Settings: Output files: "/projects/NBL/HS1198/302P8AAXX_5/tophat/tmp/segment_juncs.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) 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: /projects/NBL/HS1198/302P8AAXX_5/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:15 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:09 bmax according to bmaxDivN setting: 40210253 Using parameters --bmax 30157690 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 30157690 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:08 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: 00:00:03 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: 00:00:17 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:13 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:14 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.01051e+07 (target: 30157689) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (30157690) 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: 00:00:04 Sorting block of length 29695184 (Using difference cover) Sorting block time: 00:00:40 Returning block of 29695185 Getting block 2 of 8 Reserving size (30157690) 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 13581325 (Using difference cover) Sorting block time: 00:00:19 Returning block of 13581326 Getting block 3 of 8 Reserving size (30157690) 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: 00:00:05 Sorting block of length 18286294 (Using difference cover) Sorting block time: 00:00:30 Returning block of 18286295 Getting block 4 of 8 Reserving size (30157690) 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 14311340 (Using difference cover) Sorting block time: 00:00:23 Returning block of 14311341 Getting block 5 of 8 Reserving size (30157690) 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 21531052 (Using difference cover) Sorting block time: 00:00:31 Returning block of 21531053 Getting block 6 of 8 Reserving size (30157690) 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 28643045 (Using difference cover) Sorting block time: 00:00:43 Returning block of 28643046 Getting block 7 of 8 Reserving size (30157690) 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 21348771 (Using difference cover) Sorting block time: 00:00:34 Returning block of 21348772 Getting block 8 of 8 Reserving size (30157690) 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: 00:00:04 Sorting block of length 13443997 (Using difference cover) Sorting block time: 00:00:17 Returning block of 13443998 Exited Ebwt loop fchr[A]: 0 fchr[C]: 43276511 fchr[G]: 81037712 fchr[T]: 117761872 fchr[$]: 160841015 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 294737820 bytes to primary EBWT file: /projects/NBL/HS1198/302P8AAXX_5/tophat/tmp/segment_juncs.1.ebwt Wrote 20105132 bytes to secondary EBWT file: /projects/NBL/HS1198/302P8AAXX_5/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 160841015 bwtLen: 160841016 sz: 40210254 bwtSz: 40210254 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5026282 offsSz: 20105128 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 359021 numSides: 718042 numLines: 718042 ebwtTotLen: 45954688 ebwtTotSz: 45954688 Total time for call to driver() for forward index: 00:06:35 Reading reference sizes Time reading reference sizes: 00:00:03 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:09 bmax according to bmaxDivN setting: 40210253 Using parameters --bmax 30157690 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 30157690 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:06 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:02 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: 00:00:13 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.68068e+07 (target: 30157689) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (30157690) 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: 00:00:04 Sorting block of length 29939606 (Using difference cover) Sorting block time: 00:00:31 Returning block of 29939607 Getting block 2 of 6 Reserving size (30157690) 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: 00:00:05 Sorting block of length 26229188 (Using difference cover) Sorting block time: 00:00:31 Returning block of 26229189 Getting block 3 of 6 Reserving size (30157690) 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: 00:00:05 Sorting block of length 28475408 (Using difference cover) Sorting block time: 00:00:34 Returning block of 28475409 Getting block 4 of 6 Reserving size (30157690) 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 24638111 (Using difference cover) Sorting block time: 00:00:30 Returning block of 24638112 Getting block 5 of 6 Reserving size (30157690) 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 28010259 (Using difference cover) Sorting block time: 00:00:33 Returning block of 28010260 Getting block 6 of 6 Reserving size (30157690) 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: 00:00:03 Sorting block of length 23548438 (Using difference cover) Sorting block time: 00:00:25 Returning block of 23548439 Exited Ebwt loop fchr[A]: 0 fchr[C]: 43276511 fchr[G]: 81037712 fchr[T]: 117761872 fchr[$]: 160841015 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 294737820 bytes to primary EBWT file: /projects/NBL/HS1198/302P8AAXX_5/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 20105132 bytes to secondary EBWT file: /projects/NBL/HS1198/302P8AAXX_5/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 160841015 bwtLen: 160841016 sz: 40210254 bwtSz: 40210254 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5026282 offsSz: 20105128 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 359021 numSides: 718042 numLines: 718042 ebwtTotLen: 45954688 ebwtTotSz: 45954688 Total time for backward call to driver() for mirror index: 00:04:35