Writing bisulfite genomes out into a single MFA (multi FastA) file Bisulfite Genome Indexer version v0.19.1 (last modified 26 April 2018) Step I - Prepare genome folders - completed Total number of conversions performed: C->T: 9963208 G->A: 10083370 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! 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: 4 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: 00:00:01 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: 10673160 Using parameters --bmax 8004870 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 8004870 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples 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: 4 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 V-Sorting samples time: 00:00:01 Allocating rank array Ranking v-sort output Time to join reference sequences: 00:00:01 bmax according to bmaxDivN setting: 10673160 Using parameters --bmax 8004870 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 8004870 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes V-Sorting samples time: 00:00:01 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 0; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.09895e+06 (target: 8004869) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (8004870) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 6732952 for bucket 1 (Using difference cover) Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.09895e+06 (target: 8004869) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (8004870) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 6810255 for bucket 1 (Using difference cover) Sorting block time: 00:00:06 Returning block of 6732953 for bucket 1 Getting block 2 of 7 Reserving size (8004870) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 6839681 for bucket 2 (Using difference cover) Sorting block time: 00:00:07 Returning block of 6810256 for bucket 1 Getting block 2 of 7 Reserving size (8004870) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 7007342 for bucket 2 (Using difference cover) Sorting block time: 00:00:06 Returning block of 6839682 for bucket 2 Getting block 3 of 7 Reserving size (8004870) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 4933045 for bucket 3 (Using difference cover) Sorting block time: 00:00:07 Returning block of 7007343 for bucket 2 Getting block 3 of 7 Reserving size (8004870) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% Sorting block time: 00:00:05 Returning block of 4933046 for bucket 3 bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 3962325 for bucket 3 (Using difference cover) Getting block 4 of 7 Reserving size (8004870) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 7753100 for bucket 4 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3962326 for bucket 3 Getting block 4 of 7 Reserving size (8004870) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 6998309 for bucket 4 (Using difference cover) Sorting block time: 00:00:08 Returning block of 7753101 for bucket 4 Getting block 5 of 7 Reserving size (8004870) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% bucket 5: 20% bucket 5: 30% bucket 5: 40% bucket 5: 50% bucket 5: 60% bucket 5: 70% bucket 5: 80% Sorting block time: 00:00:06 Returning block of 6998310 for bucket 4 bucket 5: 90% bucket 5: 100% Sorting block of length 4911173 for bucket 5 (Using difference cover) Getting block 5 of 7 Reserving size (8004870) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% bucket 5: 20% bucket 5: 30% bucket 5: 40% bucket 5: 50% bucket 5: 60% bucket 5: 70% bucket 5: 80% bucket 5: 90% bucket 5: 100% Sorting block of length 4175410 for bucket 5 (Using difference cover) Sorting block time: 00:00:05 Returning block of 4911174 for bucket 5 Getting block 6 of 7 Reserving size (8004870) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% Sorting block time: 00:00:04 Returning block of 4175411 for bucket 5 bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% Getting block 6 of 7 Reserving size (8004870) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 100% Sorting block of length 4817997 for bucket 6 (Using difference cover) bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 7641519 for bucket 6 (Using difference cover) Sorting block time: 00:00:05 Returning block of 4817998 for bucket 6 Getting block 7 of 7 Reserving size (8004870) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 6704686 for bucket 7 (Using difference cover) Sorting block time: 00:00:07 Returning block of 7641520 for bucket 6 Getting block 7 of 7 Reserving size (8004870) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 6097474 for bucket 7 (Using difference cover) Sorting block time: 00:00:06 Returning block of 6704687 for bucket 7 Exited Ebwt loop fchr[A]: 0 fchr[C]: 11345849 fchr[G]: 11345849 fchr[T]: 21429219 fchr[$]: 42692640 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 18428509 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 10673168 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 42692640 bwtLen: 42692641 sz: 10673160 bwtSz: 10673161 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2668291 offsSz: 10673164 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 222358 numLines: 222358 ebwtTotLen: 14230912 ebwtTotSz: 14230912 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:01:10 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 10673160 Using parameters --bmax 8004870 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 8004870 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Sorting block time: 00:00:06 Returning block of 6097475 for bucket 7 V-Sorting samples time: 00:00:01 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Exited Ebwt loop fchr[A]: 0 fchr[C]: 21429219 fchr[G]: 31392427 fchr[T]: 31392427 fchr[$]: 42692640 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 18428509 bytes to primary EBWT file: BS_GA.1.bt2 Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Wrote 10673168 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 42692640 bwtLen: 42692641 sz: 10673160 bwtSz: 10673161 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2668291 offsSz: 10673164 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 222358 numLines: 222358 ebwtTotLen: 14230912 ebwtTotSz: 14230912 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:01:11 Reading reference sizes Time reading reference sizes: 00:00:01 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: 10673160 Using parameters --bmax 8004870 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 8004870 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 6; iterating... V-Sorting samples time: 00:00:02 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: 00:00:01 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.09895e+06 (target: 8004869) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (8004870) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 4518217 for bucket 1 (Using difference cover) Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.33658e+06 (target: 8004869) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (8004870) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 2967628 for bucket 1 (Using difference cover) Sorting block time: 00:00:05 Returning block of 4518218 for bucket 1 Getting block 2 of 7 Reserving size (8004870) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 7301783 for bucket 2 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2967629 for bucket 1 Getting block 2 of 8 Reserving size (8004870) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 7048883 for bucket 2 (Using difference cover) Sorting block time: 00:00:07 Returning block of 7301784 for bucket 2 Getting block 3 of 7 Reserving size (8004870) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% Sorting block time: 00:00:07 Returning block of 7048884 for bucket 2 bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 7676290 for bucket 3 (Using difference cover) Getting block 3 of 8 Reserving size (8004870) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 4081125 for bucket 3 (Using difference cover) Sorting block time: 00:00:05 Returning block of 4081126 for bucket 3 Getting block 4 of 8 Reserving size (8004870) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% Sorting block time: 00:00:08 Returning block of 7676291 for bucket 3 bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 6731482 for bucket 4 (Using difference cover) Getting block 4 of 7 Reserving size (8004870) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 5402512 for bucket 4 (Using difference cover) Sorting block time: 00:00:07 Returning block of 6731483 for bucket 4 Sorting block time: 00:00:06 Returning block of 5402513 for bucket 4 Getting block 5 of 8 Reserving size (8004870) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% Getting block 5 of 7 Reserving size (8004870) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 20% bucket 5: 10% bucket 5: 30% bucket 5: 20% bucket 5: 40% bucket 5: 30% bucket 5: 50% bucket 5: 40% bucket 5: 50% bucket 5: 60% bucket 5: 60% bucket 5: 70% bucket 5: 70% bucket 5: 80% bucket 5: 80% bucket 5: 90% bucket 5: 90% bucket 5: 100% Sorting block of length 6390781 for bucket 5 (Using difference cover) bucket 5: 100% Sorting block of length 4339570 for bucket 5 (Using difference cover) Sorting block time: 00:00:05 Returning block of 4339571 for bucket 5 Getting block 6 of 7 Reserving size (8004870) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% bucket 6: 50% bucket 6: 60% Sorting block time: 00:00:07 Returning block of 6390782 for bucket 5 bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 5465041 for bucket 6 (Using difference cover) Getting block 6 of 8 Reserving size (8004870) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 5383222 for bucket 6 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5465042 for bucket 6 Getting block 7 of 7 Reserving size (8004870) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% Sorting block time: 00:00:05 Returning block of 5383223 for bucket 6 bucket 7: 100% Sorting block of length 7989221 for bucket 7 (Using difference cover) Getting block 7 of 8 Reserving size (8004870) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 2768842 for bucket 7 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2768843 for bucket 7 Getting block 8 of 8 Reserving size (8004870) for bucket 8 Calculating Z arrays for bucket 8 Entering block accumulator loop for bucket 8: bucket 8: 10% bucket 8: 20% bucket 8: 30% bucket 8: 40% bucket 8: 50% bucket 8: 60% bucket 8: 70% bucket 8: 80% bucket 8: 90% bucket 8: 100% Sorting block of length 7320670 for bucket 8 (Using difference cover) Sorting block time: 00:00:07 Returning block of 7989222 for bucket 7 Exited Ebwt loop fchr[A]: 0 fchr[C]: 11345849 fchr[G]: 11345849 fchr[T]: 21429219 fchr[$]: 42692640 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 18428509 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 10673168 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 42692640 bwtLen: 42692641 sz: 10673160 bwtSz: 10673161 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2668291 offsSz: 10673164 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 222358 numLines: 222358 ebwtTotLen: 14230912 ebwtTotSz: 14230912 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:01:09 Sorting block time: 00:00:05 Returning block of 7320671 for bucket 8 Exited Ebwt loop fchr[A]: 0 fchr[C]: 21429219 fchr[G]: 31392427 fchr[T]: 31392427 fchr[$]: 42692640 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 18428509 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 10673168 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 42692640 bwtLen: 42692641 sz: 10673160 bwtSz: 10673161 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2668291 offsSz: 10673164 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 222358 numLines: 222358 ebwtTotLen: 14230912 ebwtTotSz: 14230912 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:01:09Command completed. Elapsed time: 0:02:27. Running peak memory: 0.225GB. PID: 167590; Command: bismark_genome_preparation; Return code: 0; Memory used: 0.225GB > `touch /project/shefflab/genomes_parallel/hg38_chr22/bismark_bt1_index/default/_refgenie_build/hg38_chr22_bismark_bt1_index__default.flag` (167768) Command completed. Elapsed time: 0:00:00. Running peak memory: 0.225GB. PID: 167768; Command: touch; Return code: 0; Memory used: 0.0GB > `cd /project/shefflab/genomes_parallel/hg38_chr22/bismark_bt1_index/default; find . -type f -not -path './_refgenie_build*' -exec md5sum {} \; | sort -k 2 | awk '{print $1}' | md5sum` Default tag for 'hg38_chr22/bismark_bt1_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:02:28 * Total elapsed time (all runs): 0:02:27 * Peak memory (this run): 0.2254 GB * Pipeline completed time: 2019-10-17 08:20:39 Finished building asset 'bismark_bt1_index' Using 'default' as the default tag for 'hg38_chr22/bismark_bt2_index' Inputs required to build 'bismark_bt2_index': Building asset 'bismark_bt2_index' Output content: /project/shefflab/genomes_parallel/hg38_chr22; logs: /project/shefflab/genomes_parallel/hg38_chr22/bismark_bt2_index/default/_refgenie_build ### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build --genome hg38_chr22 --asset star_index bwa_index bowtie2_index bismark_bt1_index bismark_bt2_index hisat2_index --fasta /project/shefflab/www/refgenie_raw/hg38_chr22.fa.gz --gencode_gtf /project/shefflab/www/refgenie_raw/hg38_chr22_gencode.gtf.gz --ensembl_gtf /project/shefflab/www/refgenie_raw/hg38_chr22_ensembl.gtf.gz --gff /project/shefflab/www/refgenie_raw/hg38_chr22_ensembl_rb.gff.gz --refgene /project/shefflab/www/refgenie_raw/hg38_chr22_refGene.txt.gz` * Compute host: udc-ba34-36 * Working dir: /sfs/qumulo/qhome/mjs5kd/code/databio_genomes_parallel * Outfolder: /project/shefflab/genomes_parallel/hg38_chr22/bismark_bt2_index/default/_refgenie_build/ * Pipeline started at: (10-17 08:20:39) elapsed: 0.0 _TIME_ ### Version log: * Python version: 3.6.6 * Pypiper dir: `/sfs/qumulo/qhome/mjs5kd/.local/lib/python3.6/site-packages/pypiper` * Pypiper version: 0.12.1 * Pipeline dir: `/sfs/qumulo/qhome/mjs5kd/.local/bin` * Pipeline version: None ### Arguments passed to pipeline: * `asset_registry_paths`: `['star_index', 'bwa_index', 'bowtie2_index', 'bismark_bt1_index', 'bismark_bt2_index', 'hisat2_index']` * `command`: `build` * `config_file`: `/home/mjs5kd/.local/lib/python3.6/site-packages/refgenie/refgenie.yaml` * `context`: `None` * `dbnsfp`: `None` * `docker`: `False` * `ensembl_gtf`: `/project/shefflab/www/refgenie_raw/hg38_chr22_ensembl.gtf.gz` * `fasta`: `/project/shefflab/www/refgenie_raw/hg38_chr22.fa.gz` * `gencode_gtf`: `/project/shefflab/www/refgenie_raw/hg38_chr22_gencode.gtf.gz` * `genome`: `hg38_chr22` * `genome_config`: `None` * `genome_description`: `None` * `gff`: `/project/shefflab/www/refgenie_raw/hg38_chr22_ensembl_rb.gff.gz` * `logdev`: `False` * `new_start`: `False` * `outfolder`: `/project/shefflab/genomes_parallel` * `recover`: `False` * `refgene`: `/project/shefflab/www/refgenie_raw/hg38_chr22_refGene.txt.gz` * `requirements`: `False` * `silent`: `False` * `tag_description`: `None` * `tags`: `None` * `verbosity`: `None` * `volumes`: `None` ---------------------------------------- Target to produce: `/project/shefflab/genomes_parallel/hg38_chr22/bismark_bt2_index/default/_refgenie_build/hg38_chr22_bismark_bt2_index__default.flag` > `ln -sf /project/shefflab/genomes_parallel/hg38_chr22/fasta/default/hg38_chr22.fa /project/shefflab/genomes_parallel/hg38_chr22/bismark_bt2_index/default` (167795) Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB. PID: 167795; Command: ln; Return code: 0; Memory used: 0.0GB > `bismark_genome_preparation --bowtie2 /project/shefflab/genomes_parallel/hg38_chr22/bismark_bt2_index/default` (167796)

Writing bisulfite genomes out into a single MFA (multi FastA) file Bisulfite Genome Indexer version v0.19.1 (last modified 26 April 2018) Step I - Prepare genome folders - completed Total number of conversions performed: C->T: 9963208 G->A: 10083370 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! 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: 4 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: 00:00:01 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: 10673160 Using parameters --bmax 8004870 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 8004870 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples 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: 4 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: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences V-Sorting samples time: 00:00:01 Allocating rank array Ranking v-sort output Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 10673160 Using parameters --bmax 8004870 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 8004870 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes V-Sorting samples time: 00:00:01 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 0; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.09895e+06 (target: 8004869) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (8004870) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 6732952 for bucket 1 (Using difference cover) Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.09895e+06 (target: 8004869) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (8004870) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 6810255 for bucket 1 (Using difference cover) Sorting block time: 00:00:07 Returning block of 6732953 for bucket 1 Getting block 2 of 7 Reserving size (8004870) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 6839681 for bucket 2 (Using difference cover) Sorting block time: 00:00:06 Returning block of 6810256 for bucket 1 Getting block 2 of 7 Reserving size (8004870) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 7007342 for bucket 2 (Using difference cover) Sorting block time: 00:00:07 Returning block of 6839682 for bucket 2 Getting block 3 of 7 Reserving size (8004870) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 4933045 for bucket 3 (Using difference cover) Sorting block time: 00:00:07 Returning block of 7007343 for bucket 2 Getting block 3 of 7 Reserving size (8004870) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 3962325 for bucket 3 (Using difference cover) Sorting block time: 00:00:05 Returning block of 4933046 for bucket 3 Getting block 4 of 7 Reserving size (8004870) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% Sorting block time: 00:00:04 Returning block of 3962326 for bucket 3 bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 7753100 for bucket 4 (Using difference cover) Getting block 4 of 7 Reserving size (8004870) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 6998309 for bucket 4 (Using difference cover) Sorting block time: 00:00:07 Returning block of 7753101 for bucket 4 Sorting block time: 00:00:07 Returning block of 6998310 for bucket 4 Getting block 5 of 7 Reserving size (8004870) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: Getting block 5 of 7 Reserving size (8004870) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% bucket 5: 10% bucket 5: 20% bucket 5: 20% bucket 5: 30% bucket 5: 30% bucket 5: 40% bucket 5: 40% bucket 5: 50% bucket 5: 50% bucket 5: 60% bucket 5: 60% bucket 5: 70% bucket 5: 70% bucket 5: 80% bucket 5: 80% bucket 5: 90% bucket 5: 90% bucket 5: 100% Sorting block of length 4175410 for bucket 5 (Using difference cover) bucket 5: 100% Sorting block of length 4911173 for bucket 5 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4175411 for bucket 5 Getting block 6 of 7 Reserving size (8004870) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% Sorting block time: 00:00:06 Returning block of 4911174 for bucket 5 bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% Getting block 6 of 7 Reserving size (8004870) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 100% Sorting block of length 7641519 for bucket 6 (Using difference cover) bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 4817997 for bucket 6 (Using difference cover) Sorting block time: 00:00:05 Returning block of 4817998 for bucket 6 Sorting block time: 00:00:07 Returning block of 7641520 for bucket 6 Getting block 7 of 7 Reserving size (8004870) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% Getting block 7 of 7 Reserving size (8004870) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 100% Sorting block of length 6704686 for bucket 7 (Using difference cover) bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 6097474 for bucket 7 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6097475 for bucket 7 Sorting block time: 00:00:07 Returning block of 6704687 for bucket 7 Exited Ebwt loop fchr[A]: 0 fchr[C]: 21429219 fchr[G]: 31392427 fchr[T]: 31392427 fchr[$]: 42692640 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 18428509 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 10673168 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 42692640 bwtLen: 42692641 sz: 10673160 bwtSz: 10673161 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2668291 offsSz: 10673164 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 222358 numLines: 222358 ebwtTotLen: 14230912 ebwtTotSz: 14230912 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:01:11 Reading reference sizes Exited Ebwt loop fchr[A]: 0 fchr[C]: 11345849 fchr[G]: 11345849 fchr[T]: 21429219 fchr[$]: 42692640 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 18428509 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 10673168 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 42692640 bwtLen: 42692641 sz: 10673160 bwtSz: 10673161 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2668291 offsSz: 10673164 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 222358 numLines: 222358 ebwtTotLen: 14230912 ebwtTotSz: 14230912 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:01:12 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: 10673160 Using parameters --bmax 8004870 --dcv 1024 Doing ahead-of-time memory usage test Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Passed! Constructing with these parameters: --bmax 8004870 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Time to join reference sequences: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 10673160 Using parameters --bmax 8004870 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 8004870 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:01 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks V-Sorting samples time: 00:00:02 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 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Invoking Larsson-Sadakane on ranks time: 00:00:01 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.33658e+06 (target: 8004869) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (8004870) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.09895e+06 (target: 8004869) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (8004870) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 50% bucket 1: 10% bucket 1: 60% bucket 1: 20% bucket 1: 70% bucket 1: 30% bucket 1: 80% bucket 1: 40% bucket 1: 90% bucket 1: 50% bucket 1: 100% Sorting block of length 2967628 for bucket 1 (Using difference cover) bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 4518217 for bucket 1 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2967629 for bucket 1 Getting block 2 of 8 Reserving size (8004870) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 7048883 for bucket 2 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4518218 for bucket 1 Getting block 2 of 7 Reserving size (8004870) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 7301783 for bucket 2 (Using difference cover) Sorting block time: 00:00:07 Returning block of 7048884 for bucket 2 Getting block 3 of 8 Reserving size (8004870) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 4081125 for bucket 3 (Using difference cover) Sorting block time: 00:00:07 Returning block of 7301784 for bucket 2 Getting block 3 of 7 Reserving size (8004870) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 7676290 for bucket 3 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4081126 for bucket 3 Getting block 4 of 8 Reserving size (8004870) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 6731482 for bucket 4 (Using difference cover) Sorting block time: 00:00:08 Returning block of 7676291 for bucket 3 Sorting block time: 00:00:06 Returning block of 6731483 for bucket 4 Getting block 4 of 7 Reserving size (8004870) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% Getting block 5 of 8 Reserving size (8004870) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 4: 30% bucket 5: 10% bucket 4: 40% bucket 5: 20% bucket 4: 50% bucket 5: 30% bucket 4: 60% bucket 5: 40% bucket 4: 70% bucket 5: 50% bucket 4: 80% bucket 5: 60% bucket 4: 90% bucket 5: 70% bucket 4: 100% Sorting block of length 5402512 for bucket 4 (Using difference cover) bucket 5: 80% bucket 5: 90% bucket 5: 100% Sorting block of length 6390781 for bucket 5 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5402513 for bucket 4 Sorting block time: 00:00:06 Returning block of 6390782 for bucket 5 Getting block 5 of 7 Reserving size (8004870) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% bucket 5: 20% bucket 5: 30% bucket 5: 40% bucket 5: 50% bucket 5: 60% Getting block 6 of 8 Reserving size (8004870) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 5: 70% bucket 6: 10% bucket 5: 80% bucket 6: 20% bucket 5: 90% bucket 6: 30% bucket 5: 100% Sorting block of length 4339570 for bucket 5 (Using difference cover) bucket 6: 40% bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 5383222 for bucket 6 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4339571 for bucket 5 Getting block 6 of 7 Reserving size (8004870) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% Sorting block time: 00:00:05 Returning block of 5383223 for bucket 6 bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 5465041 for bucket 6 (Using difference cover) Getting block 7 of 8 Reserving size (8004870) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 2768842 for bucket 7 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2768843 for bucket 7 Getting block 8 of 8 Reserving size (8004870) for bucket 8 Calculating Z arrays for bucket 8 Entering block accumulator loop for bucket 8: bucket 8: 10% bucket 8: 20% bucket 8: 30% bucket 8: 40% bucket 8: 50% bucket 8: 60% bucket 8: 70% bucket 8: 80% bucket 8: 90% bucket 8: 100% Sorting block of length 7320670 for bucket 8 (Using difference cover) Sorting block time: 00:00:06 Returning block of 5465042 for bucket 6 Getting block 7 of 7 Reserving size (8004870) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 7989221 for bucket 7 (Using difference cover) Sorting block time: 00:00:08 Returning block of 7320671 for bucket 8 Exited Ebwt loop fchr[A]: 0 fchr[C]: 21429219 fchr[G]: 31392427 fchr[T]: 31392427 fchr[$]: 42692640 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 18428509 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 10673168 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 42692640 bwtLen: 42692641 sz: 10673160 bwtSz: 10673161 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2668291 offsSz: 10673164 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 222358 numLines: 222358 ebwtTotLen: 14230912 ebwtTotSz: 14230912 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:01:07 Sorting block time: 00:00:08 Returning block of 7989222 for bucket 7 Exited Ebwt loop fchr[A]: 0 fchr[C]: 11345849 fchr[G]: 11345849 fchr[T]: 21429219 fchr[$]: 42692640 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 18428509 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 10673168 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 42692640 bwtLen: 42692641 sz: 10673160 bwtSz: 10673161 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2668291 offsSz: 10673164 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 222358 numLines: 222358 ebwtTotLen: 14230912 ebwtTotSz: 14230912 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:01:09Command completed. Elapsed time: 0:02:27. Running peak memory: 0.21GB. PID: 167796; Command: bismark_genome_preparation; Return code: 0; Memory used: 0.21GB > `touch /project/shefflab/genomes_parallel/hg38_chr22/bismark_bt2_index/default/_refgenie_build/hg38_chr22_bismark_bt2_index__default.flag` (167973) Command completed. Elapsed time: 0:00:00. Running peak memory: 0.21GB. PID: 167973; Command: touch; Return code: 0; Memory used: 0.0GB > `cd /project/shefflab/genomes_parallel/hg38_chr22/bismark_bt2_index/default; find . -type f -not -path './_refgenie_build*' -exec md5sum {} \; | sort -k 2 | awk '{print $1}' | md5sum` Default tag for 'hg38_chr22/bismark_bt2_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:02:27 * Total elapsed time (all runs): 0:02:27 * Peak memory (this run): 0.2099 GB * Pipeline completed time: 2019-10-17 08:23:07 Finished building asset 'bismark_bt2_index' Using 'default' as the default tag for 'hg38_chr22/hisat2_index' Inputs required to build 'hisat2_index': Building asset 'hisat2_index' Output content: /project/shefflab/genomes_parallel/hg38_chr22; logs: /project/shefflab/genomes_parallel/hg38_chr22/hisat2_index/default/_refgenie_build ### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build --genome hg38_chr22 --asset star_index bwa_index bowtie2_index bismark_bt1_index bismark_bt2_index hisat2_index --fasta /project/shefflab/www/refgenie_raw/hg38_chr22.fa.gz --gencode_gtf /project/shefflab/www/refgenie_raw/hg38_chr22_gencode.gtf.gz --ensembl_gtf /project/shefflab/www/refgenie_raw/hg38_chr22_ensembl.gtf.gz --gff /project/shefflab/www/refgenie_raw/hg38_chr22_ensembl_rb.gff.gz --refgene /project/shefflab/www/refgenie_raw/hg38_chr22_refGene.txt.gz` * Compute host: udc-ba34-36 * Working dir: /sfs/qumulo/qhome/mjs5kd/code/databio_genomes_parallel * Outfolder: /project/shefflab/genomes_parallel/hg38_chr22/hisat2_index/default/_refgenie_build/ * Pipeline started at: (10-17 08:23:07) elapsed: 0.0 _TIME_ ### Version log: * Python version: 3.6.6 * Pypiper dir: `/sfs/qumulo/qhome/mjs5kd/.local/lib/python3.6/site-packages/pypiper` * Pypiper version: 0.12.1 * Pipeline dir: `/sfs/qumulo/qhome/mjs5kd/.local/bin` * Pipeline version: None ### Arguments passed to pipeline: * `asset_registry_paths`: `['star_index', 'bwa_index', 'bowtie2_index', 'bismark_bt1_index', 'bismark_bt2_index', 'hisat2_index']` * `command`: `build` * `config_file`: `/home/mjs5kd/.local/lib/python3.6/site-packages/refgenie/refgenie.yaml` * `context`: `None` * `dbnsfp`: `None` * `docker`: `False` * `ensembl_gtf`: `/project/shefflab/www/refgenie_raw/hg38_chr22_ensembl.gtf.gz` * `fasta`: `/project/shefflab/www/refgenie_raw/hg38_chr22.fa.gz` * `gencode_gtf`: `/project/shefflab/www/refgenie_raw/hg38_chr22_gencode.gtf.gz` * `genome`: `hg38_chr22` * `genome_config`: `None` * `genome_description`: `None` * `gff`: `/project/shefflab/www/refgenie_raw/hg38_chr22_ensembl_rb.gff.gz` * `logdev`: `False` * `new_start`: `False` * `outfolder`: `/project/shefflab/genomes_parallel` * `recover`: `False` * `refgene`: `/project/shefflab/www/refgenie_raw/hg38_chr22_refGene.txt.gz` * `requirements`: `False` * `silent`: `False` * `tag_description`: `None` * `tags`: `None` * `verbosity`: `None` * `volumes`: `None` ---------------------------------------- Target to produce: `/project/shefflab/genomes_parallel/hg38_chr22/hisat2_index/default/_refgenie_build/hg38_chr22_hisat2_index__default.flag` > `hisat2-build /project/shefflab/genomes_parallel/hg38_chr22/fasta/default/hg38_chr22.fa /project/shefflab/genomes_parallel/hg38_chr22/hisat2_index/default/hg38_chr22` (167999)

Settings: Output files: "/project/shefflab/genomes_parallel/hg38_chr22/hisat2_index/default/hg38_chr22.*.ht2" 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 Local offset rate: 3 (one in 8) Local fTable chars: 6 Local sequence length: 57344 Local sequence overlap between two consecutive indexes: 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: /project/shefflab/genomes_parallel/hg38_chr22/fasta/default/hg38_chr22.fa 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: 00:00:01 Time to read SNPs and splice sites: 00:00:00 Using parameters --bmax 8004870 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 8004870 --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: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 5; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.33658e+06 (target: 8004869) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering GFM loop Getting block 1 of 8 Reserving size (8004870) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 6672392 for bucket 1 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6672393 for bucket 1 Getting block 2 of 8 Reserving size (8004870) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 7588704 for bucket 2 (Using difference cover) Sorting block time: 00:00:03 Returning block of 7588705 for bucket 2 Getting block 3 of 8 Reserving size (8004870) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 7761634 for bucket 3 (Using difference cover) Sorting block time: 00:00:03 Returning block of 7761635 for bucket 3 Getting block 4 of 8 Reserving size (8004870) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 2627464 for bucket 4 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2627465 for bucket 4 Getting block 5 of 8 Reserving size (8004870) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% bucket 5: 20% bucket 5: 30% bucket 5: 40% bucket 5: 50% bucket 5: 60% bucket 5: 70% bucket 5: 80% bucket 5: 90% bucket 5: 100% Sorting block of length 6003157 for bucket 5 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6003158 for bucket 5 Getting block 6 of 8 Reserving size (8004870) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 2681253 for bucket 6 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2681254 for bucket 6 Getting block 7 of 8 Reserving size (8004870) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 6665458 for bucket 7 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6665459 for bucket 7 Getting block 8 of 8 Reserving size (8004870) for bucket 8 Calculating Z arrays for bucket 8 Entering block accumulator loop for bucket 8: bucket 8: 10% bucket 8: 20% bucket 8: 30% bucket 8: 40% bucket 8: 50% bucket 8: 60% bucket 8: 70% bucket 8: 80% bucket 8: 90% bucket 8: 100% Sorting block of length 2692571 for bucket 8 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2692572 for bucket 8 Exited GFM loop fchr[A]: 0 fchr[C]: 11345849 fchr[G]: 21309057 fchr[T]: 31392427 fchr[$]: 42692640 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 18433322 bytes to primary GFM file: /project/shefflab/genomes_parallel/hg38_chr22/hisat2_index/default/hg38_chr22.1.ht2 Wrote 10673168 bytes to secondary GFM file: /project/shefflab/genomes_parallel/hg38_chr22/hisat2_index/default/hg38_chr22.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Returning from initFromVector Wrote 18962269 bytes to primary GFM file: /project/shefflab/genomes_parallel/hg38_chr22/hisat2_index/default/hg38_chr22.5.ht2 Wrote 10860276 bytes to secondary GFM file: /project/shefflab/genomes_parallel/hg38_chr22/hisat2_index/default/hg38_chr22.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HierEbwt constructor Headers: len: 42692640 gbwtLen: 42692641 nodes: 42692641 sz: 10673160 gbwtSz: 10673161 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2668291 offsSz: 10673164 lineSz: 64 sideSz: 64 sideGbwtSz: 48 sideGbwtLen: 192 numSides: 222358 numLines: 222358 gbwtTotLen: 14230912 gbwtTotSz: 14230912 reverse: 0 linearFM: Yes Total time for call to driver() for forward index: 00:00:40Command completed. Elapsed time: 0:00:40. Running peak memory: 0.096GB. PID: 167999; Command: hisat2-build; Return code: 0; Memory used: 0.096GB > `touch /project/shefflab/genomes_parallel/hg38_chr22/hisat2_index/default/_refgenie_build/hg38_chr22_hisat2_index__default.flag` (168009) Command completed. Elapsed time: 0:00:00. Running peak memory: 0.096GB. PID: 168009; Command: touch; Return code: 0; Memory used: 0.0GB > `cd /project/shefflab/genomes_parallel/hg38_chr22/hisat2_index/default; find . -type f -not -path './_refgenie_build*' -exec md5sum {} \; | sort -k 2 | awk '{print $1}' | md5sum` Default tag for 'hg38_chr22/hisat2_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:40 * Total elapsed time (all runs): 0:00:40 * Peak memory (this run): 0.0959 GB * Pipeline completed time: 2019-10-17 08:23:47 Finished building asset 'hisat2_index'