Settings: Output files: "/project/shefflab/genomes/hg18/hisat2_index/default/hg18.*.ht2" 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 Local offset rate: 3 (one in 8) Local fTable chars: 6 Local sequence length: 57344 Local sequence overlap between two consecutive indexes: 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: /project/shefflab/genomes/hg18/fasta/default/hg18.fa Reading reference sizes Time reading reference sizes: 00:00:24 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:13 Time to read SNPs and splice sites: 00:00:00 Using parameters --bmax 540266568 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 540266568 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:51 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:14 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:34 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 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.60178e+08 (target: 540266567) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering GFM loop Getting block 1 of 8 Reserving size (540266568) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 447150746 for bucket 1 (Using difference cover) Sorting block time: 00:03:25 Returning block of 447150747 for bucket 1 Getting block 2 of 8 Reserving size (540266568) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 457899971 for bucket 2 (Using difference cover) Sorting block time: 00:03:36 Returning block of 457899972 for bucket 2 Getting block 3 of 8 Reserving size (540266568) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 353936055 for bucket 3 (Using difference cover) Sorting block time: 00:02:53 Returning block of 353936056 for bucket 3 Getting block 4 of 8 Reserving size (540266568) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 216139682 for bucket 4 (Using difference cover) Sorting block time: 00:01:43 Returning block of 216139683 for bucket 4 Getting block 5 of 8 Reserving size (540266568) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% bucket 5: 20% bucket 5: 30% bucket 5: 40% bucket 5: 50% bucket 5: 60% bucket 5: 70% bucket 5: 80% bucket 5: 90% bucket 5: 100% Sorting block of length 460006621 for bucket 5 (Using difference cover) Sorting block time: 00:03:45 Returning block of 460006622 for bucket 5 Getting block 6 of 8 Reserving size (540266568) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 280879014 for bucket 6 (Using difference cover) Sorting block time: 00:02:05 Returning block of 280879015 for bucket 6 Getting block 7 of 8 Reserving size (540266568) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 342869993 for bucket 7 (Using difference cover) Sorting block time: 00:02:45 Returning block of 342869994 for bucket 7 Getting block 8 of 8 Reserving size (540266568) for bucket 8 Calculating Z arrays for bucket 8 Entering block accumulator loop for bucket 8: bucket 8: 10% bucket 8: 20% bucket 8: 30% bucket 8: 40% bucket 8: 50% bucket 8: 60% bucket 8: 70% bucket 8: 80% bucket 8: 90% bucket 8: 100% Sorting block of length 322539607 for bucket 8 (Using difference cover) Sorting block time: 00:02:30 Returning block of 322539608 for bucket 8 Exited GFM loop fchr[A]: 0 fchr[C]: 850568906 fchr[G]: 1439951472 fchr[T]: 2029686830 fchr[$]: 2881421696 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 964771868 bytes to primary GFM file: /project/shefflab/genomes/hg18/hisat2_index/default/hg18.1.ht2 Wrote 720355432 bytes to secondary GFM file: /project/shefflab/genomes/hg18/hisat2_index/default/hg18.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Returning from initFromVector Wrote 1266926365 bytes to primary GFM file: /project/shefflab/genomes/hg18/hisat2_index/default/hg18.5.ht2 Wrote 733549128 bytes to secondary GFM file: /project/shefflab/genomes/hg18/hisat2_index/default/hg18.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HierEbwt constructor Headers: len: 2881421696 gbwtLen: 2881421697 nodes: 2881421697 sz: 720355424 gbwtSz: 720355425 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 180088857 offsSz: 720355428 lineSz: 64 sideSz: 64 sideGbwtSz: 48 sideGbwtLen: 192 numSides: 15007405 numLines: 15007405 gbwtTotLen: 960473920 gbwtTotSz: 960473920 reverse: 0 linearFM: Yes Total time for call to driver() for forward index: 01:13:02Command completed. Elapsed time: 1:13:03. Running peak memory: 5.249GB. PID: 151665; Command: hisat2-build; Return code: 0; Memory used: 5.249GB > `touch /project/shefflab/genomes/hg18/hisat2_index/default/_refgenie_build/hg18_hisat2_index__default.flag` (158792) Command completed. Elapsed time: 0:00:00. Running peak memory: 5.249GB. PID: 158792; Command: touch; Return code: 0; Memory used: 0.0GB > `cd /project/shefflab/genomes/hg18/hisat2_index/default; find . -type f -not -path './_refgenie_build*' -exec md5sum {} \; | sort -k 2 | awk '{print $1}' | md5sum` Asset digest: ce677d99e0e73e317563d4b84362ab1c Default tag for 'hg18/hisat2_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 1:13:11 * Total elapsed time (all runs): 1:13:03 * Peak memory (this run): 5.2487 GB * Pipeline completed time: 2020-01-20 14:36:38 Finished building 'hisat2_index' asset