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: 640 G->A: 772 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: 00:00:00 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: 580 Using parameters --bmax 435 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 435 --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 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 2, merged 5; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 3; 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 Avg bucket size: 289.25 (target: 434) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (435) 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 110 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 111 for bucket 1 Getting block 2 of 8 Reserving size (435) 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 429 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 430 for bucket 2 Getting block 3 of 8 Reserving size (435) 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 400 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 401 for bucket 3 Getting block 4 of 8 Reserving size (435) 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 395 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 396 for bucket 4 Getting block 5 of 8 Reserving size (435) 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 163 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 164 for bucket 5 Getting block 6 of 8 Reserving size (435) 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 327 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 328 for bucket 6 Getting block 7 of 8 Reserving size (435) 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 325 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 326 for bucket 7 Getting block 8 of 8 Reserving size (435) 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 165 for bucket 8 (Using difference cover) Sorting block time: 00:00:00 Returning block of 166 for bucket 8 Exited Ebwt loop fchr[A]: 0 fchr[C]: 558 fchr[G]: 558 fchr[T]: 1330 fchr[$]: 2321 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4195585 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 588 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2321 bwtLen: 2322 sz: 581 bwtSz: 581 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 146 offsSz: 584 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 13 numLines: 13 ebwtTotLen: 832 ebwtTotSz: 832 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: 580 Using parameters --bmax 435 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 435 --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 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 2, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 289.25 (target: 434) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (435) 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 430 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 431 for bucket 1 Getting block 2 of 8 Reserving size (435) 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 427 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 428 for bucket 2 Getting block 3 of 8 Reserving size (435) 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 102 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 103 for bucket 3 Getting block 4 of 8 Reserving size (435) 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 386 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 387 for bucket 4 Getting block 5 of 8 Reserving size (435) 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 319 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 320 for bucket 5 Getting block 6 of 8 Reserving size (435) 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 130 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 131 for bucket 6 Getting block 7 of 8 Reserving size (435) 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 394 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 395 for bucket 7 Getting block 8 of 8 Reserving size (435) 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 126 for bucket 8 (Using difference cover) Sorting block time: 00:00:00 Returning block of 127 for bucket 8 Exited Ebwt loop fchr[A]: 0 fchr[C]: 558 fchr[G]: 558 fchr[T]: 1330 fchr[$]: 2321 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4195585 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 588 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2321 bwtLen: 2322 sz: 581 bwtSz: 581 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 146 offsSz: 584 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 13 numLines: 13 ebwtTotLen: 832 ebwtTotSz: 832 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:00 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 Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 580 Using parameters --bmax 435 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 435 --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 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 0; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 330.714 (target: 434) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (435) 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 272 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 273 for bucket 1 Getting block 2 of 7 Reserving size (435) 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 294 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 295 for bucket 2 Getting block 3 of 7 Reserving size (435) 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 294 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 295 for bucket 3 Getting block 4 of 7 Reserving size (435) 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 428 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 429 for bucket 4 Getting block 5 of 7 Reserving size (435) 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 350 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 351 for bucket 5 Getting block 6 of 7 Reserving size (435) 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 310 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 311 for bucket 6 Getting block 7 of 7 Reserving size (435) 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 367 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 368 for bucket 7 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1330 fchr[G]: 1970 fchr[T]: 1970 fchr[$]: 2321 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4195585 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 588 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2321 bwtLen: 2322 sz: 581 bwtSz: 581 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 146 offsSz: 584 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 13 numLines: 13 ebwtTotLen: 832 ebwtTotSz: 832 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: 580 Using parameters --bmax 435 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 435 --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 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: 289.25 (target: 434) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (435) 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 338 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 339 for bucket 1 Getting block 2 of 8 Reserving size (435) 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 282 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 283 for bucket 2 Getting block 3 of 8 Reserving size (435) 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 357 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 358 for bucket 3 Getting block 4 of 8 Reserving size (435) 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 386 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 387 for bucket 4 Getting block 5 of 8 Reserving size (435) 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 298 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 299 for bucket 5 Getting block 6 of 8 Reserving size (435) 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 213 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 214 for bucket 6 Getting block 7 of 8 Reserving size (435) 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 345 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 346 for bucket 7 Getting block 8 of 8 Reserving size (435) 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 95 for bucket 8 (Using difference cover) Sorting block time: 00:00:00 Returning block of 96 for bucket 8 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1330 fchr[G]: 1970 fchr[T]: 1970 fchr[$]: 2321 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4195585 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 588 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2321 bwtLen: 2322 sz: 581 bwtSz: 581 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 146 offsSz: 584 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 13 numLines: 13 ebwtTotLen: 832 ebwtTotSz: 832 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:00Command completed. Elapsed time: 0:00:06. Running peak memory: 0.008GB. PID: 172885; Command: bismark_genome_preparation; Return code: 0; Memory used: 0.008GB > `touch /project/shefflab/genomes_parallel/human_alu/bismark_bt1_index/default/_refgenie_build/human_alu_bismark_bt1_index__default.flag` (172927) Command completed. Elapsed time: 0:00:00. Running peak memory: 0.008GB. PID: 172927; Command: touch; Return code: 0; Memory used: 0.0GB > `cd /project/shefflab/genomes_parallel/human_alu/bismark_bt1_index/default; find . -type f -not -path './_refgenie_build*' -exec md5sum {} \; | sort -k 2 | awk '{print $1}' | md5sum` Default tag for 'human_alu/bismark_bt1_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:06 * Total elapsed time (all runs): 0:00:06 * Peak memory (this run): 0.0083 GB * Pipeline completed time: 2019-10-17 08:56:43 Finished building asset 'bismark_bt1_index' Using 'default' as the default tag for 'human_alu/bismark_bt2_index' Inputs required to build 'bismark_bt2_index': Building asset 'bismark_bt2_index' Output content: /project/shefflab/genomes_parallel/human_alu; logs: /project/shefflab/genomes_parallel/human_alu/bismark_bt2_index/default/_refgenie_build ### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build --genome human_alu --asset bwa_index bowtie2_index bismark_bt1_index bismark_bt2_index hisat2_index --fasta /project/shefflab/www/refgenie_raw/human_alu.fa.gz --gencode_gtf /project/shefflab/www/refgenie_raw/human_alu_gencode.gtf.gz --ensembl_gtf /project/shefflab/www/refgenie_raw/human_alu_ensembl.gtf.gz --gff /project/shefflab/www/refgenie_raw/human_alu_ensembl_rb.gff.gz --refgene /project/shefflab/www/refgenie_raw/human_alu_refGene.txt.gz` * Compute host: udc-ba34-36 * Working dir: /sfs/qumulo/qhome/mjs5kd/code/databio_genomes_parallel * Outfolder: /project/shefflab/genomes_parallel/human_alu/bismark_bt2_index/default/_refgenie_build/ * Pipeline started at: (10-17 08:56:43) 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`: `['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/human_alu_ensembl.gtf.gz` * `fasta`: `/project/shefflab/www/refgenie_raw/human_alu.fa.gz` * `gencode_gtf`: `/project/shefflab/www/refgenie_raw/human_alu_gencode.gtf.gz` * `genome`: `human_alu` * `genome_config`: `None` * `genome_description`: `None` * `gff`: `/project/shefflab/www/refgenie_raw/human_alu_ensembl_rb.gff.gz` * `logdev`: `False` * `new_start`: `False` * `outfolder`: `/project/shefflab/genomes_parallel` * `recover`: `False` * `refgene`: `/project/shefflab/www/refgenie_raw/human_alu_refGene.txt.gz` * `requirements`: `False` * `silent`: `False` * `tag_description`: `None` * `tags`: `None` * `verbosity`: `None` * `volumes`: `None` ---------------------------------------- Target to produce: `/project/shefflab/genomes_parallel/human_alu/bismark_bt2_index/default/_refgenie_build/human_alu_bismark_bt2_index__default.flag` > `ln -sf /project/shefflab/genomes_parallel/human_alu/fasta/default/human_alu.fa /project/shefflab/genomes_parallel/human_alu/bismark_bt2_index/default` (172953) Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB. PID: 172953; Command: ln; Return code: 0; Memory used: 0.0GB > `bismark_genome_preparation --bowtie2 /project/shefflab/genomes_parallel/human_alu/bismark_bt2_index/default` (172954)

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: 640 G->A: 772 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: 00:00:00 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: 580 Using parameters --bmax 435 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 435 --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 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 2, merged 5; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 3; 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 Avg bucket size: 289.25 (target: 434) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (435) 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 110 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 111 for bucket 1 Getting block 2 of 8 Reserving size (435) 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 429 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 430 for bucket 2 Getting block 3 of 8 Reserving size (435) 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 400 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 401 for bucket 3 Getting block 4 of 8 Reserving size (435) 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 395 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 396 for bucket 4 Getting block 5 of 8 Reserving size (435) 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 163 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 164 for bucket 5 Getting block 6 of 8 Reserving size (435) 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 327 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 328 for bucket 6 Getting block 7 of 8 Reserving size (435) 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 325 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 326 for bucket 7 Getting block 8 of 8 Reserving size (435) 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 165 for bucket 8 (Using difference cover) Sorting block time: 00:00:00 Returning block of 166 for bucket 8 Exited Ebwt loop fchr[A]: 0 fchr[C]: 558 fchr[G]: 558 fchr[T]: 1330 fchr[$]: 2321 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4195585 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 588 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2321 bwtLen: 2322 sz: 581 bwtSz: 581 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 146 offsSz: 584 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 13 numLines: 13 ebwtTotLen: 832 ebwtTotSz: 832 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: 580 Using parameters --bmax 435 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 435 --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 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 2, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 289.25 (target: 434) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (435) 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 430 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 431 for bucket 1 Getting block 2 of 8 Reserving size (435) 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 427 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 428 for bucket 2 Getting block 3 of 8 Reserving size (435) 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 102 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 103 for bucket 3 Getting block 4 of 8 Reserving size (435) 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 386 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 387 for bucket 4 Getting block 5 of 8 Reserving size (435) 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 319 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 320 for bucket 5 Getting block 6 of 8 Reserving size (435) 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 130 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 131 for bucket 6 Getting block 7 of 8 Reserving size (435) 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 394 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 395 for bucket 7 Getting block 8 of 8 Reserving size (435) 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 126 for bucket 8 (Using difference cover) Sorting block time: 00:00:00 Returning block of 127 for bucket 8 Exited Ebwt loop fchr[A]: 0 fchr[C]: 558 fchr[G]: 558 fchr[T]: 1330 fchr[$]: 2321 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4195585 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 588 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2321 bwtLen: 2322 sz: 581 bwtSz: 581 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 146 offsSz: 584 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 13 numLines: 13 ebwtTotLen: 832 ebwtTotSz: 832 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:01 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 Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 580 Using parameters --bmax 435 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 435 --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 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 0; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 330.714 (target: 434) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (435) 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 272 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 273 for bucket 1 Getting block 2 of 7 Reserving size (435) 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 294 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 295 for bucket 2 Getting block 3 of 7 Reserving size (435) 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 294 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 295 for bucket 3 Getting block 4 of 7 Reserving size (435) 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 428 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 429 for bucket 4 Getting block 5 of 7 Reserving size (435) 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 350 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 351 for bucket 5 Getting block 6 of 7 Reserving size (435) 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 310 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 311 for bucket 6 Getting block 7 of 7 Reserving size (435) 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 367 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 368 for bucket 7 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1330 fchr[G]: 1970 fchr[T]: 1970 fchr[$]: 2321 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4195585 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 588 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2321 bwtLen: 2322 sz: 581 bwtSz: 581 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 146 offsSz: 584 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 13 numLines: 13 ebwtTotLen: 832 ebwtTotSz: 832 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: 580 Using parameters --bmax 435 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 435 --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 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: 289.25 (target: 434) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (435) 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 338 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 339 for bucket 1 Getting block 2 of 8 Reserving size (435) 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 282 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 283 for bucket 2 Getting block 3 of 8 Reserving size (435) 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 357 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 358 for bucket 3 Getting block 4 of 8 Reserving size (435) 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 386 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 387 for bucket 4 Getting block 5 of 8 Reserving size (435) 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 298 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 299 for bucket 5 Getting block 6 of 8 Reserving size (435) 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 213 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 214 for bucket 6 Getting block 7 of 8 Reserving size (435) 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 345 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 346 for bucket 7 Getting block 8 of 8 Reserving size (435) 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 95 for bucket 8 (Using difference cover) Sorting block time: 00:00:00 Returning block of 96 for bucket 8 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1330 fchr[G]: 1970 fchr[T]: 1970 fchr[$]: 2321 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4195585 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 588 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2321 bwtLen: 2322 sz: 581 bwtSz: 581 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 146 offsSz: 584 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 13 numLines: 13 ebwtTotLen: 832 ebwtTotSz: 832 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:01Command completed. Elapsed time: 0:00:06. Running peak memory: 0.008GB. PID: 172954; Command: bismark_genome_preparation; Return code: 0; Memory used: 0.008GB > `touch /project/shefflab/genomes_parallel/human_alu/bismark_bt2_index/default/_refgenie_build/human_alu_bismark_bt2_index__default.flag` (172979) Command completed. Elapsed time: 0:00:00. Running peak memory: 0.008GB. PID: 172979; Command: touch; Return code: 0; Memory used: 0.0GB > `cd /project/shefflab/genomes_parallel/human_alu/bismark_bt2_index/default; find . -type f -not -path './_refgenie_build*' -exec md5sum {} \; | sort -k 2 | awk '{print $1}' | md5sum` Default tag for 'human_alu/bismark_bt2_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:06 * Total elapsed time (all runs): 0:00:06 * Peak memory (this run): 0.0084 GB * Pipeline completed time: 2019-10-17 08:56:49 Finished building asset 'bismark_bt2_index' Using 'default' as the default tag for 'human_alu/hisat2_index' Inputs required to build 'hisat2_index': Building asset 'hisat2_index' Output content: /project/shefflab/genomes_parallel/human_alu; logs: /project/shefflab/genomes_parallel/human_alu/hisat2_index/default/_refgenie_build ### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build --genome human_alu --asset bwa_index bowtie2_index bismark_bt1_index bismark_bt2_index hisat2_index --fasta /project/shefflab/www/refgenie_raw/human_alu.fa.gz --gencode_gtf /project/shefflab/www/refgenie_raw/human_alu_gencode.gtf.gz --ensembl_gtf /project/shefflab/www/refgenie_raw/human_alu_ensembl.gtf.gz --gff /project/shefflab/www/refgenie_raw/human_alu_ensembl_rb.gff.gz --refgene /project/shefflab/www/refgenie_raw/human_alu_refGene.txt.gz` * Compute host: udc-ba34-36 * Working dir: /sfs/qumulo/qhome/mjs5kd/code/databio_genomes_parallel * Outfolder: /project/shefflab/genomes_parallel/human_alu/hisat2_index/default/_refgenie_build/ * Pipeline started at: (10-17 08:56:49) 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`: `['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/human_alu_ensembl.gtf.gz` * `fasta`: `/project/shefflab/www/refgenie_raw/human_alu.fa.gz` * `gencode_gtf`: `/project/shefflab/www/refgenie_raw/human_alu_gencode.gtf.gz` * `genome`: `human_alu` * `genome_config`: `None` * `genome_description`: `None` * `gff`: `/project/shefflab/www/refgenie_raw/human_alu_ensembl_rb.gff.gz` * `logdev`: `False` * `new_start`: `False` * `outfolder`: `/project/shefflab/genomes_parallel` * `recover`: `False` * `refgene`: `/project/shefflab/www/refgenie_raw/human_alu_refGene.txt.gz` * `requirements`: `False` * `silent`: `False` * `tag_description`: `None` * `tags`: `None` * `verbosity`: `None` * `volumes`: `None` ---------------------------------------- Target to produce: `/project/shefflab/genomes_parallel/human_alu/hisat2_index/default/_refgenie_build/human_alu_hisat2_index__default.flag` > `hisat2-build /project/shefflab/genomes_parallel/human_alu/fasta/default/human_alu.fa /project/shefflab/genomes_parallel/human_alu/hisat2_index/default/human_alu` (173006)

Settings: Output files: "/project/shefflab/genomes_parallel/human_alu/hisat2_index/default/human_alu.*.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/human_alu/fasta/default/human_alu.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: 00:00:00 Time to read SNPs and splice sites: 00:00:00 Using parameters --bmax 435 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 435 --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 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 2, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 2; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 2; 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: 289.25 (target: 434) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering GFM loop Getting block 1 of 8 Reserving size (435) 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 251 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 252 for bucket 1 Getting block 2 of 8 Reserving size (435) 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 313 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 314 for bucket 2 Getting block 3 of 8 Reserving size (435) 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 261 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 262 for bucket 3 Getting block 4 of 8 Reserving size (435) 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 217 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 218 for bucket 4 Getting block 5 of 8 Reserving size (435) 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 432 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 433 for bucket 5 Getting block 6 of 8 Reserving size (435) 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 229 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 230 for bucket 6 Getting block 7 of 8 Reserving size (435) 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 300 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 301 for bucket 7 Getting block 8 of 8 Reserving size (435) 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 311 for bucket 8 (Using difference cover) Sorting block time: 00:00:00 Returning block of 312 for bucket 8 Exited GFM loop fchr[A]: 0 fchr[C]: 558 fchr[G]: 1198 fchr[T]: 1970 fchr[$]: 2321 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 4195966 bytes to primary GFM file: /project/shefflab/genomes_parallel/human_alu/hisat2_index/default/human_alu.1.ht2 Wrote 588 bytes to secondary GFM file: /project/shefflab/genomes_parallel/human_alu/hisat2_index/default/human_alu.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Returning from initFromVector Wrote 67165 bytes to primary GFM file: /project/shefflab/genomes_parallel/human_alu/hisat2_index/default/human_alu.5.ht2 Wrote 596 bytes to secondary GFM file: /project/shefflab/genomes_parallel/human_alu/hisat2_index/default/human_alu.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HierEbwt constructor Headers: len: 2321 gbwtLen: 2322 nodes: 2322 sz: 581 gbwtSz: 581 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 146 offsSz: 584 lineSz: 64 sideSz: 64 sideGbwtSz: 48 sideGbwtLen: 192 numSides: 13 numLines: 13 gbwtTotLen: 832 gbwtTotSz: 832 reverse: 0 linearFM: Yes Total time for call to driver() for forward index: 00:00:00Command completed. Elapsed time: 0:00:00. Running peak memory: 0.005GB. PID: 173006; Command: hisat2-build; Return code: 0; Memory used: 0.005GB > `touch /project/shefflab/genomes_parallel/human_alu/hisat2_index/default/_refgenie_build/human_alu_hisat2_index__default.flag` (173007) Command completed. Elapsed time: 0:00:00. Running peak memory: 0.005GB. PID: 173007; Command: touch; Return code: 0; Memory used: 0.0GB > `cd /project/shefflab/genomes_parallel/human_alu/hisat2_index/default; find . -type f -not -path './_refgenie_build*' -exec md5sum {} \; | sort -k 2 | awk '{print $1}' | md5sum` Default tag for 'human_alu/hisat2_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:01 * Total elapsed time (all runs): 0:00:00 * Peak memory (this run): 0.0054 GB * Pipeline completed time: 2019-10-17 08:56:50 Finished building asset 'hisat2_index'