Settings: Output files: "/projects/NBL/HS1198/30UBRAAXX_7/tophat_wj/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/HS1198/30UBRAAXX_7/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:12 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:10 bmax according to bmaxDivN setting: 39843196 Using parameters --bmax 29882397 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 29882397 --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: 00:00:14 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.27675e+07 (target: 29882396) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (29882397) 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 14525001 (Using difference cover) Sorting block time: 00:00:12 Returning block of 14525002 Getting block 2 of 7 Reserving size (29882397) 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 29557154 (Using difference cover) Sorting block time: 00:00:32 Returning block of 29557155 Getting block 3 of 7 Reserving size (29882397) 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 16226625 (Using difference cover) Sorting block time: 00:00:21 Returning block of 16226626 Getting block 4 of 7 Reserving size (29882397) 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 21359237 (Using difference cover) Sorting block time: 00:00:24 Returning block of 21359238 Getting block 5 of 7 Reserving size (29882397) 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 21602775 (Using difference cover) Sorting block time: 00:00:23 Returning block of 21602776 Getting block 6 of 7 Reserving size (29882397) 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 26849563 (Using difference cover) Sorting block time: 00:00:29 Returning block of 26849564 Getting block 7 of 7 Reserving size (29882397) 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 29252425 (Using difference cover) Sorting block time: 00:00:30 Returning block of 29252426 Exited Ebwt loop fchr[A]: 0 fchr[C]: 43127064 fchr[G]: 80769938 fchr[T]: 116432238 fchr[$]: 159372786 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 292329182 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_7/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 19921604 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_7/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 159372786 bwtLen: 159372787 sz: 39843197 bwtSz: 39843197 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4980400 offsSz: 19921600 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 355743 numSides: 711486 numLines: 711486 ebwtTotLen: 45535104 ebwtTotSz: 45535104 Total time for call to driver() for forward index: 00:04:33 Reading reference sizes Time reading reference sizes: 00:00:02 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: 39843196 Using parameters --bmax 29882397 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 29882397 --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: 00:00:12 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: 00:00:09 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: 00:00:10 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: 00:00:10 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.99216e+07 (target: 29882396) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (29882397) 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 18027411 (Using difference cover) Sorting block time: 00:00:16 Returning block of 18027412 Getting block 2 of 8 Reserving size (29882397) 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 19582664 (Using difference cover) Sorting block time: 00:00:21 Returning block of 19582665 Getting block 3 of 8 Reserving size (29882397) 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 26225929 (Using difference cover) Sorting block time: 00:00:29 Returning block of 26225930 Getting block 4 of 8 Reserving size (29882397) 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 27128934 (Using difference cover) Sorting block time: 00:00:30 Returning block of 27128935 Getting block 5 of 8 Reserving size (29882397) 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 26591608 (Using difference cover) Sorting block time: 00:00:29 Returning block of 26591609 Getting block 6 of 8 Reserving size (29882397) 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 3503989 (Using difference cover) Sorting block time: 00:00:05 Returning block of 3503990 Getting block 7 of 8 Reserving size (29882397) 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 27137307 (Using difference cover) Sorting block time: 00:00:30 Returning block of 27137308 Getting block 8 of 8 Reserving size (29882397) 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 11174937 (Using difference cover) Sorting block time: 00:00:09 Returning block of 11174938 Exited Ebwt loop fchr[A]: 0 fchr[C]: 43127064 fchr[G]: 80769938 fchr[T]: 116432238 fchr[$]: 159372786 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 292329182 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_7/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 19921604 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_7/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 159372786 bwtLen: 159372787 sz: 39843197 bwtSz: 39843197 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4980400 offsSz: 19921600 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 355743 numSides: 711486 numLines: 711486 ebwtTotLen: 45535104 ebwtTotSz: 45535104 Total time for backward call to driver() for mirror index: 00:04:52