Settings: Output files: "/scratch/8792817.1.linga/tophat2/tmp/segment_juncs.*.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: /scratch/8792817.1.linga/tophat2/tmp/segment_juncs.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 bmax according to bmaxDivN setting: 2493262 Using parameters --bmax 1869947 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1869947 --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 Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.42472e+06 (target: 1869946) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1869947) 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: 00:00:00 Sorting block of length 953388 (Using difference cover) Sorting block time: 00:00:00 Returning block of 953389 Getting block 2 of 7 Reserving size (1869947) 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: 00:00:00 Sorting block of length 1520914 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1520915 Getting block 3 of 7 Reserving size (1869947) 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: 00:00:00 Sorting block of length 1374681 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1374682 Getting block 4 of 7 Reserving size (1869947) 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: 00:00:00 Sorting block of length 1048411 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1048412 Getting block 5 of 7 Reserving size (1869947) 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: 00:00:00 Sorting block of length 1683614 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1683615 Getting block 6 of 7 Reserving size (1869947) 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: 00:00:00 Sorting block of length 1580925 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1580926 Getting block 7 of 7 Reserving size (1869947) 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: 00:00:00 Sorting block of length 1811111 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1811112 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2472577 fchr[G]: 4982075 fchr[T]: 7494532 fchr[$]: 9973050 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 20978418 bytes to primary EBWT file: /scratch/8792817.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2493268 bytes to secondary EBWT file: /scratch/8792817.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 9973050 bwtLen: 9973051 sz: 2493263 bwtSz: 2493263 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 623316 offsSz: 2493264 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 51943 numLines: 51943 ebwtTotLen: 3324352 ebwtTotSz: 3324352 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:08 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: 2493262 Using parameters --bmax 1869947 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1869947 --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 Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.24663e+06 (target: 1869946) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1869947) 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: 00:00:00 Sorting block of length 1418927 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1418928 Getting block 2 of 8 Reserving size (1869947) 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: 00:00:00 Sorting block of length 1774854 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1774855 Getting block 3 of 8 Reserving size (1869947) 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: 00:00:01 Sorting block of length 1137218 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1137219 Getting block 4 of 8 Reserving size (1869947) 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: 00:00:00 Sorting block of length 968470 (Using difference cover) Sorting block time: 00:00:00 Returning block of 968471 Getting block 5 of 8 Reserving size (1869947) 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: 00:00:01 Sorting block of length 1380455 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1380456 Getting block 6 of 8 Reserving size (1869947) 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: 00:00:00 Sorting block of length 532424 (Using difference cover) Sorting block time: 00:00:00 Returning block of 532425 Getting block 7 of 8 Reserving size (1869947) 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: 00:00:01 Sorting block of length 1738208 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1738209 Getting block 8 of 8 Reserving size (1869947) 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: 00:00:00 Sorting block of length 1022487 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1022488 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2472577 fchr[G]: 4982075 fchr[T]: 7494532 fchr[$]: 9973050 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 20978418 bytes to primary EBWT file: /scratch/8792817.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2493268 bytes to secondary EBWT file: /scratch/8792817.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 9973050 bwtLen: 9973051 sz: 2493263 bwtSz: 2493263 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 623316 offsSz: 2493264 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 51943 numLines: 51943 ebwtTotLen: 3324352 ebwtTotSz: 3324352 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:07