nohup: ignoring input Settings: Output files: "GCA_009914755.4.*.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: GCA_009914755.4.fa Reading reference sizes Time reading reference sizes: 00:00:30 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:01:05 Time to read SNPs and splice sites: 00:00:00 Using parameters --bmax 584492263 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 584492263 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:38 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:24 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:41 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 Split 1, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 4.45327e+08 (target: 584492262) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering GFM loop Getting block 1 of 7 Reserving size (584492263) for bucket 1 Getting block 2 of 7 Reserving size (584492263) for bucket 2 Getting block 3 of 7 Calculating Z arrays for bucket 1 Getting block 4 of 7 Reserving size (584492263) for bucket 3 Entering block accumulator loop for bucket 1: Reserving size (584492263) for bucket 4 Getting block 5 of 7 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 3 Reserving size (584492263) for bucket 5 Entering block accumulator loop for bucket 4: Getting block 7 of 7 Calculating Z arrays for bucket 5 Getting block 6 of 7 Reserving size (584492263) for bucket 6 Calculating Z arrays for bucket 2 Reserving size (584492263) for bucket 7 Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 5: Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 2: Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 7: bucket 4: 10% bucket 7: 10% bucket 6: 10% bucket 1: 10% bucket 3: 10% bucket 5: 10% bucket 7: 20% bucket 2: 10% bucket 4: 20% bucket 1: 20% bucket 6: 20% bucket 7: 30% bucket 3: 20% bucket 4: 30% bucket 1: 30% bucket 2: 20% bucket 5: 20% bucket 6: 30% bucket 7: 40% bucket 1: 40% bucket 4: 40% bucket 3: 30% bucket 7: 50% bucket 6: 40% bucket 2: 30% bucket 5: 30% bucket 1: 50% bucket 4: 50% bucket 7: 60% bucket 3: 40% bucket 6: 50% bucket 1: 60% bucket 2: 40% bucket 7: 70% bucket 4: 60% bucket 5: 40% bucket 6: 60% bucket 3: 50% bucket 1: 70% bucket 7: 80% bucket 4: 70% bucket 2: 50% bucket 6: 70% bucket 5: 50% bucket 3: 60% bucket 7: 90% bucket 1: 80% bucket 4: 80% bucket 7: 100% Sorting block of length 303706319 for bucket 7 (Using difference cover) bucket 6: 80% bucket 1: 90% bucket 2: 60% bucket 3: 70% bucket 5: 60% bucket 4: 90% bucket 6: 90% bucket 1: 100% Sorting block of length 439414275 for bucket 1 (Using difference cover) bucket 3: 80% bucket 2: 70% bucket 4: 100% Sorting block of length 456512234 for bucket 4 (Using difference cover) bucket 5: 70% bucket 6: 100% Sorting block of length 479407635 for bucket 6 (Using difference cover) bucket 3: 90% bucket 2: 80% bucket 5: 80% bucket 3: 100% Sorting block of length 583499314 for bucket 3 (Using difference cover) bucket 2: 90% bucket 5: 90% bucket 2: 100% Sorting block of length 490037421 for bucket 2 (Using difference cover) bucket 5: 100% Sorting block of length 364714866 for bucket 5 (Using difference cover) Sorting block time: 00:03:44 Returning block of 303706320 for bucket 7 Sorting block time: 00:04:03 Returning block of 364714867 for bucket 5 Sorting block time: 00:05:16 Returning block of 439414276 for bucket 1 Sorting block time: 00:05:45 Returning block of 456512235 for bucket 4 Sorting block time: 00:06:05 Returning block of 479407636 for bucket 6 Sorting block time: 00:06:01 Returning block of 490037422 for bucket 2 Sorting block time: 00:06:52 Returning block of 583499315 for bucket 3 Exited GFM loop fchr[A]: 0 fchr[C]: 923878813 fchr[G]: 1557575547 fchr[T]: 2194298091 fchr[$]: 3117292070 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 1043292552 bytes to primary GFM file: GCA_009914755.4.1.ht2 Wrote 779323024 bytes to secondary GFM file: GCA_009914755.4.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Returning from initFromVector Wrote 1367916093 bytes to primary GFM file: GCA_009914755.4.5.ht2 Wrote 793600510 bytes to secondary GFM file: GCA_009914755.4.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HierEbwt constructor Headers: len: 3117292070 gbwtLen: 3117292071 nodes: 3117292071 sz: 779323018 gbwtSz: 779323018 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 194830755 offsSz: 779323020 lineSz: 64 sideSz: 64 sideGbwtSz: 48 sideGbwtLen: 192 numSides: 16235897 numLines: 16235897 gbwtTotLen: 1039097408 gbwtTotSz: 1039097408 reverse: 0 linearFM: Yes Total time for call to driver() for forward index: 00:22:19