Settings: Output files: "/scratch/8792857.1.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/8792857.1.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: 00:00:01 bmax according to bmaxDivN setting: 3046587 Using parameters --bmax 2284941 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2284941 --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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 7; 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: 1.52329e+06 (target: 2284940) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2284941) 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 2021200 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2021201 Getting block 2 of 8 Reserving size (2284941) 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 1224750 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1224751 Getting block 3 of 8 Reserving size (2284941) 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 2228607 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2228608 Getting block 4 of 8 Reserving size (2284941) 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 1220553 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1220554 Getting block 5 of 8 Reserving size (2284941) 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 1435519 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1435520 Getting block 6 of 8 Reserving size (2284941) 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 1695534 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1695535 Getting block 7 of 8 Reserving size (2284941) 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 1441568 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1441569 Getting block 8 of 8 Reserving size (2284941) 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 918612 (Using difference cover) Sorting block time: 00:00:01 Returning block of 918613 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3045410 fchr[G]: 6069100 fchr[T]: 9079017 fchr[$]: 12186350 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 24685231 bytes to primary EBWT file: /scratch/8792857.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 3046592 bytes to secondary EBWT file: /scratch/8792857.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 12186350 bwtLen: 12186351 sz: 3046588 bwtSz: 3046588 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 761647 offsSz: 3046588 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 63471 numLines: 63471 ebwtTotLen: 4062144 ebwtTotSz: 4062144 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:20 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 reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 3046587 Using parameters --bmax 2284941 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2284941 --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: 00:00:01 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 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: 1.52329e+06 (target: 2284940) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2284941) 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 567305 (Using difference cover) Sorting block time: 00:00:00 Returning block of 567306 Getting block 2 of 8 Reserving size (2284941) 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 2270309 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2270310 Getting block 3 of 8 Reserving size (2284941) 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 1184687 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1184688 Getting block 4 of 8 Reserving size (2284941) 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 2118672 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2118673 Getting block 5 of 8 Reserving size (2284941) 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 1555787 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1555788 Getting block 6 of 8 Reserving size (2284941) 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 1140953 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1140954 Getting block 7 of 8 Reserving size (2284941) 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 2271483 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2271484 Getting block 8 of 8 Reserving size (2284941) 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 1077147 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1077148 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3045410 fchr[G]: 6069100 fchr[T]: 9079017 fchr[$]: 12186350 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 24685231 bytes to primary EBWT file: /scratch/8792857.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 3046592 bytes to secondary EBWT file: /scratch/8792857.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 12186350 bwtLen: 12186351 sz: 3046588 bwtSz: 3046588 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 761647 offsSz: 3046588 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 63471 numLines: 63471 ebwtTotLen: 4062144 ebwtTotSz: 4062144 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:21