bucket 93: 20% bucket 93: 30% bucket 93: 40% Sorting block time: 00:00:00 Returning block of 30 for bucket 71 bucket 93: 50% Getting block 94 of 203 bucket 93: 60% Reserving size (36) for bucket 94 bucket 93: 70% Calculating Z arrays for bucket 94 bucket 93: 80% bucket 93: 90% Entering block accumulator loop for bucket 94: Sorting block time: 00:00:00 Returning block of 32 for bucket 70 Sorting block time: 00:00:00 bucket 93: 100% Sorting block time: 00:00:00 Returning block of 18 for bucket 76 Sorting block time: 00:00:00 Sorting block of length 34 for bucket 93 (Using difference cover) Sorting block time: 00:00:00 Returning block of 31 for bucket 78 bucket 94: 10% Returning block of 33 for bucket 74 Returning block of 28 for bucket 75 bucket 94: 20% bucket 94: 30% Getting block 95 of 203 bucket 94: 40% Reserving size (36) for bucket 95 bucket 94: 50% Calculating Z arrays for bucket 95 bucket 94: 60% bucket 94: 70% Entering block accumulator loop for bucket 95: bucket 94: 80% Getting block 96 of 203 bucket 94: 90% bucket 95: 10% Reserving size (36) for bucket 96 bucket 94: 100% bucket 95: 20% Calculating Z arrays for bucket 96 Sorting block of length 34 for bucket 94 (Using difference cover) bucket 95: 30% Getting block 97 of 203 Entering block accumulator loop for bucket 96: bucket 95: 40% Reserving size (36) for bucket 97 bucket 95: 50% Calculating Z arrays for bucket 97 bucket 96: 10% bucket 95: 60% Getting block 98 of 203 bucket 96: 20% Entering block accumulator loop for bucket 97: bucket 95: 70% Reserving size (36) for bucket 98 bucket 96: 30% bucket 95: 80% Calculating Z arrays for bucket 98 bucket 96: 40% bucket 97: 10% bucket 95: 90% bucket 96: 50% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 98: Sorting block time: 00:00:00 bucket 97: 20% Sorting block time: 00:00:00 bucket 95: 100% Sorting block time: 00:00:00 Returning block of 36 for bucket 83 bucket 96: 60% Sorting block time: 00:00:00 Returning block of 33 for bucket 79 Returning block of 28 for bucket 81 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Getting block 99 of 203 bucket 97: 30% Sorting block of length 31 for bucket 95 Sorting block time: 00:00:00 (Using difference cover) Returning block of 32 for bucket 84 Returning block of 13 for bucket 80 bucket 96: 70% bucket 98: 10% Returning block of 35 for bucket 77 Returning block of 24 for bucket 85 Reserving size (36) for bucket 99 Returning block of 30 for bucket 82 bucket 97: 40% Getting block 100 of 203 bucket 96: 80% bucket 98: 20% Calculating Z arrays for bucket 99 bucket 97: 50% Reserving size (36) for bucket 100 bucket 96: 90% Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 98: 30% bucket 97: 60% Sorting block time: 00:00:00 Calculating Z arrays for bucket 100 Sorting block time: 00:00:00 Getting block 101 of 203 Entering block accumulator loop for bucket 99: Returning block of 29 for bucket 86 Returning block of 34 for bucket 89 Returning block of 30 for bucket 88 bucket 96: 100% bucket 98: 40% Returning block of 35 for bucket 91 bucket 97: 70% Returning block of 23 for bucket 90 Reserving size (36) for bucket 101 Entering block accumulator loop for bucket 100: Sorting block of length 23 for bucket 96 (Using difference cover) bucket 98: 50% Getting block 102 of 203 bucket 97: 80% Calculating Z arrays for bucket 101 Getting block 103 of 203 Sorting block time: 00:00:00 bucket 99: 10% bucket 98: 60% Reserving size (36) for bucket 102 bucket 97: 90% Sorting block time: 00:00:00 bucket 100: 10% Reserving size (36) for bucket 103 Getting block 104 of 203 Returning block of 11 for bucket 87 Entering block accumulator loop for bucket 101: bucket 99: 20% bucket 98: 70% Calculating Z arrays for bucket 102 Returning block of 31 for bucket 92 bucket 97: 100% bucket 100: 20% Calculating Z arrays for bucket 103 Reserving size (36) for bucket 104 bucket 99: 30% bucket 98: 80% Getting block 105 of 203 Entering block accumulator loop for bucket 102: Sorting block of length 32 for bucket 97 (Using difference cover) bucket 100: 30% Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 103: bucket 101: 10% Getting block 106 of 203 Sorting block time: 00:00:00 bucket 99: 40% bucket 98: 90% Reserving size (36) for bucket 105 bucket 100: 40% Entering block accumulator loop for bucket 104: bucket 101: 20% Reserving size (36) for bucket 106 Returning block of 35 for bucket 93 bucket 99: 50% bucket 98: 100% Calculating Z arrays for bucket 105 bucket 102: 10% Getting block 107 of 203 bucket 100: 50% bucket 103: 10% bucket 101: 30% Calculating Z arrays for bucket 106 bucket 99: 60% Sorting block of length 23 for bucket 98 (Using difference cover) bucket 102: 20% Entering block accumulator loop for bucket 105: Reserving size (36) for bucket 107 bucket 100: 60% Sorting block time: 00:00:00 bucket 103: 20% bucket 104: 10% bucket 101: 40% Getting block 108 of 203 bucket 99: 70% Entering block accumulator loop for bucket 106: bucket 102: 30% Calculating Z arrays for bucket 107 Returning block of 35 for bucket 94 bucket 100: 70% bucket 103: 30% bucket 104: 20% bucket 101: 50% Reserving size (36) for bucket 108 bucket 99: 80% Getting block 109 of 203 bucket 102: 40% bucket 105: 10% Entering block accumulator loop for bucket 107: bucket 100: 80% bucket 103: 40% bucket 104: 30% bucket 101: 60% Calculating Z arrays for bucket 108 Getting block 110 of 203 bucket 99: 90% bucket 106: 10% Reserving size (36) for bucket 109 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 102: 50% bucket 105: 20% bucket 100: 90% bucket 103: 50% bucket 104: 40% bucket 101: 70% Getting block 111 of 203 Reserving size (36) for bucket 110 Entering block accumulator loop for bucket 108: bucket 99: 100% bucket 106: 20% Returning block of 32 for bucket 95 Calculating Z arrays for bucket 109 Returning block of 24 for bucket 96 bucket 102: 60% bucket 105: 30% bucket 107: 10% Sorting block time: 00:00:00 bucket 100: 100% bucket 103: 60% Getting block 112 of 203 bucket 104: 50% bucket 101: 80% Reserving size (36) for bucket 111 Sorting block time: 00:00:00 Calculating Z arrays for bucket 110 Sorting block of length 34 for bucket 99 (Using difference cover) bucket 106: 30% Entering block accumulator loop for bucket 109: Getting block 113 of 203 bucket 102: 70% bucket 105: 40% Returning block of 33 for bucket 97 bucket 107: 20% Sorting block of length 31 for bucket 100 (Using difference cover) bucket 103: 70% Reserving size (36) for bucket 112 bucket 104: 60% Returning block of 24 for bucket 98 bucket 101: 90% Calculating Z arrays for bucket 111 bucket 108: 10% Getting block 114 of 203 Entering block accumulator loop for bucket 110: bucket 106: 40% Reserving size (36) for bucket 113 bucket 102: 80% bucket 105: 50% bucket 107: 30% Getting block 115 of 203 bucket 103: 80% Calculating Z arrays for bucket 112 bucket 104: 70% bucket 101: 100% Entering block accumulator loop for bucket 111: bucket 108: 20% Reserving size (36) for bucket 114 Getting block 116 of 203 bucket 106: 50% Calculating Z arrays for bucket 113 bucket 109: 10% bucket 102: 90% bucket 105: 60% Getting block 117 of 203 bucket 107: 40% Reserving size (36) for bucket 115 Sorting block time: 00:00:00 bucket 103: 90% bucket 104: 80% Entering block accumulator loop for bucket 112: Sorting block of length 14 for bucket 101 (Using difference cover) Sorting block time: 00:00:00 bucket 108: 30% Calculating Z arrays for bucket 114 Getting block 118 of 203 bucket 110: 10% Reserving size (36) for bucket 116 bucket 106: 60% bucket 109: 20% Entering block accumulator loop for bucket 113: bucket 102: 100% bucket 105: 70% Reserving size (36) for bucket 117 bucket 107: 50% Calculating Z arrays for bucket 115 Getting block 119 of 203 Returning block of 35 for bucket 99 bucket 103: 100% bucket 104: 90% Returning block of 32 for bucket 100 bucket 111: 10% bucket 108: 40% Entering block accumulator loop for bucket 114: Reserving size (36) for bucket 118 bucket 110: 20% Calculating Z arrays for bucket 116 bucket 106: 70% Sorting block time: 00:00:00 bucket 109: 30% Sorting block of length 29 for bucket 102 (Using difference cover) bucket 105: 80% Calculating Z arrays for bucket 117 bucket 107: 60% Entering block accumulator loop for bucket 115: Reserving size (36) for bucket 119 Sorting block of length 35 for bucket 103 (Using difference cover) bucket 104: 100% bucket 112: 10% Getting block 120 of 203 bucket 111: 20% bucket 108: 50% Calculating Z arrays for bucket 118 bucket 110: 30% Returning block of 15 for bucket 101 Entering block accumulator loop for bucket 116: bucket 106: 80% bucket 109: 40% bucket 113: 10% bucket 105: 90% bucket 107: 70% Entering block accumulator loop for bucket 117: Calculating Z arrays for bucket 119 Sorting block of length 25 for bucket 104 (Using difference cover) bucket 112: 20% Reserving size (36) for bucket 120 bucket 111: 30% bucket 108: 60% bucket 114: 10% Getting block 121 of 203 bucket 110: 40% Entering block accumulator loop for bucket 118: bucket 106: 90% bucket 109: 50% bucket 113: 20% bucket 105: 100% bucket 107: 80% Getting block 122 of 203 bucket 115: 10% Entering block accumulator loop for bucket 119: bucket 112: 30% Sorting block time: 00:00:00 Calculating Z arrays for bucket 120 bucket 111: 40% bucket 108: 70% bucket 114: 20% Reserving size (36) for bucket 121 bucket 110: 50% Getting block 123 of 203 bucket 116: 10% bucket 106: 100% bucket 109: 60% bucket 113: 30% Sorting block of length 12 for bucket 105 (Using difference cover) bucket 107: 90% bucket 117: 10% Reserving size (36) for bucket 122 bucket 115: 20% Returning block of 30 for bucket 102 bucket 112: 40% Getting block 124 of 203 Entering block accumulator loop for bucket 120: bucket 111: 50% bucket 108: 80% bucket 114: 30% Sorting block time: 00:00:00 Calculating Z arrays for bucket 121 bucket 110: 60% bucket 118: 10% Reserving size (36) for bucket 123 bucket 116: 20% Sorting block of length 29 for bucket 106 (Using difference cover) Getting block 125 of 203 bucket 109: 70% bucket 113: 40% bucket 107: 100% bucket 117: 20% Calculating Z arrays for bucket 122 bucket 115: 30% bucket 119: 10% Getting block 126 of 203 bucket 112: 50% Reserving size (36) for bucket 124 bucket 111: 60% bucket 108: 90% Returning block of 36 for bucket 103 bucket 114: 40% Entering block accumulator loop for bucket 121: bucket 110: 70% Sorting block time: 00:00:00 bucket 118: 20% Calculating Z arrays for bucket 123 bucket 116: 30% Reserving size (36) for bucket 125 bucket 109: 80% bucket 113: 50% Sorting block of length 24 for bucket 107 (Using difference cover) bucket 117: 30% Entering block accumulator loop for bucket 122: bucket 115: 40% bucket 119: 20% Reserving size (36) for bucket 126 bucket 112: 60% Calculating Z arrays for bucket 124 Getting block 127 of 203 bucket 120: 10% bucket 111: 70% bucket 108: 100% bucket 114: 50% Returning block of 26 for bucket 104 bucket 110: 80% Sorting block time: 00:00:00 bucket 118: 30% Getting block 128 of 203 Entering block accumulator loop for bucket 123: bucket 116: 40% Calculating Z arrays for bucket 125 bucket 109: 90% bucket 113: 60% bucket 117: 40% bucket 115: 50% bucket 119: 30% Calculating Z arrays for bucket 126 bucket 112: 70% Entering block accumulator loop for bucket 124: Sorting block time: 00:00:00 Reserving size (36) for bucket 127 bucket 120: 20% bucket 111: 80% Sorting block of length 14 for bucket 108 (Using difference cover) bucket 121: 10% Sorting block time: 00:00:00 bucket 114: 60% Returning block of 13 for bucket 105 bucket 110: 90% Getting block 129 of 203 bucket 118: 40% Reserving size (36) for bucket 128 bucket 116: 50% Entering block accumulator loop for bucket 125: bucket 109: 100% bucket 113: 70% bucket 117: 50% bucket 122: 10% bucket 115: 60% bucket 119: 40% Entering block accumulator loop for bucket 126: bucket 112: 80% Returning block of 30 for bucket 106 Calculating Z arrays for bucket 127 Getting block 130 of 203 bucket 120: 30% Sorting block time: 00:00:00 bucket 111: 90% Returning block of 25 for bucket 107 bucket 121: 20% bucket 114: 70% bucket 110: 100% Reserving size (36) for bucket 129 bucket 118: 50% Calculating Z arrays for bucket 128 bucket 123: 10% bucket 116: 60% Sorting block of length 27 for bucket 109 (Using difference cover) bucket 113: 80% bucket 117: 60% bucket 122: 20% bucket 115: 70% bucket 119: 50% bucket 112: 90% bucket 124: 10% Entering block accumulator loop for bucket 127: Reserving size (36) for bucket 130 Returning block of 15 for bucket 108 bucket 120: 40% bucket 111: 100% Getting block 131 of 203 bucket 121: 30% bucket 114: 80% Sorting block of length 34 for bucket 110 (Using difference cover) Calculating Z arrays for bucket 129 bucket 118: 60% Entering block accumulator loop for bucket 128: bucket 123: 20% bucket 116: 70% bucket 125: 10% bucket 113: 90% bucket 117: 70% bucket 122: 30% bucket 115: 80% bucket 119: 60% bucket 126: 10% bucket 112: 100% bucket 124: 20% Calculating Z arrays for bucket 130 bucket 120: 50% Sorting block of length 6 for bucket 111 (Using difference cover) Getting block 132 of 203 Reserving size (36) for bucket 131 bucket 121: 40% bucket 114: 90% Entering block accumulator loop for bucket 129: bucket 118: 70% bucket 123: 30% bucket 116: 80% bucket 125: 20% bucket 113: 100% bucket 117: 80% bucket 122: 40% Getting block 133 of 203 Sorting block time: 00:00:00 bucket 115: 90% bucket 119: 70% bucket 126: 20% Sorting block of length 34 for bucket 112 (Using difference cover) bucket 124: 30% bucket 127: 10% Getting block 134 of 203 Entering block accumulator loop for bucket 130: bucket 120: 60% Reserving size (36) for bucket 132 Calculating Z arrays for bucket 131 bucket 121: 50% bucket 114: 100% bucket 118: 80% bucket 128: 10% bucket 123: 40% bucket 116: 90% bucket 125: 30% Sorting block of length 35 for bucket 113 (Using difference cover) bucket 117: 90% bucket 122: 50% Reserving size (36) for bucket 133 Sorting block time: 00:00:00 Getting block 135 of 203 Returning block of 28 for bucket 109 bucket 115: 100% bucket 119: 80% bucket 126: 30% bucket 124: 40% bucket 127: 20% Reserving size (36) for bucket 134 Sorting block time: 00:00:00 bucket 120: 70% Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 131: bucket 121: 60% Sorting block of length 28 for bucket 114 (Using difference cover) bucket 129: 10% bucket 118: 90% bucket 128: 20% bucket 123: 50% bucket 116: 100% bucket 125: 40% bucket 117: 100% bucket 122: 60% Calculating Z arrays for bucket 133 Returning block of 35 for bucket 110 Reserving size (36) for bucket 135 Sorting block of length 23 for bucket 115 (Using difference cover) bucket 119: 90% bucket 126: 40% bucket 124: 50% bucket 127: 30% Calculating Z arrays for bucket 134 Returning block of 7 for bucket 111 bucket 130: 10% bucket 120: 80% Entering block accumulator loop for bucket 132: bucket 121: 70% bucket 129: 20% bucket 118: 100% bucket 128: 30% bucket 123: 60% Sorting block of length 24 for bucket 116 (Using difference cover) bucket 125: 50% Sorting block of length 29 for bucket 117 (Using difference cover) bucket 122: 70% Entering block accumulator loop for bucket 133: Calculating Z arrays for bucket 135 bucket 119: 100% bucket 126: 50% bucket 124: 60% bucket 127: 40% Entering block accumulator loop for bucket 134: bucket 130: 20% bucket 120: 90% bucket 131: 10% bucket 121: 80% bucket 129: 30% Sorting block of length 12 for bucket 118 (Using difference cover) bucket 128: 40% bucket 123: 70% bucket 125: 60% Getting block 136 of 203 bucket 122: 80% Sorting block of length 31 for bucket 119 (Using difference cover) Entering block accumulator loop for bucket 135: bucket 126: 60% bucket 124: 70% bucket 127: 50% bucket 130: 30% bucket 120: 100% bucket 131: 20% bucket 132: 10% bucket 121: 90% bucket 129: 40% bucket 128: 50% Getting block 137 of 203 bucket 123: 80% bucket 125: 70% Reserving size (36) for bucket 136 bucket 122: 90% bucket 133: 10% bucket 126: 70% bucket 124: 80% bucket 127: 60% bucket 134: 10% bucket 130: 40% Sorting block of length 27 for bucket 120 (Using difference cover) Getting block 138 of 203 bucket 131: 30% bucket 132: 20% bucket 121: 100% bucket 129: 50% bucket 128: 60% Reserving size (36) for bucket 137 bucket 123: 90% bucket 125: 80% Calculating Z arrays for bucket 136 bucket 122: 100% bucket 133: 20% bucket 135: 10% bucket 126: 80% bucket 124: 90% bucket 127: 70% bucket 134: 20% bucket 130: 50% Reserving size (36) for bucket 138 bucket 131: 40% bucket 132: 30% Sorting block of length 28 for bucket 121 (Using difference cover) bucket 129: 60% bucket 128: 70% Calculating Z arrays for bucket 137 bucket 123: 100% bucket 125: 90% Sorting block of length 29 for bucket 122 (Using difference cover) Sorting block time: 00:00:00 Entering block accumulator loop for bucket 136: Sorting block time: 00:00:00 bucket 133: 30% bucket 135: 20% bucket 126: 90% bucket 124: 100% bucket 127: 80% bucket 134: 30% bucket 130: 60% Calculating Z arrays for bucket 138 bucket 131: 50% bucket 132: 40% bucket 129: 70% bucket 128: 80% Sorting block of length 33 for bucket 123 (Using difference cover) Entering block accumulator loop for bucket 137: bucket 125: 100% Returning block of 36 for bucket 113 Returning block of 35 for bucket 112 bucket 133: 40% bucket 135: 30% bucket 126: 100% Sorting block of length 18 for bucket 124 (Using difference cover) bucket 127: 90% bucket 134: 40% Sorting block time: 00:00:00 bucket 130: 70% Entering block accumulator loop for bucket 138: bucket 131: 60% bucket 132: 50% bucket 129: 80% bucket 128: 90% Sorting block of length 34 for bucket 125 (Using difference cover) bucket 136: 10% bucket 133: 50% bucket 135: 40% Sorting block of length 9 for bucket 126 (Using difference cover) bucket 127: 100% Returning block of 29 for bucket 114 bucket 134: 50% bucket 130: 80% bucket 131: 70% bucket 132: 60% bucket 129: 90% bucket 128: 100% bucket 137: 10% bucket 136: 20% bucket 133: 60% bucket 135: 50% Sorting block of length 33 for bucket 127 (Using difference cover) bucket 134: 60% bucket 130: 90% bucket 138: 10% bucket 131: 80% bucket 132: 70% bucket 129: 100% Sorting block of length 33 for bucket 128 (Using difference cover) bucket 137: 20% bucket 136: 30% bucket 133: 70% Getting block 139 of 203 bucket 135: 60% bucket 134: 70% bucket 130: 100% bucket 138: 20% bucket 131: 90% bucket 132: 80% Sorting block time: 00:00:00 Sorting block of length 20 for bucket 129 (Using difference cover) Getting block 140 of 203 bucket 137: 30% bucket 136: 40% bucket 133: 80% Reserving size (36) for bucket 139 bucket 135: 70% bucket 134: 80% Sorting block of length 18 for bucket 130 (Using difference cover) bucket 138: 30% Returning block of 24 for bucket 115 bucket 131: 100% bucket 132: 90% Reserving size (36) for bucket 140 bucket 137: 40% bucket 136: 50% bucket 133: 90% Calculating Z arrays for bucket 139 Getting block 141 of 203 bucket 135: 80% bucket 134: 90% bucket 138: 40% Sorting block of length 27 for bucket 131 bucket 132: 100% (Using difference cover) Calculating Z arrays for bucket 140 bucket 137: 50% bucket 136: 60% bucket 133: 100% Reserving size (36) for bucket 141 Entering block accumulator loop for bucket 139: bucket 135: 90% bucket 134: 100% bucket 138: 50% Sorting block of length 30 for bucket 132 (Using difference cover) bucket 137: 60% Sorting block of length 34 for bucket 133 (Using difference cover) bucket 136: 70% Entering block accumulator loop for bucket 140: Calculating Z arrays for bucket 141 bucket 135: 100% Sorting block of length 33 for bucket 134 (Using difference cover) bucket 138: 60% bucket 137: 70% bucket 136: 80% bucket 139: 10% Sorting block of length 18 for bucket 135 (Using difference cover) Entering block accumulator loop for bucket 141: bucket 138: 70% bucket 137: 80% bucket 136: 90% bucket 140: 10% bucket 139: 20% Getting block 142 of 203 bucket 138: 80% bucket 137: 90% bucket 136: 100% bucket 140: 20% bucket 141: 10% bucket 139: 30% Reserving size (36) for bucket 142 bucket 138: 90% bucket 137: 100% Sorting block of length 30 for bucket 136 (Using difference cover) bucket 140: 30% Sorting block time: 00:00:00 bucket 141: 20% bucket 139: 40% Calculating Z arrays for bucket 142 bucket 138: 100% Sorting block of length 33 for bucket 137 (Using difference cover) Returning block of 30 for bucket 117 bucket 140: 40% bucket 141: 30% bucket 139: 50% Sorting block of length 24 for bucket 138 (Using difference cover) Entering block accumulator loop for bucket 142: bucket 140: 50% bucket 141: 40% bucket 139: 60% bucket 140: 60% bucket 141: 50% bucket 139: 70% bucket 142: 10% bucket 140: 70% bucket 141: 60% bucket 139: 80% bucket 142: 20% bucket 140: 80% bucket 141: 70% bucket 139: 90% bucket 142: 30% bucket 140: 90% bucket 141: 80% bucket 139: 100% bucket 142: 40% bucket 140: 100% bucket 141: 90% Sorting block of length 17 for bucket 139 (Using difference cover) Sorting block of length 19 for bucket 140 (Using difference cover) bucket 142: 50% bucket 141: 100% bucket 142: 60% Sorting block of length 25 for bucket 141 Sorting block time: 00:00:00 (Using difference cover) Sorting block time: 00:00:00 bucket 142: 70% Returning block of 13 for bucket 118 Returning block of 25 for bucket 116 bucket 142: 80% Getting block 143 of 203 bucket 142: 90% Sorting block time: 00:00:00 Reserving size (36) for bucket 143 Returning block of 32 for bucket 119 bucket 142: 100% Calculating Z arrays for bucket 143 Sorting block of length 27 for bucket 142 (Using difference cover) Entering block accumulator loop for bucket 143: bucket 143: 10% bucket 143: 20% bucket 143: 30% Getting block 144 of 203 bucket 143: 40% Reserving size (36) for bucket 144 bucket 143: 50% Calculating Z arrays for bucket 144 bucket 143: 60% Getting block 145 of 203 bucket 143: 70% Entering block accumulator loop for bucket 144: Reserving size (36) for bucket 145 bucket 143: 80% Calculating Z arrays for bucket 145 bucket 143: 90% bucket 144: 10% bucket 143: 100% Entering block accumulator loop for bucket 145: bucket 144: 20% Sorting block of length 23 for bucket 143 (Using difference cover) bucket 144: 30% Getting block 146 of 203 bucket 145: 10% bucket 144: 40% Reserving size (36) for bucket 146 bucket 145: 20% bucket 144: 50% Sorting block time: 00:00:00 Calculating Z arrays for bucket 146 bucket 145: 30% Returning block of 28 for bucket 120 bucket 144: 60% bucket 145: 40% Entering block accumulator loop for bucket 146: bucket 144: 70% bucket 145: 50% bucket 144: 80% bucket 145: 60% bucket 146: 10% bucket 144: 90% bucket 145: 70% bucket 146: 20% bucket 144: 100% bucket 145: 80% Sorting block of length 32 for bucket 144 (Using difference cover) bucket 146: 30% bucket 145: 90% bucket 146: 40% bucket 145: 100% bucket 146: 50% Sorting block of length 28 for bucket 145 (Using difference cover) bucket 146: 60% Getting block 147 of 203 bucket 146: 70% Sorting block time: 00:00:00 Reserving size (36) for bucket 147 Returning block of 29 for bucket 121 bucket 146: 80% Calculating Z arrays for bucket 147 bucket 146: 90% bucket 146: 100% Entering block accumulator loop for bucket 147: Sorting block of length 34 for bucket 146 (Using difference cover) bucket 147: 10% bucket 147: 20% bucket 147: 30% bucket 147: 40% bucket 147: 50% bucket 147: 60% bucket 147: 70% bucket 147: 80% bucket 147: 90% bucket 147: 100% Sorting block of length 24 for bucket 147 (Using difference cover) Getting block 148 of 203 Reserving size (36) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 148: 10% bucket 148: 20% bucket 148: 30% bucket 148: 40% bucket 148: 50% bucket 148: 60% bucket 148: 70% bucket 148: 80% bucket 148: 90% bucket 148: 100% Sorting block of length 33 for bucket 148 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 34 for bucket 123 Returning block of 30 for bucket 122 Sorting block time: 00:00:00 Returning block of 10 for bucket 126 Sorting block time: 00:00:00 Returning block of 34 for bucket 128 Getting block 149 of 203 Reserving size (36) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: bucket 149: 10% bucket 149: 20% bucket 149: 30% bucket 149: 40% Getting block 150 of 203 bucket 149: 50% Reserving size (36) for bucket 150 bucket 149: 60% Calculating Z arrays for bucket 150 bucket 149: 70% bucket 149: 80% Entering block accumulator loop for bucket 150: bucket 149: 90% bucket 149: 100% bucket 150: 10% Sorting block of length 34 for bucket 149 (Using difference cover) bucket 150: 20% bucket 150: 30% bucket 150: 40% bucket 150: 50% bucket 150: 60% bucket 150: 70% bucket 150: 80% bucket 150: 90% Getting block 151 of 203 bucket 150: 100% Reserving size (36) for bucket 151 Sorting block of length 35 for bucket 150 (Using difference cover) Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 151: 10% Getting block 152 of 203 bucket 151: 20% Reserving size (36) for bucket 152 bucket 151: 30% Calculating Z arrays for bucket 152 bucket 151: 40% bucket 151: 50% Entering block accumulator loop for bucket 152: bucket 151: 60% bucket 151: 70% bucket 152: 10% bucket 151: 80% bucket 152: 20% bucket 151: 90% bucket 152: 30% bucket 151: 100% bucket 152: 40% Sorting block of length 26 for bucket 151 (Using difference cover) bucket 152: 50% bucket 152: 60% bucket 152: 70% bucket 152: 80% bucket 152: 90% bucket 152: 100% Sorting block of length 34 for bucket 152 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 19 for bucket 124 Returning block of 34 for bucket 127 Sorting block time: 00:00:00 Returning block of 35 for bucket 125 Getting block 153 of 203 Reserving size (36) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 153: 10% bucket 153: 20% bucket 153: 30% Getting block 154 of 203 bucket 153: 40% Reserving size (36) for bucket 154 Sorting block time: 00:00:00 bucket 153: 50% Calculating Z arrays for bucket 154 Returning block of 28 for bucket 131 bucket 153: 60% Entering block accumulator loop for bucket 154: bucket 153: 70% Getting block 155 of 203 bucket 154: 10% bucket 153: 80% Reserving size (36) for bucket 155 bucket 154: 20% bucket 153: 90% Calculating Z arrays for bucket 155 bucket 154: 30% bucket 153: 100% bucket 154: 40% Sorting block of length 34 for bucket 153 (Using difference cover) Entering block accumulator loop for bucket 155: bucket 154: 50% bucket 154: 60% bucket 155: 10% bucket 154: 70% bucket 155: 20% Getting block 156 of 203 bucket 154: 80% bucket 155: 30% Reserving size (36) for bucket 156 bucket 154: 90% bucket 155: 40% Calculating Z arrays for bucket 156 bucket 154: 100% bucket 155: 50% Sorting block of length 29 for bucket 154 (Using difference cover) Entering block accumulator loop for bucket 156: bucket 155: 60% bucket 156: 10% bucket 155: 70% bucket 156: 20% bucket 155: 80% bucket 156: 30% bucket 155: 90% bucket 156: 40% bucket 155: 100% bucket 156: 50% Sorting block of length 14 for bucket 155 (Using difference cover) bucket 156: 60% bucket 156: 70% Sorting block time: 00:00:00 Returning block of 31 for bucket 132 bucket 156: 80% bucket 156: 90% bucket 156: 100% Sorting block of length 24 for bucket 156 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25 for bucket 138 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 31 for bucket 136 Sorting block time: 00:00:00 Returning block of 34 for bucket 134 Sorting block time: 00:00:00 Returning block of 35 for bucket 133 Returning block of 26 for bucket 141 Sorting block time: 00:00:00 Returning block of 21 for bucket 129 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 18 for bucket 139 Sorting block time: 00:00:00 Returning block of 19 for bucket 135 Returning block of 19 for bucket 130 Getting block 157 of 203 Reserving size (36) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 157: 10% bucket 157: 20% bucket 157: 30% Getting block 158 of 203 bucket 157: 40% Reserving size (36) for bucket 158 bucket 157: 50% Calculating Z arrays for bucket 158 bucket 157: 60% bucket 157: 70% Entering block accumulator loop for bucket 158: bucket 157: 80% bucket 157: 90% bucket 158: 10% bucket 157: 100% bucket 158: 20% Sorting block of length 15 for bucket 157 (Using difference cover) bucket 158: 30% bucket 158: 40% bucket 158: 50% bucket 158: 60% bucket 158: 70% bucket 158: 80% bucket 158: 90% Sorting block time: 00:00:00 Returning block of 28 for bucket 142 bucket 158: 100% Sorting block of length 30 for bucket 158 (Using difference cover) Sorting block time: 00:00:00 Getting block 159 of 203 Returning block of 34 for bucket 137 Reserving size (36) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 159: 10% Sorting block time: 00:00:00 Returning block of 24 for bucket 143 Sorting block time: 00:00:00 bucket 159: 20% Returning block of 20 for bucket 140 Getting block 160 of 203 bucket 159: 30% Reserving size (36) for bucket 160 Sorting block time: 00:00:00 bucket 159: 40% Sorting block time: 00:00:00 Calculating Z arrays for bucket 160 Returning block of 35 for bucket 146 Returning block of 33 for bucket 144 bucket 159: 50% Entering block accumulator loop for bucket 160: Getting block 161 of 203 bucket 159: 60% Reserving size (36) for bucket 161 bucket 160: 10% bucket 159: 70% Calculating Z arrays for bucket 161 bucket 160: 20% bucket 159: 80% Getting block 162 of 203 bucket 160: 30% Entering block accumulator loop for bucket 161: bucket 159: 90% Reserving size (36) for bucket 162 bucket 160: 40% bucket 159: 100% Calculating Z arrays for bucket 162 bucket 160: 50% Sorting block of length 18 for bucket 159 (Using difference cover) Sorting block time: 00:00:00 bucket 161: 10% bucket 160: 60% Entering block accumulator loop for bucket 162: Returning block of 34 for bucket 148 bucket 161: 20% bucket 160: 70% Sorting block time: 00:00:00 Getting block 163 of 203 bucket 161: 30% Returning block of 29 for bucket 145 bucket 160: 80% bucket 162: 10% Reserving size (36) for bucket 163 Getting block 164 of 203 bucket 161: 40% bucket 160: 90% bucket 162: 20% Calculating Z arrays for bucket 163 Reserving size (36) for bucket 164 bucket 161: 50% bucket 160: 100% bucket 162: 30% Calculating Z arrays for bucket 164 Getting block 165 of 203 Entering block accumulator loop for bucket 163: bucket 161: 60% Sorting block of length 17 for bucket 160 (Using difference cover) bucket 162: 40% Reserving size (36) for bucket 165 Entering block accumulator loop for bucket 164: bucket 161: 70% bucket 162: 50% Calculating Z arrays for bucket 165 Getting block 166 of 203 bucket 163: 10% bucket 161: 80% bucket 162: 60% bucket 164: 10% Reserving size (36) for bucket 166 Entering block accumulator loop for bucket 165: bucket 163: 20% bucket 161: 90% bucket 162: 70% bucket 164: 20% Calculating Z arrays for bucket 166 bucket 163: 30% bucket 161: 100% bucket 162: 80% bucket 164: 30% bucket 165: 10% Sorting block time: 00:00:00 bucket 163: 40% Sorting block of length 20 for bucket 161 (Using difference cover) Entering block accumulator loop for bucket 166: bucket 162: 90% Returning block of 25 for bucket 147 bucket 164: 40% bucket 165: 20% bucket 163: 50% bucket 162: 100% bucket 164: 50% bucket 165: 30% bucket 163: 60% Sorting block of length 25 for bucket 162 (Using difference cover) bucket 166: 10% bucket 164: 60% bucket 165: 40% bucket 163: 70% bucket 166: 20% bucket 164: 70% bucket 165: 50% Getting block 167 of 203 bucket 163: 80% bucket 166: 30% bucket 164: 80% bucket 165: 60% Reserving size (36) for bucket 167 bucket 163: 90% bucket 166: 40% Getting block 168 of 203 bucket 164: 90% bucket 165: 70% Calculating Z arrays for bucket 167 bucket 163: 100% bucket 166: 50% Reserving size (36) for bucket 168 bucket 164: 100% bucket 165: 80% Sorting block of length 11 for bucket 163 (Using difference cover) Getting block 169 of 203 Entering block accumulator loop for bucket 167: Sorting block time: 00:00:00 bucket 166: 60% Calculating Z arrays for bucket 168 Sorting block of length 25 for bucket 164 (Using difference cover) Sorting block time: 00:00:00 Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 165: 90% Reserving size (36) for bucket 169 Returning block of 27 for bucket 151 bucket 166: 70% Getting block 170 of 203 Entering block accumulator loop for bucket 168: Returning block of 35 for bucket 152 Returning block of 36 for bucket 150 Returning block of 35 for bucket 149 bucket 165: 100% Calculating Z arrays for bucket 169 bucket 167: 10% bucket 166: 80% Reserving size (36) for bucket 170 Sorting block of length 30 for bucket 165 (Using difference cover) Getting block 171 of 203 bucket 167: 20% Entering block accumulator loop for bucket 169: bucket 166: 90% Calculating Z arrays for bucket 170 Getting block 172 of 203 bucket 168: 10% Reserving size (36) for bucket 171 bucket 167: 30% bucket 166: 100% Reserving size (36) for bucket 172 Entering block accumulator loop for bucket 170: Getting block 173 of 203 bucket 168: 20% Calculating Z arrays for bucket 171 bucket 167: 40% Sorting block of length 13 for bucket 166 (Using difference cover) bucket 169: 10% Calculating Z arrays for bucket 172 Getting block 174 of 203 Reserving size (36) for bucket 173 bucket 168: 30% Entering block accumulator loop for bucket 171: Sorting block time: 00:00:00 bucket 167: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 169: 20% bucket 170: 10% Sorting block time: 00:00:00 Reserving size (36) for bucket 174 Entering block accumulator loop for bucket 172: Calculating Z arrays for bucket 173 Getting block 175 of 203 bucket 168: 40% Returning block of 25 for bucket 156 Returning block of 15 for bucket 155 Returning block of 35 for bucket 153 bucket 167: 60% Returning block of 30 for bucket 154 bucket 169: 30% bucket 170: 20% Calculating Z arrays for bucket 174 Reserving size (36) for bucket 175 Entering block accumulator loop for bucket 173: bucket 168: 50% bucket 171: 10% bucket 167: 70% bucket 169: 40% bucket 170: 30% Getting block 176 of 203 bucket 172: 10% Entering block accumulator loop for bucket 174: Calculating Z arrays for bucket 175 bucket 168: 60% Getting block 177 of 203 bucket 171: 20% bucket 167: 80% bucket 169: 50% bucket 170: 40% Reserving size (36) for bucket 176 bucket 172: 20% Getting block 178 of 203 bucket 173: 10% Entering block accumulator loop for bucket 175: bucket 168: 70% Reserving size (36) for bucket 177 bucket 171: 30% bucket 167: 90% bucket 169: 60% Getting block 179 of 203 bucket 170: 50% Calculating Z arrays for bucket 176 bucket 172: 30% bucket 174: 10% Reserving size (36) for bucket 178 bucket 173: 20% bucket 168: 80% Calculating Z arrays for bucket 177 bucket 171: 40% bucket 167: 100% bucket 169: 70% Reserving size (36) for bucket 179 bucket 170: 60% bucket 172: 40% Entering block accumulator loop for bucket 176: bucket 174: 20% Calculating Z arrays for bucket 178 Getting block 180 of 203 bucket 173: 30% bucket 175: 10% bucket 168: 90% bucket 171: 50% Sorting block of length 23 for bucket 167 (Using difference cover) Entering block accumulator loop for bucket 177: bucket 169: 80% Calculating Z arrays for bucket 179 bucket 170: 70% bucket 172: 50% bucket 174: 30% Reserving size (36) for bucket 180 Entering block accumulator loop for bucket 178: bucket 173: 40% bucket 175: 20% bucket 168: 100% bucket 171: 60% Getting block 181 of 203 bucket 169: 90% bucket 170: 80% Entering block accumulator loop for bucket 179: bucket 172: 60% bucket 176: 10% bucket 174: 40% Calculating Z arrays for bucket 180 bucket 173: 50% bucket 175: 30% Sorting block of length 17 for bucket 168 (Using difference cover) bucket 171: 70% bucket 177: 10% Reserving size (36) for bucket 181 Getting block 182 of 203 bucket 169: 100% bucket 170: 90% bucket 172: 70% bucket 176: 20% bucket 174: 50% bucket 178: 10% Entering block accumulator loop for bucket 180: bucket 173: 60% bucket 175: 40% bucket 171: 80% bucket 177: 20% Calculating Z arrays for bucket 181 Reserving size (36) for bucket 182 Getting block 183 of 203 Sorting block of length 33 for bucket 169 (Using difference cover) bucket 179: 10% bucket 170: 100% bucket 172: 80% bucket 176: 30% bucket 174: 60% bucket 178: 20% bucket 173: 70% bucket 175: 50% Sorting block time: 00:00:00 Sorting block time: 00:00:00 bucket 171: 90% Sorting block time: 00:00:00 bucket 177: 30% Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 181: Reserving size (36) for bucket 183 bucket 179: 20% Sorting block of length 30 for bucket 170 (Using difference cover) bucket 172: 90% bucket 176: 40% bucket 174: 70% bucket 178: 30% bucket 180: 10% bucket 173: 80% Returning block of 31 for bucket 158 Returning block of 16 for bucket 157 bucket 175: 60% Returning block of 19 for bucket 159 bucket 171: 100% bucket 177: 40% Entering block accumulator loop for bucket 182: Calculating Z arrays for bucket 183 bucket 179: 30% bucket 172: 100% bucket 176: 50% bucket 174: 80% bucket 178: 40% bucket 180: 20% bucket 173: 90% bucket 175: 70% Sorting block of length 34 for bucket 171 (Using difference cover) bucket 177: 50% bucket 181: 10% Entering block accumulator loop for bucket 183: bucket 179: 40% Sorting block of length 17 for bucket 172 (Using difference cover) bucket 176: 60% bucket 174: 90% bucket 178: 50% bucket 180: 30% bucket 173: 100% Sorting block time: 00:00:00 bucket 175: 80% bucket 177: 60% Sorting block time: 00:00:00 bucket 181: 20% bucket 182: 10% bucket 179: 50% Sorting block time: 00:00:00 bucket 176: 70% bucket 174: 100% bucket 178: 60% bucket 180: 40% Sorting block of length 35 for bucket 173 (Using difference cover) Returning block of 26 for bucket 164 bucket 175: 90% Getting block 184 of 203 Returning block of 18 for bucket 160 bucket 177: 70% bucket 181: 30% Returning block of 26 for bucket 162 bucket 182: 20% bucket 183: 10% bucket 179: 60% bucket 176: 80% Sorting block of length 10 for bucket 174 (Using difference cover) bucket 178: 70% bucket 180: 50% bucket 175: 100% Reserving size (36) for bucket 184 bucket 177: 80% bucket 181: 40% bucket 182: 30% Getting block 185 of 203 bucket 183: 20% bucket 179: 70% bucket 176: 90% bucket 178: 80% bucket 180: 60% Sorting block of length 34 for bucket 175 (Using difference cover) Calculating Z arrays for bucket 184 Getting block 186 of 203 bucket 177: 90% bucket 181: 50% bucket 182: 40% Reserving size (36) for bucket 185 bucket 183: 30% bucket 179: 80% bucket 176: 100% bucket 178: 90% bucket 180: 70% Entering block accumulator loop for bucket 184: Reserving size (36) for bucket 186 Getting block 187 of 203 bucket 177: 100% bucket 181: 60% bucket 182: 50% Calculating Z arrays for bucket 185 bucket 183: 40% bucket 179: 90% Sorting block of length 1 for bucket 176 (Using difference cover) Sorting block time: 00:00:00 bucket 178: 100% bucket 180: 80% Calculating Z arrays for bucket 186 Reserving size (36) for bucket 187 Sorting block of length 35 for bucket 177 (Using difference cover) Getting block 188 of 203 bucket 181: 70% Sorting block time: 00:00:00 bucket 182: 60% bucket 183: 50% Sorting block time: 00:00:00 Entering block accumulator loop for bucket 185: bucket 179: 100% Sorting block time: 00:00:00 Returning block of 2 for bucket 176 Sorting block of length 28 for bucket 178 (Using difference cover) bucket 180: 90% bucket 184: 10% Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 186: Getting block 189 of 203 Reserving size (36) for bucket 188 Returning block of 12 for bucket 163 bucket 181: 80% bucket 182: 70% Returning block of 31 for bucket 165 bucket 183: 60% Returning block of 21 for bucket 161 Sorting block of length 30 for bucket 179 (Using difference cover) bucket 180: 100% bucket 184: 20% Entering block accumulator loop for bucket 187: Reserving size (36) for bucket 189 Calculating Z arrays for bucket 188 bucket 181: 90% bucket 182: 80% bucket 183: 70% bucket 185: 10% Sorting block of length 23 for bucket 180 (Using difference cover) bucket 184: 30% bucket 186: 10% Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 188: bucket 181: 100% bucket 182: 90% bucket 183: 80% bucket 185: 20% Getting block 190 of 203 bucket 184: 40% bucket 186: 20% bucket 187: 10% Entering block accumulator loop for bucket 189: Sorting block of length 35 for bucket 181 (Using difference cover) bucket 182: 100% bucket 183: 90% bucket 185: 30% Sorting block time: 00:00:00 Reserving size (36) for bucket 190 Sorting block time: 00:00:00 bucket 184: 50% Getting block 191 of 203 bucket 186: 30% bucket 187: 20% bucket 188: 10% Sorting block of length 35 for bucket 182 (Using difference cover) bucket 183: 100% Returning block of 14 for bucket 166 bucket 185: 40% Calculating Z arrays for bucket 190 Returning block of 24 for bucket 167 bucket 184: 60% Reserving size (36) for bucket 191 bucket 186: 40% bucket 187: 30% Getting block 192 of 203 bucket 188: 20% bucket 189: 10% Sorting block of length 24 for bucket 183 (Using difference cover) bucket 185: 50% Getting block 193 of 203 Entering block accumulator loop for bucket 190: bucket 184: 70% Calculating Z arrays for bucket 191 bucket 186: 50% bucket 187: 40% Reserving size (36) for bucket 192 bucket 188: 30% bucket 189: 20% bucket 185: 60% Reserving size (36) for bucket 193 bucket 184: 80% bucket 186: 60% Entering block accumulator loop for bucket 191: bucket 187: 50% Calculating Z arrays for bucket 192 bucket 188: 40% bucket 189: 30% bucket 185: 70% Calculating Z arrays for bucket 193 bucket 190: 10% Getting block 194 of 203 bucket 184: 90% bucket 186: 70% bucket 187: 60% bucket 188: 50% Entering block accumulator loop for bucket 192: bucket 189: 40% bucket 185: 80% bucket 190: 20% Entering block accumulator loop for bucket 193: Reserving size (36) for bucket 194 bucket 184: 100% bucket 186: 80% bucket 191: 10% bucket 187: 70% Sorting block time: 00:00:00 bucket 188: 60% bucket 189: 50% bucket 185: 90% bucket 190: 30% Getting block 195 of 203 Calculating Z arrays for bucket 194 Sorting block of length 26 for bucket 184 (Using difference cover) bucket 186: 90% bucket 191: 20% Returning block of 18 for bucket 168 bucket 187: 80% bucket 188: 70% bucket 192: 10% bucket 189: 60% bucket 185: 100% bucket 190: 40% bucket 193: 10% Reserving size (36) for bucket 195 Entering block accumulator loop for bucket 194: bucket 186: 100% bucket 191: 30% bucket 187: 90% bucket 188: 80% bucket 192: 20% bucket 189: 70% Sorting block of length 28 for bucket 185 (Using difference cover) bucket 190: 50% bucket 193: 20% Calculating Z arrays for bucket 195 Sorting block of length 15 for bucket 186 (Using difference cover) bucket 191: 40% bucket 187: 100% bucket 188: 90% bucket 192: 30% bucket 189: 80% bucket 190: 60% bucket 193: 30% bucket 194: 10% Entering block accumulator loop for bucket 195: bucket 191: 50% Sorting block of length 31 for bucket 187 (Using difference cover) bucket 188: 100% bucket 192: 40% bucket 189: 90% Getting block 196 of 203 bucket 190: 70% bucket 193: 40% bucket 194: 20% bucket 191: 60% Sorting block of length 19 for bucket 188 (Using difference cover) Sorting block time: 00:00:00 bucket 192: 50% Sorting block time: 00:00:00 bucket 189: 100% Reserving size (36) for bucket 196 bucket 190: 80% bucket 193: 50% bucket 194: 30% bucket 195: 10% bucket 191: 70% Returning block of 35 for bucket 171 Returning block of 34 for bucket 169 bucket 192: 60% Sorting block of length 27 for bucket 189 (Using difference cover) Calculating Z arrays for bucket 196 bucket 190: 90% Sorting block time: 00:00:00 bucket 193: 60% bucket 194: 40% bucket 195: 20% bucket 191: 80% bucket 192: 70% Returning block of 31 for bucket 170 Entering block accumulator loop for bucket 196: bucket 190: 100% bucket 193: 70% bucket 194: 50% bucket 195: 30% bucket 191: 90% bucket 192: 80% Sorting block of length 10 for bucket 190 (Using difference cover) bucket 193: 80% bucket 194: 60% bucket 195: 40% bucket 191: 100% bucket 196: 10% bucket 192: 90% bucket 193: 90% bucket 194: 70% bucket 195: 50% Sorting block of length 34 for bucket 191 (Using difference cover) Sorting block time: 00:00:00 bucket 196: 20% bucket 192: 100% bucket 193: 100% bucket 194: 80% bucket 195: 60% Returning block of 18 for bucket 172 bucket 196: 30% Sorting block of length 35 for bucket 192 (Using difference cover) Sorting block of length 32 for bucket 193 (Using difference cover) Getting block 197 of 203 bucket 194: 90% bucket 195: 70% bucket 196: 40% Reserving size (36) for bucket 197 bucket 194: 100% Getting block 198 of 203 bucket 195: 80% bucket 196: 50% Calculating Z arrays for bucket 197 Sorting block of length 22 for bucket 194 (Using difference cover) Reserving size (36) for bucket 198 Getting block 199 of 203 bucket 195: 90% bucket 196: 60% Entering block accumulator loop for bucket 197: Calculating Z arrays for bucket 198 Reserving size (36) for bucket 199 bucket 195: 100% bucket 196: 70% Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 198: Sorting block of length 17 for bucket 195 Sorting block time: 00:00:00 (Using difference cover) Sorting block time: 00:00:00 Getting block 200 of 203 bucket 196: 80% bucket 197: 10% Entering block accumulator loop for bucket 199: Returning block of 35 for bucket 175 Returning block of 36 for bucket 177 Reserving size (36) for bucket 200 bucket 196: 90% bucket 197: 20% bucket 198: 10% Calculating Z arrays for bucket 200 bucket 196: 100% bucket 197: 30% bucket 198: 20% bucket 199: 10% Sorting block of length 29 for bucket 196 (Using difference cover) Entering block accumulator loop for bucket 200: bucket 197: 40% bucket 198: 30% Sorting block time: 00:00:00 bucket 199: 20% bucket 197: 50% Returning block of 11 for bucket 174 bucket 198: 40% Sorting block time: 00:00:00 bucket 200: 10% bucket 199: 30% bucket 197: 60% Returning block of 36 for bucket 173 Sorting block time: 00:00:00 bucket 198: 50% bucket 200: 20% bucket 199: 40% bucket 197: 70% Returning block of 29 for bucket 178 bucket 198: 60% bucket 200: 30% bucket 199: 50% bucket 197: 80% bucket 198: 70% bucket 200: 40% bucket 199: 60% bucket 197: 90% bucket 198: 80% bucket 200: 50% bucket 199: 70% bucket 197: 100% bucket 198: 90% bucket 200: 60% bucket 199: 80% Sorting block of length 35 for bucket 197 (Using difference cover) Getting block 201 of 203 bucket 198: 100% bucket 200: 70% bucket 199: 90% Reserving size (36) for bucket 201 Sorting block of length 30 for bucket 198 (Using difference cover) bucket 200: 80% bucket 199: 100% Calculating Z arrays for bucket 201 bucket 200: 90% Sorting block of length 10 for bucket 199 (Using difference cover) Getting block 202 of 203 Entering block accumulator loop for bucket 201: bucket 200: 100% Reserving size (36) for bucket 202 Sorting block of length 29 for bucket 200 (Using difference cover) Calculating Z arrays for bucket 202 bucket 201: 10% Getting block 203 of 203 Entering block accumulator loop for bucket 202: bucket 201: 20% Reserving size (36) for bucket 203 bucket 201: 30% Calculating Z arrays for bucket 203 bucket 202: 10% bucket 201: 40% Entering block accumulator loop for bucket 203: bucket 202: 20% bucket 201: 50% bucket 202: 30% bucket 203: 10% bucket 201: 60% bucket 202: 40% bucket 203: 20% bucket 201: 70% bucket 202: 50% bucket 203: 30% bucket 201: 80% bucket 202: 60% bucket 203: 40% bucket 201: 90% bucket 202: 70% bucket 203: 50% bucket 201: 100% bucket 202: 80% bucket 203: 60% Sorting block of length 28 for bucket 201 (Using difference cover) bucket 202: 90% bucket 203: 70% bucket 202: 100% bucket 203: 80% Sorting block of length 22 for bucket 202 (Using difference cover) bucket 203: 90% bucket 203: 100% Sorting block of length 16 for bucket 203 (Using difference cover) Sorting block time: 00:00:00 Returning block of 24 for bucket 180 Sorting block time: 00:00:00 Returning block of 36 for bucket 181 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 36 for bucket 182 Sorting block time: 00:00:00 Returning block of 25 for bucket 183 Returning block of 31 for bucket 179 Sorting block time: 00:00:00 Returning block of 16 for bucket 186 Sorting block time: 00:00:00 Returning block of 27 for bucket 184 Sorting block time: 00:00:00 Returning block of 29 for bucket 185 Sorting block time: 00:00:00 Returning block of 32 for bucket 187 Sorting block time: 00:00:00 Returning block of 20 for bucket 188 Sorting block time: 00:00:00 Returning block of 35 for bucket 191 Sorting block time: 00:00:00 Returning block of 28 for bucket 189 Sorting block time: 00:00:00 Returning block of 11 for bucket 190 Sorting block time: 00:00:00 Returning block of 23 for bucket 194 Sorting block time: 00:00:00 Returning block of 18 for bucket 195 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 36 for bucket 197 Sorting block time: 00:00:00 Returning block of 30 for bucket 196 Sorting block time: 00:00:00 Returning block of 29 for bucket 201 Sorting block time: 00:00:00 Sorting block time: 00:00:00 Returning block of 11 for bucket 199 Returning block of 33 for bucket 193 Sorting block time: 00:00:00 Returning block of 36 for bucket 192 Sorting block time: 00:00:00 Returning block of 23 for bucket 202 Sorting block time: 00:00:00 Returning block of 31 for bucket 198 Returning block of 30 for bucket 200 Sorting block time: 00:00:00 Returning block of 17 for bucket 203 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2545 fchr[G]: 3702 fchr[T]: 3702 fchr[$]: 5386 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4196346 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 1352 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 5386 bwtLen: 5387 sz: 1347 bwtSz: 1347 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 337 offsSz: 1348 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 29 numLines: 29 ebwtTotLen: 1856 ebwtTotSz: 1856 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/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_10_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_10_s456_trimmed.fq to zr1394_10_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_10_s456_trimmed.fq to zr1394_10_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_10_s456_trimmed.fq (78221457 sequences in total) Input files are zr1394_10_s456_trimmed.fq_C_to_T.fastq and zr1394_10_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_10_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1108:2120_1:Y:0:TATCTT 4 * 0 0 * * 0 0 ATTAATGAGAATGATTTTTTTTTTA B//FF>> Writing bisulfite mapping results to zr1394_10_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_10_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far Processed 65000000 sequences so far Processed 66000000 sequences so far Processed 67000000 sequences so far Processed 68000000 sequences so far Processed 69000000 sequences so far Processed 70000000 sequences so far Processed 71000000 sequences so far Processed 72000000 sequences so far Processed 73000000 sequences so far Processed 74000000 sequences so far Processed 75000000 sequences so far Processed 76000000 sequences so far Processed 77000000 sequences so far Processed 78000000 sequences so far 78221457 reads; of these: 78221457 (100.00%) were unpaired; of these: 78221422 (100.00%) aligned 0 times 35 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 78221457 reads; of these: 78221457 (100.00%) were unpaired; of these: 78221423 (100.00%) aligned 0 times 34 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 78221457 reads; of these: 78221457 (100.00%) were unpaired; of these: 78221436 (100.00%) aligned 0 times 21 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 78221457 reads; of these: 78221457 (100.00%) were unpaired; of these: 78221435 (100.00%) aligned 0 times 22 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 78221457 sequences in total Successfully deleted the temporary files zr1394_10_s456_trimmed.fq_C_to_T.fastq and zr1394_10_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 78221457 Number of alignments with a unique best hit from the different alignments: 100 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 78221357 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 16 ((converted) top strand) CT/GA: 15 ((converted) bottom strand) GA/CT: 34 (complementary to (converted) top strand) GA/GA: 35 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 722 Total methylated C's in CpG context: 40 Total methylated C's in CHG context: 25 Total methylated C's in CHH context: 190 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 42 Total unmethylated C's in CHG context: 32 Total unmethylated C's in CHH context: 393 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 48.8% C methylated in CHG context: 43.9% C methylated in CHH context: 32.6% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 30m 19s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_11_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_11_s456_trimmed.fq to zr1394_11_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_11_s456_trimmed.fq to zr1394_11_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_11_s456_trimmed.fq (54458572 sequences in total) Input files are zr1394_11_s456_trimmed.fq_C_to_T.fastq and zr1394_11_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_11_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1243:2134_1:N:0:GGCTAC 4 * 0 0 * * 0 0 TATTGATATTATAATTATTTTTTTTTATAT >> Writing bisulfite mapping results to zr1394_11_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_11_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far 54458572 reads; of these: 54458572 (100.00%) were unpaired; of these: 54458544 (100.00%) aligned 0 times 28 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate54458572 reads; of these: 54458572 (100.00%) were unpaired; of these: 54458561 (100.00%) aligned 0 times 11 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 54458572 reads; of these: 54458572 (100.00%) were unpaired; of these: 54458557 (100.00%) aligned 0 times 15 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 54458572 reads; of these: 54458572 (100.00%) were unpaired; of these: 54458558 (100.00%) aligned 0 times 14 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 54458572 sequences in total Successfully deleted the temporary files zr1394_11_s456_trimmed.fq_C_to_T.fastq and zr1394_11_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 54458572 Number of alignments with a unique best hit from the different alignments: 68 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 54458504 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 14 ((converted) top strand) CT/GA: 15 ((converted) bottom strand) GA/CT: 11 (complementary to (converted) top strand) GA/GA: 28 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 553 Total methylated C's in CpG context: 14 Total methylated C's in CHG context: 8 Total methylated C's in CHH context: 97 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 20 Total unmethylated C's in CHG context: 25 Total unmethylated C's in CHH context: 389 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 41.2% C methylated in CHG context: 24.2% C methylated in CHH context: 20.0% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 21m 29s ==================== 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/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_12_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_12_s456_trimmed.fq to zr1394_12_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_12_s456_trimmed.fq to zr1394_12_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_12_s456_trimmed.fq (59459431 sequences in total) Input files are zr1394_12_s456_trimmed.fq_C_to_T.fastq and zr1394_12_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_12_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1130:2172_1:N:0:CTTGTA 4 * 0 0 * * 0 0 TTTTTTGGTTGGATGTAATAGATTATGATTG BFB/FF//FF////7/>> Writing bisulfite mapping results to zr1394_12_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_12_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far 59459431 reads; of these: 59459431 (100.00%) were unpaired; of these: 59459416 (100.00%) aligned 0 times 15 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.0059459431% reads; of these: overall alignment rate 59459431 (100.00%) were unpaired; of these: 59459407 (100.00%) aligned 0 times 24 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 59459431 reads; of these: 5945943159459431 reads; of these: ( 59459431 (100.00%100.00) were unpaired; of these:% ) were unpaired; of these: 59459419 (59459425100.00 (%100.00) aligned 0 times% ) aligned 0 times 12 (60.00 (%0.00) aligned exactly 1 time% ) aligned exactly 1 time 0 (00.00 (%0.00) aligned >1 times% ) aligned >1 times0.00 %0.00 overall alignment rate% overall alignment rate Processed 59459431 sequences in total Successfully deleted the temporary files zr1394_12_s456_trimmed.fq_C_to_T.fastq and zr1394_12_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 59459431 Number of alignments with a unique best hit from the different alignments: 56 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 59459375 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 6 ((converted) top strand) CT/GA: 14 ((converted) bottom strand) GA/CT: 12 (complementary to (converted) top strand) GA/GA: 24 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 406 Total methylated C's in CpG context: 16 Total methylated C's in CHG context: 6 Total methylated C's in CHH context: 99 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 12 Total unmethylated C's in CHG context: 18 Total unmethylated C's in CHH context: 255 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 57.1% C methylated in CHG context: 25.0% C methylated in CHH context: 28.0% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 23m 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/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_13_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_13_s456_trimmed.fq to zr1394_13_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_13_s456_trimmed.fq to zr1394_13_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_13_s456_trimmed.fq (64352550 sequences in total) Input files are zr1394_13_s456_trimmed.fq_C_to_T.fastq and zr1394_13_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_13_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1235:2169_1:N:0:AGTCAA 4 * 0 0 * * 0 0 GGTAAGTTTTGTTTTATTAATATGTTGTTGT FBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from zr1394_13_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1235:2169_1:N:0:AGTCAA 4 * 0 0 * * 0 0 GGTAAGTTTTGTTTTATTAATATGTTGTTGT FBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from zr1394_13_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1235:2169_1:N:0:AGTCAA 4 * 0 0 * * 0 0 AATAAATTTTATTTTATTAATATATCATCAC FBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from zr1394_13_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1235:2169_1:N:0:AGTCAA 4 * 0 0 * * 0 0 AATAAATTTTATTTTATTAATATATCATCAC FBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to zr1394_13_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_13_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far 64352550 reads; of these: 64352550 (100.00%) were unpaired; of these: 64352530 (100.00%) aligned 0 times 20 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 6435255064352550 reads; of these: reads; of these: 6435255064352550 ( (100.00100.00%%) were unpaired; of these:) were unpaired; of these: 6435254064352538 ( (100.00100.00%%) aligned 0 times) aligned 0 times 1012 ( (0.000.00%%) aligned exactly 1 time) aligned exactly 1 time 00 ( (0.000.00%%) aligned >1 times) aligned >1 times 0.000.00%% overall alignment rate overall alignment rate 64352550 reads; of these: 64352550 (100.00%) were unpaired; of these: 64352522 (100.00%) aligned 0 times 28 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 64352550 sequences in total Successfully deleted the temporary files zr1394_13_s456_trimmed.fq_C_to_T.fastq and zr1394_13_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 64352550 Number of alignments with a unique best hit from the different alignments: 66 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 64352484 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 9 ((converted) top strand) CT/GA: 9 ((converted) bottom strand) GA/CT: 20 (complementary to (converted) top strand) GA/GA: 28 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 513 Total methylated C's in CpG context: 17 Total methylated C's in CHG context: 8 Total methylated C's in CHH context: 126 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 22 Total unmethylated C's in CHG context: 23 Total unmethylated C's in CHH context: 317 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 43.6% C methylated in CHG context: 25.8% C methylated in CHH context: 28.4% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 25m 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/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_14_s456_trimmed.fq to zr1394_14_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_14_s456_trimmed.fq to zr1394_14_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_14_s456_trimmed.fq (87834637 sequences in total) Input files are zr1394_14_s456_trimmed.fq_C_to_T.fastq and zr1394_14_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_14_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1225:2220_1:N:0:AGTTCC 4 * 0 0 * * 0 0 TTATTTTTAAATTAAATTTATTTATTTTA FF>> Writing bisulfite mapping results to zr1394_14_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far Processed 65000000 sequences so far Processed 66000000 sequences so far Processed 67000000 sequences so far Processed 68000000 sequences so far Processed 69000000 sequences so far Processed 70000000 sequences so far Processed 71000000 sequences so far Processed 72000000 sequences so far Processed 73000000 sequences so far Processed 74000000 sequences so far Processed 75000000 sequences so far Processed 76000000 sequences so far Processed 77000000 sequences so far Processed 78000000 sequences so far Processed 79000000 sequences so far Processed 80000000 sequences so far Processed 81000000 sequences so far Processed 82000000 sequences so far Processed 83000000 sequences so far Processed 84000000 sequences so far Processed 85000000 sequences so far Processed 86000000 sequences so far Processed 87000000 sequences so far 87834637 reads; of these: 87834637 (100.00%) were unpaired; of these: 87834600 (100.00%) aligned 0 times 37 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 87834637 reads; of these: 87834637 (100.00%) were unpaired; of these: 87834619 (100.00%) aligned 0 times 18 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 87834637 reads; of these: 87834637 (100.00%) were unpaired; of these: 87834617 (100.00%) aligned 0 times 20 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 87834637 reads; of these: 87834637 (100.00%) were unpaired; of these: 87834609 (100.00%) aligned 0 times 28 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 87834637 sequences in total Successfully deleted the temporary files zr1394_14_s456_trimmed.fq_C_to_T.fastq and zr1394_14_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 87834637 Number of alignments with a unique best hit from the different alignments: 96 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 87834541 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 14 ((converted) top strand) CT/GA: 17 ((converted) bottom strand) GA/CT: 37 (complementary to (converted) top strand) GA/GA: 28 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 809 Total methylated C's in CpG context: 27 Total methylated C's in CHG context: 16 Total methylated C's in CHH context: 153 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 30 Total unmethylated C's in CHG context: 28 Total unmethylated C's in CHH context: 555 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 47.4% C methylated in CHG context: 36.4% C methylated in CHH context: 21.6% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 34m 5s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_15_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_15_s456_trimmed.fq to zr1394_15_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_15_s456_trimmed.fq to zr1394_15_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_15_s456_trimmed.fq (67984205 sequences in total) Input files are zr1394_15_s456_trimmed.fq_C_to_T.fastq and zr1394_15_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_15_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1117:2111_1:Y:0:ATGNCA 4 * 0 0 * * 0 0 TAATGGAGTGTAATTTTATTTTTAATTTTGT />> Writing bisulfite mapping results to zr1394_15_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_15_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far Processed 65000000 sequences so far Processed 66000000 sequences so far Processed 67000000 sequences so far 67984205 reads; of these: 67984205 (100.00%) were unpaired; of these: 67984179 (100.00%) aligned 0 times 26 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 67984205 reads; of these: 67984205 (67984205100.00 reads; of these:% ) were unpaired; of these: 67984205 (67984183 (100.00%) aligned 0 times 100.00 %22) were unpaired; of these: ( 0.00 %67984187) aligned exactly 1 time ( 100.00 %0) aligned 0 times ( 0.00 %18) aligned >1 times ( 0.000.00%%) aligned exactly 1 time overall alignment rate 0 (0.00%) aligned >1 times 0.00% overall alignment rate 67984205 reads; of these: 67984205 (100.00%) were unpaired; of these: 67984173 (100.00%) aligned 0 times 32 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 67984205 sequences in total Successfully deleted the temporary files zr1394_15_s456_trimmed.fq_C_to_T.fastq and zr1394_15_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 67984205 Number of alignments with a unique best hit from the different alignments: 92 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 67984113 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 13 ((converted) top strand) CT/GA: 21 ((converted) bottom strand) GA/CT: 26 (complementary to (converted) top strand) GA/GA: 32 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 734 Total methylated C's in CpG context: 18 Total methylated C's in CHG context: 9 Total methylated C's in CHH context: 167 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 25 Total unmethylated C's in CHG context: 30 Total unmethylated C's in CHH context: 485 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 41.9% C methylated in CHG context: 23.1% C methylated in CHH context: 25.6% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 26m 58s ==================== 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/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_16_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_16_s456_trimmed.fq to zr1394_16_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_16_s456_trimmed.fq to zr1394_16_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_16_s456_trimmed.fq (74531056 sequences in total) Input files are zr1394_16_s456_trimmed.fq_C_to_T.fastq and zr1394_16_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_16_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1095:2123_1:Y:0:NCGTCC 4 * 0 0 * * 0 0 TATATTAAAAATTAATTTTTAATATTTGTGT FFBBFFFFFFFF/FFFF/FFB/FFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from zr1394_16_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1095:2123_1:Y:0:NCGTCC 4 * 0 0 * * 0 0 TATATTAAAAATTAATTTTTAATATTTGTGT FFBBFFFFFFFF/FFFF/FFB/FFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from zr1394_16_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1095:2123_1:Y:0:NCGTCC 4 * 0 0 * * 0 0 TACATTAAAAATCAATTCCCAATACTCACAC FFBBFFFFFFFF/FFFF/FFB/FFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from zr1394_16_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1095:2123_1:Y:0:NCGTCC 4 * 0 0 * * 0 0 TACATTAAAAATCAATTCCCAATACTCACAC FFBBFFFFFFFF/FFFF/FFB/FFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to zr1394_16_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_16_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far Processed 65000000 sequences so far Processed 66000000 sequences so far Processed 67000000 sequences so far Processed 68000000 sequences so far Processed 69000000 sequences so far Processed 70000000 sequences so far Processed 71000000 sequences so far Processed 72000000 sequences so far Processed 73000000 sequences so far Processed 74000000 sequences so far 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 74531017 (100.00%) aligned 0 times 39 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 74531031 (100.00%) aligned 0 times 25 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 74531039 (100.00%) aligned 0 times 17 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 74531056 reads; of these: 74531056 (100.00%) were unpaired; of these: 74531026 (100.00%) aligned 0 times 30 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 74531056 sequences in total Successfully deleted the temporary files zr1394_16_s456_trimmed.fq_C_to_T.fastq and zr1394_16_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 74531056 Number of alignments with a unique best hit from the different alignments: 99 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 74530957 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12 ((converted) top strand) CT/GA: 18 ((converted) bottom strand) GA/CT: 39 (complementary to (converted) top strand) GA/GA: 30 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 800 Total methylated C's in CpG context: 24 Total methylated C's in CHG context: 27 Total methylated C's in CHH context: 204 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 21 Total unmethylated C's in CHG context: 25 Total unmethylated C's in CHH context: 499 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 53.3% C methylated in CHG context: 51.9% C methylated in CHH context: 29.0% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 28m 58s ==================== 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/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_17_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_17_s456_trimmed.fq to zr1394_17_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_17_s456_trimmed.fq to zr1394_17_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_17_s456_trimmed.fq (42070546 sequences in total) Input files are zr1394_17_s456_trimmed.fq_C_to_T.fastq and zr1394_17_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_17_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1337:2117_1:Y:0:GTCCGC 4 * 0 0 * * 0 0 AATAATTAAATATTTTTTATTAATTAATTA >> Writing bisulfite mapping results to zr1394_17_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_17_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 42070534 (100.00%) aligned 0 times 12 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 42070530 (100.00%) aligned 0 times 16 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 42070525 (100.00%) aligned 0 times 21 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 42070546 reads; of these: 42070546 (100.00%) were unpaired; of these: 42070533 (100.00%) aligned 0 times 13 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 42070546 sequences in total Successfully deleted the temporary files zr1394_17_s456_trimmed.fq_C_to_T.fastq and zr1394_17_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 42070546 Number of alignments with a unique best hit from the different alignments: 58 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 42070488 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 9 ((converted) top strand) CT/GA: 16 ((converted) bottom strand) GA/CT: 12 (complementary to (converted) top strand) GA/GA: 21 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 415 Total methylated C's in CpG context: 12 Total methylated C's in CHG context: 7 Total methylated C's in CHH context: 98 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 9 Total unmethylated C's in CHG context: 16 Total unmethylated C's in CHH context: 273 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 57.1% C methylated in CHG context: 30.4% C methylated in CHH context: 26.4% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 16m 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/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_18_s456_trimmed.fq to zr1394_18_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_18_s456_trimmed.fq to zr1394_18_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_18_s456_trimmed.fq (55048106 sequences in total) Input files are zr1394_18_s456_trimmed.fq_C_to_T.fastq and zr1394_18_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_18_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1154:2201_1:N:0:GTGAAA 4 * 0 0 * * 0 0 ATAGTAGGTTAGTTAGTTGAGTTATGTT FFFBFFB/<>> Writing bisulfite mapping results to zr1394_18_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far 55048106 reads; of these: 55048106 (100.00%) were unpaired; of these: 55048087 (100.00%) aligned 0 times 19 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00%55048106 overall alignment rate reads; of these: 55048106 (100.00%) were unpaired; of these: 55048097 (100.00%) aligned 0 times 9 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 55048106 reads; of these: 55048106 (55048106100.00 reads; of these:% ) were unpaired; of these: 55048106 (55048090 (100.00%) aligned 0 times 100.00 %16) were unpaired; of these: ( 0.00 %55048093) aligned exactly 1 time ( 100.00 %0) aligned 0 times ( 0.00 %13) aligned >1 times ( 0.000.00%%) aligned exactly 1 time overall alignment rate 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 55048106 sequences in total Successfully deleted the temporary files zr1394_18_s456_trimmed.fq_C_to_T.fastq and zr1394_18_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 55048106 Number of alignments with a unique best hit from the different alignments: 53 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 55048053 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 7 ((converted) top strand) CT/GA: 11 ((converted) bottom strand) GA/CT: 16 (complementary to (converted) top strand) GA/GA: 19 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 411 Total methylated C's in CpG context: 11 Total methylated C's in CHG context: 10 Total methylated C's in CHH context: 98 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 11 Total unmethylated C's in CHG context: 15 Total unmethylated C's in CHH context: 266 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 50.0% C methylated in CHG context: 40.0% C methylated in CHH context: 26.9% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 21m 30s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_1_s456_trimmed.fq to zr1394_1_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_1_s456_trimmed.fq to zr1394_1_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_1_s456_trimmed.fq (46792286 sequences in total) Input files are zr1394_1_s456_trimmed.fq_C_to_T.fastq and zr1394_1_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_1_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1447:2175_1:N:0:ATCACG 4 * 0 0 * * 0 0 TAAAAAGATTAAAGTTTAAGATAGATAGATT FFFFFFFFFFFFFFFFFFFFBFFFFFFFB>> Writing bisulfite mapping results to zr1394_1_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far 46792286 reads; of these: 46792286 (100.00%) were unpaired; of these: 46792286 reads; of these:46792277 ( 100.0046792286% () aligned 0 times 9 (0.00100.00%%) aligned exactly 1 time) were unpaired; of these: 046792275 ( (0.00100.00%%) aligned >1 times) aligned 0 times 0.00 %11 overall alignment rate ( 0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 46792286 reads; of these: 46792286 (100.00%) were unpaired; of these: 46792269 (100.00%) aligned 0 times 17 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 46792286 reads; of these: 46792286 (100.00%) were unpaired; of these: 46792265 (100.00%) aligned 0 times 21 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 46792286 sequences in total Successfully deleted the temporary files zr1394_1_s456_trimmed.fq_C_to_T.fastq and zr1394_1_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 46792286 Number of alignments with a unique best hit from the different alignments: 51 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 46792235 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 6 ((converted) top strand) CT/GA: 7 ((converted) bottom strand) GA/CT: 21 (complementary to (converted) top strand) GA/GA: 17 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 404 Total methylated C's in CpG context: 13 Total methylated C's in CHG context: 10 Total methylated C's in CHH context: 97 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 25 Total unmethylated C's in CHG context: 32 Total unmethylated C's in CHH context: 227 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 34.2% C methylated in CHG context: 23.8% C methylated in CHH context: 29.9% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 18m 8s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_2_s456_trimmed.fq to zr1394_2_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_2_s456_trimmed.fq to zr1394_2_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_2_s456_trimmed.fq (46105140 sequences in total) Input files are zr1394_2_s456_trimmed.fq_C_to_T.fastq and zr1394_2_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_2_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1359:2236_1:N:0:CGATGT 4 * 0 0 * * 0 0 AATGTAATGATGTTAAATATGTATTAGAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from zr1394_2_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1359:2236_1:N:0:CGATGT 4 * 0 0 * * 0 0 AATGTAATGATGTTAAATATGTATTAGAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from zr1394_2_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1359:2236_1:N:0:CGATGT 4 * 0 0 * * 0 0 AATATAATAATATTAAATACATATTAAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from zr1394_2_s456_trimmed.fq_G_to_A.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1359:2236_1:N:0:CGATGT 4 * 0 0 * * 0 0 AATATAATAATATTAAATACATATTAAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UU >>> Writing bisulfite mapping results to zr1394_2_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far 46105140 reads; of these: 46105140 (100.00%) were unpaired; of these: 46105123 (100.00%) aligned 0 times 17 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 46105140 reads; of these: 46105140 (100.00%) were unpaired; of these: 46105123 (100.00%) aligned 0 times 17 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 46105140 reads; of these: 46105140 (100.00%) were unpaired; of these: 46105126 (100.00%) aligned 0 times 14 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 46105140 reads; of these: 46105140 (100.00%) were unpaired; of these: 46105122 (100.00%) aligned 0 times 18 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 46105140 sequences in total Successfully deleted the temporary files zr1394_2_s456_trimmed.fq_C_to_T.fastq and zr1394_2_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 46105140 Number of alignments with a unique best hit from the different alignments: 55 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 46105085 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 12 ((converted) top strand) CT/GA: 12 ((converted) bottom strand) GA/CT: 14 (complementary to (converted) top strand) GA/GA: 17 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 395 Total methylated C's in CpG context: 19 Total methylated C's in CHG context: 17 Total methylated C's in CHH context: 114 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 20 Total unmethylated C's in CHG context: 16 Total unmethylated C's in CHH context: 209 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 48.7% C methylated in CHG context: 51.5% C methylated in CHH context: 35.3% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 18m 0s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_3_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_3_s456_trimmed.fq to zr1394_3_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_3_s456_trimmed.fq to zr1394_3_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_3_s456_trimmed.fq (48376729 sequences in total) Input files are zr1394_3_s456_trimmed.fq_C_to_T.fastq and zr1394_3_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_3_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1217:2194_1:N:0:TTAGGC 4 * 0 0 * * 0 0 TTAATTTTTTTAAAATATTTTATTTTATTTA FFF>> Writing bisulfite mapping results to zr1394_3_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_3_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 48376709 (100.00%) aligned 0 times 20 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 48376716 (100.00%) aligned 0 times 13 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 48376706 (100.00%) aligned 0 times 23 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 48376729 reads; of these: 48376729 (100.00%) were unpaired; of these: 48376717 (100.00%) aligned 0 times 12 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 48376729 sequences in total Successfully deleted the temporary files zr1394_3_s456_trimmed.fq_C_to_T.fastq and zr1394_3_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 48376729 Number of alignments with a unique best hit from the different alignments: 59 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 48376670 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 8 ((converted) top strand) CT/GA: 15 ((converted) bottom strand) GA/CT: 23 (complementary to (converted) top strand) GA/GA: 13 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 444 Total methylated C's in CpG context: 15 Total methylated C's in CHG context: 22 Total methylated C's in CHH context: 118 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 27 Total unmethylated C's in CHG context: 19 Total unmethylated C's in CHH context: 243 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 35.7% C methylated in CHG context: 53.7% C methylated in CHH context: 32.7% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 18m 37s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_4_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_4_s456_trimmed.fq to zr1394_4_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_4_s456_trimmed.fq to zr1394_4_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_4_s456_trimmed.fq (44905078 sequences in total) Input files are zr1394_4_s456_trimmed.fq_C_to_T.fastq and zr1394_4_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_4_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1202:2117_1:N:0:TGACCA 4 * 0 0 * * 0 0 AAATATTATTTTTGTTTTTTTGATTGAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFB>> Writing bisulfite mapping results to zr1394_4_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_4_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far 44905078 reads; of these: 44905078 (100.00%) were unpaired; of these: 44905053 (100.00%) aligned 0 times 25 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 4490507844905078 reads; of these: reads; of these: 4490507844905078 ( (100.00%) were unpaired; of these: 44905059100.00 (%100.00) were unpaired; of these:% ) aligned 0 times 44905067 (19100.00 (%0.00) aligned 0 times% ) aligned exactly 1 time 11 (00.00 (%0.00) aligned exactly 1 time% ) aligned >1 times 00.00 (%0.00 overall alignment rate% ) aligned >1 times 0.00% overall alignment rate 44905078 reads; of these: 44905078 (100.00%) were unpaired; of these: 44905059 (100.00%) aligned 0 times 19 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 44905078 sequences in total Successfully deleted the temporary files zr1394_4_s456_trimmed.fq_C_to_T.fastq and zr1394_4_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 44905078 Number of alignments with a unique best hit from the different alignments: 70 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 44905008 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 17 ((converted) top strand) CT/GA: 9 ((converted) bottom strand) GA/CT: 19 (complementary to (converted) top strand) GA/GA: 25 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 562 Total methylated C's in CpG context: 12 Total methylated C's in CHG context: 13 Total methylated C's in CHH context: 123 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 21 Total unmethylated C's in CHG context: 19 Total unmethylated C's in CHH context: 374 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 36.4% C methylated in CHG context: 40.6% C methylated in CHH context: 24.7% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 17m 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/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_5_s456_trimmed.fq to zr1394_5_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_5_s456_trimmed.fq to zr1394_5_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_5_s456_trimmed.fq (47401736 sequences in total) Input files are zr1394_5_s456_trimmed.fq_C_to_T.fastq and zr1394_5_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_5_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1173:2158_1:N:0:ACAGTG 4 * 0 0 * * 0 0 ATATTAAATATTATAAATTTATTATATATT B/FF/FFFFFFFF>> Writing bisulfite mapping results to zr1394_5_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 47401722 (100.00%) aligned 0 times 14 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 47401717 (100.00%) aligned 0 times 19 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 47401706 (100.00%) aligned 0 times 30 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 47401736 reads; of these: 47401736 (100.00%) were unpaired; of these: 47401723 (100.00%) aligned 0 times 13 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 47401736 sequences in total Successfully deleted the temporary files zr1394_5_s456_trimmed.fq_C_to_T.fastq and zr1394_5_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 47401736 Number of alignments with a unique best hit from the different alignments: 64 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 47401672 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 8 ((converted) top strand) CT/GA: 12 ((converted) bottom strand) GA/CT: 14 (complementary to (converted) top strand) GA/GA: 30 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 497 Total methylated C's in CpG context: 21 Total methylated C's in CHG context: 25 Total methylated C's in CHH context: 156 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 18 Total unmethylated C's in CHG context: 21 Total unmethylated C's in CHH context: 256 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 53.8% C methylated in CHG context: 54.3% C methylated in CHH context: 37.9% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 18m 33s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_6_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_6_s456_trimmed.fq to zr1394_6_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_6_s456_trimmed.fq to zr1394_6_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_6_s456_trimmed.fq (46455148 sequences in total) Input files are zr1394_6_s456_trimmed.fq_C_to_T.fastq and zr1394_6_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_6_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1223:2248_1:N:0:GCCAAT 4 * 0 0 * * 0 0 AATTAATAAATAAATAATAAAATATGATAAA FFFFFFFFFFFFFFFFFFFFFFFBF/>> Writing bisulfite mapping results to zr1394_6_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_6_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far 46455148 reads; of these: 46455148 (100.00%) were unpaired; of these: 46455134 (100.00%) aligned 0 times 14 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 46455148 reads; of these: 46455148 (100.00%) were unpaired; of these: 46455138 (100.00%) aligned 0 times 10 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 46455148 reads; of these: 46455148 (100.00%) were unpaired; of these: 46455127 (100.00%) aligned 0 times 21 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 46455148 reads; of these: 46455148 (100.00%) were unpaired; of these: 46455135 (100.00%) aligned 0 times 13 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 46455148 sequences in total Successfully deleted the temporary files zr1394_6_s456_trimmed.fq_C_to_T.fastq and zr1394_6_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 46455148 Number of alignments with a unique best hit from the different alignments: 49 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 46455099 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 5 ((converted) top strand) CT/GA: 11 ((converted) bottom strand) GA/CT: 12 (complementary to (converted) top strand) GA/GA: 21 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 386 Total methylated C's in CpG context: 26 Total methylated C's in CHG context: 20 Total methylated C's in CHH context: 110 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 13 Total unmethylated C's in CHG context: 15 Total unmethylated C's in CHH context: 202 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 66.7% C methylated in CHG context: 57.1% C methylated in CHH context: 35.3% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 18m 11s ==================== 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/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_7_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_7_s456_trimmed.fq to zr1394_7_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_7_s456_trimmed.fq to zr1394_7_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_7_s456_trimmed.fq (49730113 sequences in total) Input files are zr1394_7_s456_trimmed.fq_C_to_T.fastq and zr1394_7_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_7_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1323:2170_1:N:0:CAGATC 4 * 0 0 * * 0 0 GTTGTATTATGTATTTTTAAAATATAGTGTT FFFFFFFFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to zr1394_7_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_7_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 49730102 (100.00%) aligned 0 times 11 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 49730096 (100.00%) aligned 0 times 17 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 49730097 (100.00%) aligned 0 times 16 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 49730113 reads; of these: 49730113 (100.00%) were unpaired; of these: 49730100 (100.00%) aligned 0 times 13 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 49730113 sequences in total Successfully deleted the temporary files zr1394_7_s456_trimmed.fq_C_to_T.fastq and zr1394_7_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 49730113 Number of alignments with a unique best hit from the different alignments: 52 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 49730061 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 13 ((converted) top strand) CT/GA: 15 ((converted) bottom strand) GA/CT: 11 (complementary to (converted) top strand) GA/GA: 13 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 398 Total methylated C's in CpG context: 9 Total methylated C's in CHG context: 6 Total methylated C's in CHH context: 84 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 20 Total unmethylated C's in CHG context: 17 Total unmethylated C's in CHH context: 262 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 31.0% C methylated in CHG context: 26.1% C methylated in CHH context: 24.3% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 19m 16s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_8_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_8_s456_trimmed.fq to zr1394_8_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_8_s456_trimmed.fq to zr1394_8_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_8_s456_trimmed.fq (38697189 sequences in total) Input files are zr1394_8_s456_trimmed.fq_C_to_T.fastq and zr1394_8_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_8_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1180:2121_1:Y:0:ACTTGA 4 * 0 0 * * 0 0 GTTTTATAATATATGTATTATGAGTTTTT FFFBF/B/>> Writing bisulfite mapping results to zr1394_8_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_8_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far 38697189 reads; of these: 38697189 (38697189100.00 reads; of these:%) were unpaired; of these: 3869718938697183 ( (100.00%) aligned 0 times 6 (0.00%) aligned exactly 1 time 100.000% () were unpaired; of these:0.00 % ) aligned >1 times38697183 (0.00%100.00 overall alignment rate% ) aligned 0 times 6 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 38697189 reads; of these: 38697189 (100.00%) were unpaired; of these: 38697176 (100.00%) aligned 0 times 13 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 38697189 reads; of these: 38697189 (100.00%) were unpaired; of these: 38697177 (100.00%) aligned 0 times 12 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 38697189 sequences in total Successfully deleted the temporary files zr1394_8_s456_trimmed.fq_C_to_T.fastq and zr1394_8_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 38697189 Number of alignments with a unique best hit from the different alignments: 33 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 38697156 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 9 ((converted) top strand) CT/GA: 5 ((converted) bottom strand) GA/CT: 6 (complementary to (converted) top strand) GA/GA: 13 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 244 Total methylated C's in CpG context: 8 Total methylated C's in CHG context: 8 Total methylated C's in CHH context: 51 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 5 Total unmethylated C's in CHG context: 10 Total unmethylated C's in CHH context: 162 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 61.5% C methylated in CHG context: 44.4% C methylated in CHH context: 23.9% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 14m 58s ==================== 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/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_9_s456_trimmed.fq to zr1394_9_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_9_s456_trimmed.fq to zr1394_9_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_9_s456_trimmed.fq (77350922 sequences in total) Input files are zr1394_9_s456_trimmed.fq_C_to_T.fastq and zr1394_9_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_9_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:1:1101:1382:2160_1:N:0:GATCAG 4 * 0 0 * * 0 0 TATTTAAAAAATTTTTATTATTTTAATATTA B>> Writing bisulfite mapping results to zr1394_9_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Processed 30000000 sequences so far Processed 31000000 sequences so far Processed 32000000 sequences so far Processed 33000000 sequences so far Processed 34000000 sequences so far Processed 35000000 sequences so far Processed 36000000 sequences so far Processed 37000000 sequences so far Processed 38000000 sequences so far Processed 39000000 sequences so far Processed 40000000 sequences so far Processed 41000000 sequences so far Processed 42000000 sequences so far Processed 43000000 sequences so far Processed 44000000 sequences so far Processed 45000000 sequences so far Processed 46000000 sequences so far Processed 47000000 sequences so far Processed 48000000 sequences so far Processed 49000000 sequences so far Processed 50000000 sequences so far Processed 51000000 sequences so far Processed 52000000 sequences so far Processed 53000000 sequences so far Processed 54000000 sequences so far Processed 55000000 sequences so far Processed 56000000 sequences so far Processed 57000000 sequences so far Processed 58000000 sequences so far Processed 59000000 sequences so far Processed 60000000 sequences so far Processed 61000000 sequences so far Processed 62000000 sequences so far Processed 63000000 sequences so far Processed 64000000 sequences so far Processed 65000000 sequences so far Processed 66000000 sequences so far Processed 67000000 sequences so far Processed 68000000 sequences so far Processed 69000000 sequences so far Processed 70000000 sequences so far Processed 71000000 sequences so far Processed 72000000 sequences so far Processed 73000000 sequences so far Processed 74000000 sequences so far Processed 75000000 sequences so far Processed 76000000 sequences so far Processed 77000000 sequences so far 77350922 reads; of these: 77350922 (100.00%) were unpaired; of these: 77350901 (100.00%) aligned 0 times 21 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 77350922 reads; of these: 77350922 (100.00%) were unpaired; of these: 77350903 (100.00%) aligned 0 times 19 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 77350922 reads; of these: 77350922 (100.00%) were unpaired; of these: 77350900 (100.00%) aligned 0 times 22 (0.00%) aligned exactly 1 time 077350922 ( reads; of these:0.00 % ) aligned >1 times77350922 (0.00% overall alignment rate 100.00%) were unpaired; of these: 77350903 (100.00%) aligned 0 times 19 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 77350922 sequences in total Successfully deleted the temporary files zr1394_9_s456_trimmed.fq_C_to_T.fastq and zr1394_9_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 77350922 Number of alignments with a unique best hit from the different alignments: 74 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 77350848 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 15 ((converted) top strand) CT/GA: 16 ((converted) bottom strand) GA/CT: 21 (complementary to (converted) top strand) GA/GA: 22 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 604 Total methylated C's in CpG context: 22 Total methylated C's in CHG context: 16 Total methylated C's in CHH context: 124 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 30 Total unmethylated C's in CHG context: 24 Total unmethylated C's in CHH context: 388 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 42.3% C methylated in CHG context: 40.0% C methylated in CHH context: 24.2% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 30m 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/phiX174/ (absolute path is '/gscratch/srlab/sr320/data/phiX174/)' 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/sr320/091422-oly-phage'): /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_all_s456_trimmed.fq Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Current working directory is: /gscratch/scrubbed/sr320/091422-oly-phage Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/phiX174/ chr NC_001422.1 (5386 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file zr1394_all_s456_trimmed.fq to zr1394_all_s456_trimmed.fq_C_to_T.fastq Writing a G -> A converted version of the input file zr1394_all_s456_trimmed.fq to zr1394_all_s456_trimmed.fq_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr1394_all_s456_trimmed.fq (605809374 sequences in total) Input files are zr1394_all_s456_trimmed.fq_C_to_T.fastq and zr1394_all_s456_trimmed.fq_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/phiX174/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from zr1394_all_s456_trimmed.fq_C_to_T.fastq with options -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/phiX174/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-C00124:164:C7URDANXX:2:1101:1108:2120_1:Y:0:TATCTT 4 * 0 0 * * 0 0 ATTAATGAGAATGATTTTTTTTTTA B//FF>> Writing bisulfite mapping results to zr1394_all_s456_trimmed_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_all_s456_trimmed.fq Processed 1000000 sequences so far Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Processed 10000000 sequences so far Processed 11000000 sequences so far Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Processed 20000000 sequences so far Processed 21000000 sequences so far Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far 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Processed 567000000 sequences so far Processed 568000000 sequences so far Processed 569000000 sequences so far Processed 570000000 sequences so far Processed 571000000 sequences so far Processed 572000000 sequences so far Processed 573000000 sequences so far Processed 574000000 sequences so far Processed 575000000 sequences so far Processed 576000000 sequences so far Processed 577000000 sequences so far Processed 578000000 sequences so far Processed 579000000 sequences so far Processed 580000000 sequences so far Processed 581000000 sequences so far Processed 582000000 sequences so far Processed 583000000 sequences so far Processed 584000000 sequences so far Processed 585000000 sequences so far Processed 586000000 sequences so far Processed 587000000 sequences so far Processed 588000000 sequences so far Processed 589000000 sequences so far Processed 590000000 sequences so far Processed 591000000 sequences so far Processed 592000000 sequences so far Processed 593000000 sequences so far Processed 594000000 sequences so far Processed 595000000 sequences so far Processed 596000000 sequences so far Processed 597000000 sequences so far Processed 598000000 sequences so far Processed 599000000 sequences so far Processed 600000000 sequences so far Processed 601000000 sequences so far Processed 602000000 sequences so far Processed 603000000 sequences so far Processed 604000000 sequences so far Processed 605000000 sequences so far 605809374 reads; of these: 605809374 (100.00%) were unpaired; of these: 605809121 (100.00%) aligned 0 times 253 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 605809374 reads; of these: 605809374 (100.00%) were unpaired; of these: 605809209 (100.00%605809374) aligned 0 times reads; of these: 165605809374 ( (0.00%) aligned exactly 1 time605809374100.00 reads; of these:% ) were unpaired; of these: 0 ( 0.00 %605809244) aligned >1 times ( 100.000.00%%) aligned 0 times overall alignment rate 130 ( 0.00605809374% () aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 100.00%) were unpaired; of these: 605809154 (100.00%) aligned 0 times 220 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Processed 605809374 sequences in total Successfully deleted the temporary files zr1394_all_s456_trimmed.fq_C_to_T.fastq and zr1394_all_s456_trimmed.fq_G_to_A.fastq Final Alignment report ====================== Sequences analysed in total: 605809374 Number of alignments with a unique best hit from the different alignments: 713 Mapping efficiency: 0.0% Sequences with no alignments under any condition: 605808661 Sequences did not map uniquely: 0 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 101 ((converted) top strand) CT/GA: 139 ((converted) bottom strand) GA/CT: 220 (complementary to (converted) top strand) GA/GA: 253 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 5561 Total methylated C's in CpG context: 187 Total methylated C's in CHG context: 121 Total methylated C's in CHH context: 1287 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 197 Total unmethylated C's in CHG context: 224 Total unmethylated C's in CHH context: 3545 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 48.7% C methylated in CHG context: 35.1% C methylated in CHH context: 26.6% Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 Bismark completed in 0d 3h 55m 38s ==================== Bismark run complete ==================== Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_10_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_10_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_10_s456_trimmed_bismark_bt2.bam: 100 Total number duplicated alignments removed: 36 (36.00%) Duplicated alignments were found at: 19 different position(s) Total count of deduplicated leftover sequences: 64 (64.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_10_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_11_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_11_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_11_s456_trimmed_bismark_bt2.bam: 68 Total number duplicated alignments removed: 27 (39.71%) Duplicated alignments were found at: 10 different position(s) Total count of deduplicated leftover sequences: 41 (60.29% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_11_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_12_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_12_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_12_s456_trimmed_bismark_bt2.bam: 56 Total number duplicated alignments removed: 11 (19.64%) Duplicated alignments were found at: 9 different position(s) Total count of deduplicated leftover sequences: 45 (80.36% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_12_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_13_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_13_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_13_s456_trimmed_bismark_bt2.bam: 66 Total number duplicated alignments removed: 22 (33.33%) Duplicated alignments were found at: 12 different position(s) Total count of deduplicated leftover sequences: 44 (66.67% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_13_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_14_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_14_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_14_s456_trimmed_bismark_bt2.bam: 96 Total number duplicated alignments removed: 41 (42.71%) Duplicated alignments were found at: 11 different position(s) Total count of deduplicated leftover sequences: 55 (57.29% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_15_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_15_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_15_s456_trimmed_bismark_bt2.bam: 92 Total number duplicated alignments removed: 37 (40.22%) Duplicated alignments were found at: 9 different position(s) Total count of deduplicated leftover sequences: 55 (59.78% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_15_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_16_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_16_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_16_s456_trimmed_bismark_bt2.bam: 99 Total number duplicated alignments removed: 39 (39.39%) Duplicated alignments were found at: 13 different position(s) Total count of deduplicated leftover sequences: 60 (60.61% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_16_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_17_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_17_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_17_s456_trimmed_bismark_bt2.bam: 58 Total number duplicated alignments removed: 16 (27.59%) Duplicated alignments were found at: 5 different position(s) Total count of deduplicated leftover sequences: 42 (72.41% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_17_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_18_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_18_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_18_s456_trimmed_bismark_bt2.bam: 53 Total number duplicated alignments removed: 11 (20.75%) Duplicated alignments were found at: 7 different position(s) Total count of deduplicated leftover sequences: 42 (79.25% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_1_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_1_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_1_s456_trimmed_bismark_bt2.bam: 51 Total number duplicated alignments removed: 13 (25.49%) Duplicated alignments were found at: 8 different position(s) Total count of deduplicated leftover sequences: 38 (74.51% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_2_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_2_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_2_s456_trimmed_bismark_bt2.bam: 55 Total number duplicated alignments removed: 7 (12.73%) Duplicated alignments were found at: 4 different position(s) Total count of deduplicated leftover sequences: 48 (87.27% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_3_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_3_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_3_s456_trimmed_bismark_bt2.bam: 59 Total number duplicated alignments removed: 7 (11.86%) Duplicated alignments were found at: 4 different position(s) Total count of deduplicated leftover sequences: 52 (88.14% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_3_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_4_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_4_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_4_s456_trimmed_bismark_bt2.bam: 70 Total number duplicated alignments removed: 23 (32.86%) Duplicated alignments were found at: 10 different position(s) Total count of deduplicated leftover sequences: 47 (67.14% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_4_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_5_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_5_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_5_s456_trimmed_bismark_bt2.bam: 64 Total number duplicated alignments removed: 11 (17.19%) Duplicated alignments were found at: 6 different position(s) Total count of deduplicated leftover sequences: 53 (82.81% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_6_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_6_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_6_s456_trimmed_bismark_bt2.bam: 49 Total number duplicated alignments removed: 10 (20.41%) Duplicated alignments were found at: 5 different position(s) Total count of deduplicated leftover sequences: 39 (79.59% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_6_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_7_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_7_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_7_s456_trimmed_bismark_bt2.bam: 52 Total number duplicated alignments removed: 9 (17.31%) Duplicated alignments were found at: 7 different position(s) Total count of deduplicated leftover sequences: 43 (82.69% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_7_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_8_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_8_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_8_s456_trimmed_bismark_bt2.bam: 33 Total number duplicated alignments removed: 5 (15.15%) Duplicated alignments were found at: 4 different position(s) Total count of deduplicated leftover sequences: 28 (84.85% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_8_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_9_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_9_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_9_s456_trimmed_bismark_bt2.bam: 74 Total number duplicated alignments removed: 16 (21.62%) Duplicated alignments were found at: 8 different position(s) Total count of deduplicated leftover sequences: 58 (78.38% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_s456_trimmed.fq" Neither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the @PG line of the SAM/BAM file Processing single-end Bismark output file(s) (SAM format): zr1394_all_s456_trimmed_bismark_bt2.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr1394_all_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Trying to determine the type of mapping from the SAM header line Treating file as single-end data (extracted from @PG line) Output file is: zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_all_s456_trimmed_bismark_bt2.bam: 713 Total number duplicated alignments removed: 407 (57.08%) Duplicated alignments were found at: 79 different position(s) Total count of deduplicated leftover sequences: 306 (42.92% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_all_s456_trimmed.fq" *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Treating file(s) as single-end data (as extracted from @PG line) Summarising Bismark methylation extractor parameters: =============================================================== Bismark single-end SAM format specified (default) Number of cores to be used: 14 Output will be written to the current directory ('/gscratch/scrubbed/sr320/091422-oly-phage') Summarising bedGraph parameters: =============================================================== Generating additional output in bedGraph and coverage format bedGraph format: coverage format: Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting cytosine methylation information in CpG context only (default) The bedGraph UNIX sort command will use the following memory setting: '75%'. Temporary directory used for sorting is the output directory Checking file >>zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_10_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 64 lines in total Total number of methylation call strings processed: 64 Final Cytosine Methylation Report ================================= Total number of C's analysed: 442 Total methylated C's in CpG context: 33 Total methylated C's in CHG context: 22 Total methylated C's in CHH context: 130 Total C to T conversions in CpG context: 24 Total C to T conversions in CHG context: 23 Total C to T conversions in CHH context: 210 C methylated in CpG context: 57.9% C methylated in CHG context: 48.9% C methylated in CHH context: 38.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_11_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 41 lines in total Total number of methylation call strings processed: 41 Final Cytosine Methylation Report ================================= Total number of C's analysed: 311 Total methylated C's in CpG context: 10 Total methylated C's in CHG context: 7 Total methylated C's in CHH context: 64 Total C to T conversions in CpG context: 17 Total C to T conversions in CHG context: 19 Total C to T conversions in CHH context: 194 C methylated in CpG context: 37.0% C methylated in CHG context: 26.9% C methylated in CHH context: 24.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_12_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 45 lines in total Total number of methylation call strings processed: 45 Final Cytosine Methylation Report ================================= Total number of C's analysed: 323 Total methylated C's in CpG context: 13 Total methylated C's in CHG context: 6 Total methylated C's in CHH context: 75 Total C to T conversions in CpG context: 12 Total C to T conversions in CHG context: 17 Total C to T conversions in CHH context: 200 C methylated in CpG context: 52.0% C methylated in CHG context: 26.1% C methylated in CHH context: 27.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_13_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 44 lines in total Total number of methylation call strings processed: 44 Final Cytosine Methylation Report ================================= Total number of C's analysed: 326 Total methylated C's in CpG context: 16 Total methylated C's in CHG context: 8 Total methylated C's in CHH context: 95 Total C to T conversions in CpG context: 12 Total C to T conversions in CHG context: 16 Total C to T conversions in CHH context: 179 C methylated in CpG context: 57.1% C methylated in CHG context: 33.3% C methylated in CHH context: 34.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 55 lines in total Total number of methylation call strings processed: 55 Final Cytosine Methylation Report ================================= Total number of C's analysed: 417 Total methylated C's in CpG context: 24 Total methylated C's in CHG context: 15 Total methylated C's in CHH context: 93 Total C to T conversions in CpG context: 24 Total C to T conversions in CHG context: 25 Total C to T conversions in CHH context: 236 C methylated in CpG context: 50.0% C methylated in CHG context: 37.5% C methylated in CHH context: 28.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_15_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 55 lines in total Total number of methylation call strings processed: 55 Final Cytosine Methylation Report ================================= Total number of C's analysed: 397 Total methylated C's in CpG context: 16 Total methylated C's in CHG context: 9 Total methylated C's in CHH context: 108 Total C to T conversions in CpG context: 22 Total C to T conversions in CHG context: 23 Total C to T conversions in CHH context: 219 C methylated in CpG context: 42.1% C methylated in CHG context: 28.1% C methylated in CHH context: 33.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_16_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 60 lines in total Total number of methylation call strings processed: 60 Final Cytosine Methylation Report ================================= Total number of C's analysed: 442 Total methylated C's in CpG context: 24 Total methylated C's in CHG context: 25 Total methylated C's in CHH context: 134 Total C to T conversions in CpG context: 15 Total C to T conversions in CHG context: 19 Total C to T conversions in CHH context: 225 C methylated in CpG context: 61.5% C methylated in CHG context: 56.8% C methylated in CHH context: 37.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_17_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 42 lines in total Total number of methylation call strings processed: 42 Final Cytosine Methylation Report ================================= Total number of C's analysed: 280 Total methylated C's in CpG context: 12 Total methylated C's in CHG context: 7 Total methylated C's in CHH context: 67 Total C to T conversions in CpG context: 8 Total C to T conversions in CHG context: 13 Total C to T conversions in CHH context: 173 C methylated in CpG context: 60.0% C methylated in CHG context: 35.0% C methylated in CHH context: 27.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Finished processing child process. Exiting.. Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 42 lines in total Total number of methylation call strings processed: 42 Final Cytosine Methylation Report ================================= Total number of C's analysed: 308 Total methylated C's in CpG context: 11 Total methylated C's in CHG context: 10 Total methylated C's in CHH context: 85 Total C to T conversions in CpG context: 11 Total C to T conversions in CHG context: 15 Total C to T conversions in CHH context: 176 C methylated in CpG context: 50.0% C methylated in CHG context: 40.0% C methylated in CHH context: 32.6% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 30 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 30 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Now reading in Bismark result file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 38 lines in total Total number of methylation call strings processed: 38 Final Cytosine Methylation Report ================================= Total number of C's analysed: 285 Total methylated C's in CpG context: 11 Total methylated C's in CHG context: 10 Total methylated C's in CHH context: 66 Total C to T conversions in CpG context: 22 Total C to T conversions in CHG context: 30 Total C to T conversions in CHH context: 146 C methylated in CpG context: 33.3% C methylated in CHG context: 25.0% C methylated in CHH context: 31.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 48 lines in total Total number of methylation call strings processed: 48 Final Cytosine Methylation Report ================================= Total number of C's analysed: 343 Total methylated C's in CpG context: 19 Total methylated C's in CHG context: 17 Total methylated C's in CHH context: 98 Total C to T conversions in CpG context: 20 Total C to T conversions in CHG context: 16 Total C to T conversions in CHH context: 173 C methylated in CpG context: 48.7% C methylated in CHG context: 51.5% C methylated in CHH context: 36.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_3_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 52 lines in total Total number of methylation call strings processed: 52 Final Cytosine Methylation Report ================================= Total number of C's analysed: 378 Total methylated C's in CpG context: 14 Total methylated C's in CHG context: 22 Total methylated C's in CHH context: 111 Total C to T conversions in CpG context: 24 Total C to T conversions in CHG context: 17 Total C to T conversions in CHH context: 190 C methylated in CpG context: 36.8% C methylated in CHG context: 56.4% C methylated in CHH context: 36.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_4_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 47 lines in total Total number of methylation call strings processed: 47 Final Cytosine Methylation Report ================================= Total number of C's analysed: 347 Total methylated C's in CpG context: 12 Total methylated C's in CHG context: 9 Total methylated C's in CHH context: 80 Total C to T conversions in CpG context: 19 Total C to T conversions in CHG context: 14 Total C to T conversions in CHH context: 213 C methylated in CpG context: 38.7% C methylated in CHG context: 39.1% C methylated in CHH context: 27.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 53 lines in total Total number of methylation call strings processed: 53 Final Cytosine Methylation Report ================================= Total number of C's analysed: 394 Total methylated C's in CpG context: 21 Total methylated C's in CHG context: 24 Total methylated C's in CHH context: 133 Total C to T conversions in CpG context: 12 Total C to T conversions in CHG context: 15 Total C to T conversions in CHH context: 189 C methylated in CpG context: 63.6% C methylated in CHG context: 61.5% C methylated in CHH context: 41.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_6_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 39 lines in total Total number of methylation call strings processed: 39 Final Cytosine Methylation Report ================================= Total number of C's analysed: 289 Total methylated C's in CpG context: 26 Total methylated C's in CHG context: 19 Total methylated C's in CHH context: 82 Total C to T conversions in CpG context: 13 Total C to T conversions in CHG context: 14 Total C to T conversions in CHH context: 135 C methylated in CpG context: 66.7% C methylated in CHG context: 57.6% C methylated in CHH context: 37.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_7_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 43 lines in total Total number of methylation call strings processed: 43 Final Cytosine Methylation Report ================================= Total number of C's analysed: 320 Total methylated C's in CpG context: 9 Total methylated C's in CHG context: 6 Total methylated C's in CHH context: 71 Total C to T conversions in CpG context: 16 Total C to T conversions in CHG context: 13 Total C to T conversions in CHH context: 205 C methylated in CpG context: 36.0% C methylated in CHG context: 31.6% C methylated in CHH context: 25.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 Finished processing child process. Exiting.. 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_8_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 28 lines in total Total number of methylation call strings processed: 28 Final Cytosine Methylation Report ================================= Total number of C's analysed: 195 Total methylated C's in CpG context: 8 Total methylated C's in CHG context: 7 Total methylated C's in CHH context: 45 Total C to T conversions in CpG context: 5 Total C to T conversions in CHG context: 9 Total C to T conversions in CHH context: 121 C methylated in CpG context: 61.5% C methylated in CHG context: 43.8% C methylated in CHH context: 27.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 29 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 29 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 58 lines in total Total number of methylation call strings processed: 58 Final Cytosine Methylation Report ================================= Total number of C's analysed: 448 Total methylated C's in CpG context: 19 Total methylated C's in CHG context: 15 Total methylated C's in CHH context: 95 Total C to T conversions in CpG context: 30 Total C to T conversions in CHG context: 21 Total C to T conversions in CHH context: 268 C methylated in CpG context: 38.8% C methylated in CHG context: 41.7% C methylated in CHH context: 26.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Now reading in Bismark result file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_001422.1 LN:5386 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/phiX174/ -p 4 --non_directional /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_all_s456_trimmed.fq" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13 zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 306 lines in total Total number of methylation call strings processed: 306 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2096 Total methylated C's in CpG context: 142 Total methylated C's in CHG context: 107 Total methylated C's in CHH context: 580 Total C to T conversions in CpG context: 96 Total C to T conversions in CHG context: 144 Total C to T conversions in CHH context: 1027 C methylated in CpG context: 59.7% C methylated in CHG context: 42.6% C methylated in CHH context: 36.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.1.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.2.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.3.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.4.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.5.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.6.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.7.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.8.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.9.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.10.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.11.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.12.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.13.mbias zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 31 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CpG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept CHH_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHH_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt /gscratch/scrubbed/sr320/091422-oly-phage/CpG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt Writing bedGraph to file: zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr1394_all_s456_trimmed_bismark_bt2.deduplicated.txt to merged temp file Sorting input file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 19 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> zr1394_10_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_10_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_10_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_10_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_10_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_11_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_11_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_11_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_11_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_11_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_12_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_12_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_12_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_12_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_12_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_13_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_13_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_13_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_13_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_13_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_14_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_14_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_14_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_14_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_14_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_15_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_15_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_15_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_15_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_15_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_16_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_16_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_16_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_16_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_16_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_17_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_17_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_17_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_17_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_17_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_18_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_18_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_18_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_18_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_18_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_1_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_1_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_1_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_1_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_1_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_2_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_2_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_2_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_2_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_2_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_3_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_3_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_3_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_3_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_3_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_4_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_4_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_4_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_4_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_4_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_5_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_5_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_5_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_5_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_5_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_6_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_6_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_6_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_6_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_6_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_7_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_7_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_7_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_7_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_7_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_8_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_8_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_8_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_8_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_8_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_9_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_9_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_9_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_9_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_9_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_all_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_all_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_all_s456_trimmed_bismark_bt2_SE_report.txt ... Complete Using the following deduplication report: > zr1394_all_s456_trimmed_bismark_bt2.deduplication_report.txt < Processing deduplication report zr1394_all_s456_trimmed_bismark_bt2.deduplication_report.txt ... Complete Using the following splitting report: > zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt < Processing splitting report zr1394_all_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr1394_all_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt < Processing M-bias report zr1394_all_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Found Bismark/Bowtie2 single-end files No Bismark/Bowtie2 paired-end BAM files detected No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 19 Bismark BAM file(s)... >> Reading from Bismark report: zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt >> Reading from Bismark report: zr1394_all_s456_trimmed_bismark_bt2_SE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html << Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_10_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 45 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 >>zr1394_10_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_10_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_11_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 18 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 >>zr1394_11_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_11_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_12_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 17 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 >>zr1394_12_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_12_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_13_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 24 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 >>zr1394_13_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_13_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_14_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 34 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 >>zr1394_14_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_14_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_15_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 29 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 >>zr1394_15_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_15_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_16_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 25 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 >>zr1394_16_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_16_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_17_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 17 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 >>zr1394_17_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_17_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_18_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 17 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 >>zr1394_18_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_18_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_1_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 27 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 >>zr1394_1_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_1_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_2_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 28 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 >>zr1394_2_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_2_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_3_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 26 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 >>zr1394_3_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_3_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_4_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 22 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 >>zr1394_4_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_4_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_5_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 28 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 >>zr1394_5_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_5_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_6_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 30 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 >>zr1394_6_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_6_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_7_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 16 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 >>zr1394_7_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_7_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_8_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 13 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 >>zr1394_8_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_8_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_9_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 39 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 >>zr1394_9_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_9_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr1394_all_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/091422-oly-phage/< Genome directory: >/gscratch/srlab/sr320/data/phiX174/< 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/phiX174/ chr NC_001422.1 (5386 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: zr1394_all_s456.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001422.1 Writing cytosine report for last chromosome NC_001422.1 (stored 138 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 >>zr1394_all_s456.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr1394_all_s456.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq!