Settings: Output files: "Po_0_R2//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: Po_0_R2//tmp/segment_juncs.fa 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: 00:00:05 bmax according to bmaxDivN setting: 29813717 Using parameters --bmax 22360288 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 22360288 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:04 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: 00:00:16 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: 00:00:11 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 2; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:09 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: 00:00:08 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.98758e+07 (target: 22360287) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (22360288) 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: 00:00:02 Sorting block of length 21438988 (Using difference cover) Sorting block time: 00:00:10 Returning block of 21438989 Getting block 2 of 6 Reserving size (22360288) 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 20388971 (Using difference cover) Sorting block time: 00:00:10 Returning block of 20388972 Getting block 3 of 6 Reserving size (22360288) 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 18622917 (Using difference cover) Sorting block time: 00:00:08 Returning block of 18622918 Getting block 4 of 6 Reserving size (22360288) 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 21254807 (Using difference cover) Sorting block time: 00:00:11 Returning block of 21254808 Getting block 5 of 6 Reserving size (22360288) 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 18766098 (Using difference cover) Sorting block time: 00:00:10 Returning block of 18766099 Getting block 6 of 6 Reserving size (22360288) 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: 00:00:02 Sorting block of length 18783083 (Using difference cover) Sorting block time: 00:00:10 Returning block of 18783084 Exited Ebwt loop fchr[A]: 0 fchr[C]: 34734197 fchr[G]: 59458757 fchr[T]: 84437161 fchr[$]: 119254869 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 211685169 bytes to primary EBWT file: Po_0_R2//tmp/segment_juncs.1.ebwt Wrote 14906864 bytes to secondary EBWT file: Po_0_R2//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 119254869 bwtLen: 119254870 sz: 29813718 bwtSz: 29813718 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3726715 offsSz: 14906860 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 266194 numSides: 532388 numLines: 532388 ebwtTotLen: 34072832 ebwtTotSz: 34072832 reverse: 0 Total time for call to driver() for forward index: 00:02:33 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: 00:00:05 bmax according to bmaxDivN setting: 29813717 Using parameters --bmax 22360288 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 22360288 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:03 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: 00:00:08 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: 00:00:06 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: 00:00:06 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:07 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.32505e+07 (target: 22360287) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (22360288) 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: 00:00:02 Sorting block of length 5825180 (Using difference cover) Sorting block time: 00:00:03 Returning block of 5825181 Getting block 2 of 9 Reserving size (22360288) 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 18537023 (Using difference cover) Sorting block time: 00:00:08 Returning block of 18537024 Getting block 3 of 9 Reserving size (22360288) 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: 00:00:02 Sorting block of length 6683202 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6683203 Getting block 4 of 9 Reserving size (22360288) 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: 00:00:02 Sorting block of length 18623690 (Using difference cover) Sorting block time: 00:00:08 Returning block of 18623691 Getting block 5 of 9 Reserving size (22360288) 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: 00:00:02 Sorting block of length 19408940 (Using difference cover) Sorting block time: 00:00:07 Returning block of 19408941 Getting block 6 of 9 Reserving size (22360288) 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 11777446 (Using difference cover) Sorting block time: 00:00:05 Returning block of 11777447 Getting block 7 of 9 Reserving size (22360288) 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 15239620 (Using difference cover) Sorting block time: 00:00:12 Returning block of 15239621 Getting block 8 of 9 Reserving size (22360288) 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 12473120 (Using difference cover) Sorting block time: 00:00:06 Returning block of 12473121 Getting block 9 of 9 Reserving size (22360288) 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 10686640 (Using difference cover) Sorting block time: 00:00:09 Returning block of 10686641 Exited Ebwt loop fchr[A]: 0 fchr[C]: 34734197 fchr[G]: 59458757 fchr[T]: 84437161 fchr[$]: 119254869 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 211685169 bytes to primary EBWT file: Po_0_R2//tmp/segment_juncs.rev.1.ebwt Wrote 14906864 bytes to secondary EBWT file: Po_0_R2//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 119254869 bwtLen: 119254870 sz: 29813718 bwtSz: 29813718 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3726715 offsSz: 14906860 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 266194 numSides: 532388 numLines: 532388 ebwtTotLen: 34072832 ebwtTotSz: 34072832 reverse: 0 Total time for backward call to driver() for mirror index: 00:02:28