[seanb80@n2193 BGI_Small_Assembly]$ /gscratch/srlab/programs/bowtie2-2.1.0/bowtie2-build Ostrea_lurida.scafSeq BGI_Oly_Small Settings: Output files: "BGI_Oly_Small.*.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: Ostrea_lurida.scafSeq Reading reference sizes Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:04 bmax according to bmaxDivN setting: 159851748 Using parameters --bmax 119888811 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 119888811 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:09 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:02 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:05 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 Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:21 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:18 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 7.99259e+07 (target: 119888810) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:06 Sorting block of length 116016512 (Using difference cover) Sorting block time: 00:00:25 Returning block of 116016513 Getting block 2 of 8 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:07 Sorting block of length 11223891 (Using difference cover) Sorting block time: 00:00:03 Returning block of 11223892 Getting block 3 of 8 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:09 Sorting block of length 113346107 (Using difference cover) Sorting block time: 00:00:24 Returning block of 113346108 Getting block 4 of 8 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:09 Sorting block of length 69406192 (Using difference cover) Sorting block time: 00:00:14 Returning block of 69406193 Getting block 5 of 8 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:09 Sorting block of length 73042110 (Using difference cover) Sorting block time: 00:00:15 Returning block of 73042111 Getting block 6 of 8 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:10 Sorting block of length 106084568 (Using difference cover) Sorting block time: 00:00:22 Returning block of 106084569 Getting block 7 of 8 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:09 Sorting block of length 61768278 (Using difference cover) Sorting block time: 00:00:13 Returning block of 61768279 Getting block 8 of 8 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:07 Sorting block of length 88519329 (Using difference cover) Sorting block time: 00:00:18 Returning block of 88519330 Exited Ebwt loop fchr[A]: 0 fchr[C]: 205278688 fchr[G]: 319794570 fchr[T]: 434310904 fchr[$]: 639406994 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 249415523 bytes to primary EBWT file: BGI_Oly_Small.1.bt2 Wrote 159851756 bytes to secondary EBWT file: BGI_Oly_Small.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 639406994 bwtLen: 639406995 sz: 159851749 bwtSz: 159851749 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 39962938 offsSz: 159851752 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3330245 numLines: 3330245 ebwtTotLen: 213135680 ebwtTotSz: 213135680 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:05:01 Reading reference sizes Time reading reference sizes: 00:00:04 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:04 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 159851748 Using parameters --bmax 119888811 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 119888811 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:09 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:02 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:05 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 Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:22 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:18 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 9.13439e+07 (target: 119888810) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:06 Sorting block of length 104088635 (Using difference cover) Sorting block time: 00:00:22 Returning block of 104088636 Getting block 2 of 7 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:08 Sorting block of length 101190051 (Using difference cover) Sorting block time: 00:00:22 Returning block of 101190052 Getting block 3 of 7 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:10 Sorting block of length 110737392 (Using difference cover) Sorting block time: 00:00:23 Returning block of 110737393 Getting block 4 of 7 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:10 Sorting block of length 97035638 (Using difference cover) Sorting block time: 00:00:20 Returning block of 97035639 Getting block 5 of 7 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:09 Sorting block of length 43823266 (Using difference cover) Sorting block time: 00:00:09 Returning block of 43823267 Getting block 6 of 7 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:09 Sorting block of length 91809344 (Using difference cover) Sorting block time: 00:00:19 Returning block of 91809345 Getting block 7 of 7 Reserving size (119888811) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:06 Sorting block of length 90722662 (Using difference cover) Sorting block time: 00:00:19 Returning block of 90722663 Exited Ebwt loop fchr[A]: 0 fchr[C]: 205278688 fchr[G]: 319794570 fchr[T]: 434310904 fchr[$]: 639406994 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 249415523 bytes to primary EBWT file: BGI_Oly_Small.rev.1.bt2 Wrote 159851756 bytes to secondary EBWT file: BGI_Oly_Small.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 639406994 bwtLen: 639406995 sz: 159851749 bwtSz: 159851749 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 39962938 offsSz: 159851752 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3330245 numLines: 3330245 ebwtTotLen: 213135680 ebwtTotSz: 213135680 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:04:55