Settings: Output files: "CB_Gut_tp121/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: CB_Gut_tp121/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: 4757519 Using parameters --bmax 3568140 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3568140 --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: 00:00:01 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 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: 2.37876e+06 (target: 3568139) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3568140) 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 918697 (Using difference cover) Sorting block time: 00:00:00 Returning block of 918698 Getting block 2 of 8 Reserving size (3568140) 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 3498094 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3498095 Getting block 3 of 8 Reserving size (3568140) 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 1851770 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1851771 Getting block 4 of 8 Reserving size (3568140) 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 2591370 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2591371 Getting block 5 of 8 Reserving size (3568140) 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 3493307 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3493308 Getting block 6 of 8 Reserving size (3568140) 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 3081789 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3081790 Getting block 7 of 8 Reserving size (3568140) 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 3525140 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3525141 Getting block 8 of 8 Reserving size (3568140) 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 69902 (Using difference cover) Sorting block time: 00:00:00 Returning block of 69903 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4548850 fchr[G]: 9503944 fchr[T]: 14267777 fchr[$]: 19030076 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 35309184 bytes to primary EBWT file: CB_Gut_tp121/tmp/segment_juncs.1.bt2 Wrote 4757524 bytes to secondary EBWT file: CB_Gut_tp121/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19030076 bwtLen: 19030077 sz: 4757519 bwtSz: 4757520 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1189380 offsSz: 4757520 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 99115 numLines: 99115 ebwtTotLen: 6343360 ebwtTotSz: 6343360 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:16 Reading reference sizes Time reading reference sizes: 00:00:01 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: 4757519 Using parameters --bmax 3568140 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3568140 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:01 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 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: 2.37876e+06 (target: 3568139) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3568140) 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 963250 (Using difference cover) Sorting block time: 00:00:00 Returning block of 963251 Getting block 2 of 8 Reserving size (3568140) 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 3234025 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3234026 Getting block 3 of 8 Reserving size (3568140) 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 3434940 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3434941 Getting block 4 of 8 Reserving size (3568140) 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 2363896 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2363897 Getting block 5 of 8 Reserving size (3568140) 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 1467004 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1467005 Getting block 6 of 8 Reserving size (3568140) 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 3206173 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3206174 Getting block 7 of 8 Reserving size (3568140) 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 1099418 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1099419 Getting block 8 of 8 Reserving size (3568140) 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 3261363 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3261364 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4548850 fchr[G]: 9503944 fchr[T]: 14267777 fchr[$]: 19030076 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 35309184 bytes to primary EBWT file: CB_Gut_tp121/tmp/segment_juncs.rev.1.bt2 Wrote 4757524 bytes to secondary EBWT file: CB_Gut_tp121/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19030076 bwtLen: 19030077 sz: 4757519 bwtSz: 4757520 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1189380 offsSz: 4757520 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 99115 numLines: 99115 ebwtTotLen: 6343360 ebwtTotSz: 6343360 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:17