========================================================== Starting on : Tue Sep 1 20:10:57 EDT 2020 Running on node : scc-kb3 Current job ID : 9166325 Current job name : mm10_bowtie Task index number : ========================================================== Settings: Output files: "genome.*.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.fa Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:50 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:29 bmax according to bmaxDivN setting: 663217578 Using parameters --bmax 497413184 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 497413184 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:06:09 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:01:45 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:01:51 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: 2.65287e+09 (target: 497413183) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 2652870314 for bucket 1 (Using difference cover) Sorting block time: 01:20:16 Returning block of 2652870315 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 773305605 fchr[G]: 1325972558 fchr[T]: 1878682421 fchr[$]: 2652870314 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 888499392 bytes to primary EBWT file: genome.1.bt2 Wrote 663217584 bytes to secondary EBWT file: genome.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2652870314 bwtLen: 2652870315 sz: 663217579 bwtSz: 663217579 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 165804395 offsSz: 663217580 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 13817033 numLines: 13817033 ebwtTotLen: 884290112 ebwtTotSz: 884290112 color: 0 reverse: 0 Total time for call to driver() for forward index: 01:50:19 Reading reference sizes Time reading reference sizes: 00:00:29 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:28 Time to reverse reference sequence: 00:00:08 bmax according to bmaxDivN setting: 663217578 Using parameters --bmax 497413184 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 497413184 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:03:45 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:46 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:01:09 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: 2.65287e+09 (target: 497413183) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 2652870314 for bucket 1 (Using difference cover) Sorting block time: 01:00:51 Returning block of 2652870315 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 773305605 fchr[G]: 1325972558 fchr[T]: 1878682421 fchr[$]: 2652870314 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 888499392 bytes to primary EBWT file: genome.rev.1.bt2 Wrote 663217584 bytes to secondary EBWT file: genome.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2652870314 bwtLen: 2652870315 sz: 663217579 bwtSz: 663217579 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 165804395 offsSz: 663217580 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 13817033 numLines: 13817033 ebwtTotLen: 884290112 ebwtTotSz: 884290112 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 02:30:41 Finished .............. Wed Sep 2 00:31:59 EDT 2020