Settings: Output files: "../output/10-hisat-deseq2/GCF_031168955.1.index.*.ht2" Line rate: 7 (line is 128 bytes) Lines per side: 1 (side is 128 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: ../data/ncbi_dataset/data/GCF_031168955.1/GCF_031168955.1_ASM3116895v1_genomic.fna 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: 00:00:02 Time to read SNPs and splice sites: 00:00:01 Generation 0 (555444193 -> 555444193 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 5 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 1 (555668541 -> 555668541 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 5 RESIZED NODES: 0 MADE NEW NODES: 1 Generation 2 (556117282 -> 556117282 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 5 RESIZED NODES: 0 MADE NEW NODES: 1 Generation 3 (557014927 -> 557014927 nodes, 0 ranks) BUILT FROM_INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 5 RESIZED NODES: 0 MADE NEW NODES: 1 RESIZE NODES: 10 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 1 3 32577101 7 34540049 8 31130827 8 33322782 39 30495781 3 33723165 8 31251349 14 33895102 39 27466881 8 32682168 8 26728451 8 29456178 3 29711409 39 22088961 7 28143471 7 25028802 3 33527348 6 18306390 2 24735367 146 4 FINISHED RECURSIVE SORTS: 3 SORT NODES: 6 MERGE, UPDATE RANK: 8 Generation 4 (558811586 -> 557941980 nodes, 347556972 ranks) ALLOCATE FROM_TABLE: 12 COUNT NUMBER IN EACH BIN: 3 FINISHED FIRST ROUND: 3 14 29531844 14 29482994 14 29548953 14 29453223 14 29509861 13 27396884 13 27423245 13 27410566 13 27380693 13 27419072 13 27371201 13 27417511 13 27394945 13 27381696 13 27381237 13 27416559 13 27370878 13 27394939 13 27396419 13 26859260 FINISHED RECURSIVE SORTS: 3 BUILD TABLE: 9 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 3 MERGEUPDATERANK: 7 TOTAL TIME: 33 Generation 5 (558559987 -> 557905527 nodes, 447173183 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 14 29529152 14 29482625 14 29545778 14 29457233 14 29507489 13 27396253 13 27419411 13 27407152 13 27378227 13 27414521 13 27370782 13 27413168 13 27391335 13 27381096 13 27379916 13 27414000 13 27370344 13 27392317 13 27395890 13 26858838 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 5 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 5 TOTAL TIME: 14 Generation 6 (558059915 -> 557997756 nodes, 488033829 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 14 29534374 14 29488734 14 29550765 14 29465149 14 29512242 13 27401623 13 27422351 13 27411812 13 27381406 13 27417444 13 27376114 13 27415900 13 27394189 13 27386601 13 27383860 13 27418046 13 27375944 13 27395767 13 27401310 13 26864125 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 5 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 4 TOTAL TIME: 13 Generation 7 (558138390 -> 558077038 nodes, 520901965 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 14 29539248 14 29494843 14 29553908 14 29471542 14 29515478 13 27404700 13 27424907 13 27416051 13 27384145 13 27419322 13 27380781 13 27418842 13 27396220 13 27391836 13 27387691 13 27422281 13 27381391 13 27398175 13 27406129 13 26869548 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 5 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 3 TOTAL TIME: 12 Generation 8 (558181901 -> 558131068 nodes, 539273927 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 14 29542047 14 29499787 14 29554695 14 29475045 14 29517015 13 27406815 13 27426552 13 27419166 13 27386579 13 27421224 13 27384672 13 27420939 13 27398078 13 27396772 13 27390913 13 27425431 13 27384062 13 27399068 13 27408506 13 26873702 FINISHED RECURSIVE SORTS: 3 BUILD TABLE: 6 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 2 TOTAL TIME: 12 Generation 9 (558203646 -> 558163040 nodes, 549213118 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 14 29543160 14 29503386 14 29554809 14 29475910 14 29517911 13 27409088 13 27428298 13 27420867 13 27387848 13 27421518 13 27387431 13 27422556 13 27399530 13 27400898 13 27393000 13 27426887 13 27385005 13 27399477 13 27409394 13 26876067 FINISHED RECURSIVE SORTS: 3 BUILD TABLE: 6 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 2 TOTAL TIME: 12 Generation 10 (558222058 -> 558190630 nodes, 553946345 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 14 29543605 14 29507402 14 29555227 14 29476560 14 29519984 13 27411830 13 27430023 13 27422264 13 27388851 13 27421928 13 27387821 13 27425271 13 27400263 13 27403238 13 27395257 13 27426622 13 27386366 13 27399484 13 27408970 13 26879664 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 5 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 2 TOTAL TIME: 11 Generation 11 (558246671 -> 558220698 nodes, 556303271 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 3 14 29544189 14 29512407 14 29555227 14 29476777 14 29521970 13 27415177 13 27431861 13 27423595 13 27389933 13 27422041 13 27386843 13 27429091 13 27402311 13 27405098 13 27397866 13 27425811 13 27390221 13 27399484 13 27408705 13 26882091 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 6 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 2 TOTAL TIME: 12 Generation 12 (558257399 -> 558233138 nodes, 557538929 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 3 14 29544330 14 29514623 14 29555151 14 29476992 14 29521409 13 27414589 13 27431861 13 27425502 13 27389933 13 27422041 13 27386642 13 27434218 13 27402928 13 27402467 13 27399792 13 27425208 13 27394651 13 27399484 13 27408705 13 26882612 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 6 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 2 TOTAL TIME: 12 Generation 13 (558242638 -> 558228626 nodes, 558074429 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 4 14 29544330 14 29512891 14 29555151 14 29476992 14 29521409 13 27411403 13 27431861 13 27428280 13 27389933 13 27422041 13 27386642 13 27432068 13 27402928 13 27402467 13 27400168 13 27424783 13 27394651 13 27399484 13 27408705 13 26882439 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 6 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 2 TOTAL TIME: 12 Generation 14 (558232679 -> 558228771 nodes, 558221708 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 14 29544330 14 29512449 14 29555151 14 29476992 14 29521409 13 27411403 13 27431861 13 27432123 13 27388585 13 27422041 13 27386642 13 27431770 13 27402928 13 27400857 13 27400168 13 27424783 13 27394651 13 27399484 13 27408705 13 26882439 FINISHED RECURSIVE SORTS: 3 BUILD TABLE: 6 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 2 TOTAL TIME: 12 Generation 15 (558228771 -> 558228771 nodes, 558228771 ranks) COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 14 29544330 14 29512449 14 29555151 14 29476992 14 29521409 13 27411403 13 27431861 13 27432123 13 27388585 13 27422041 13 27386642 13 27431770 13 27402928 13 27400857 13 27400168 13 27424783 13 27394651 13 27399484 13 27408705 13 26882439 FINISHED RECURSIVE SORTS: 2 Generating edges... NODE.TO -> GENOME POS: 2 BUILD FROM_INDEX 2 COUNTED NEW EDGES: 0 MADE NEW EDGES: 5 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 11 8039719 11 7877868 15 7744644 16 8048620 12 7528178 13 8257331 8 7552766 13 7844179 15 7632267 16 7448508 12 8221736 12 7633345 13 7764511 13 7305089 17 7808015 11 7069246 16 7338387 14 7287307 15 7036984 14 6612065 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 14 6853826 10 7395109 10 6666001 11 6819315 11 6566036 12 6681334 14 6370893 14 6672162 10 6361783 12 6428543 12 6328108 21 6241300 19 6159769 22 6199392 16 6257398 11 6243240 9 6043500 11 6126731 14 5474438 14 5440520 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 15 6607296 17 6452152 11 6650584 12 6672853 16 6445538 17 6415232 15 6457807 13 6442059 14 6304666 13 6309564 12 6317228 12 6554911 10 6261619 15 6430938 15 6434023 14 6244438 14 6559785 8 6194800 11 5919748 13 5621290 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 17 7612981 20 7967844 20 7655043 15 8214599 17 8007028 14 7670412 15 7753041 11 7739038 12 7916796 12 7495637 13 8029649 12 7442698 10 8985516 8 7626499 12 7322832 12 7100697 14 7254484 14 6897477 10 7100586 9 5984158 FINISHED RECURSIVE SORTS: 1 SORTED NEW EDGES: 7 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 2 14 29360128 14 29360128 14 29360128 14 29360128 14 29360128 14 29360128 14 29360128 13 27262976 13 27262976 13 27262976 13 27262976 13 27262976 13 27262976 13 27262976 13 27262976 13 27262976 13 27262976 13 27262976 13 27262976 13 25552163 FINISHED RECURSIVE SORTS: 2 RE-SORTED NODES: 9 PROCESS EDGES: 3 REMOVE Y: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 14 29362149 14 29363350 14 29381892 14 29392885 14 29362973 14 29366956 14 29386719 13 27294130 13 27276414 13 27291905 13 27271814 13 27271534 13 27278606 13 27269515 13 27267221 13 27265606 13 27265143 13 27265574 13 27264666 13 25554658 FINISHED RECURSIVE SORTS: 2 SORT, Make index: 8 TOTAL: 37 Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 152050765 fchr[G]: 279380163 fchr[T]: 406676694 fchr[$]: 558453709 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 347918103 bytes to primary GFM file: ../output/10-hisat-deseq2/GCF_031168955.1.index.1.ht2 Wrote 139557200 bytes to secondary GFM file: ../output/10-hisat-deseq2/GCF_031168955.1.index.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Warning: a local graph exploded (offset: 211411279, length: 57244) Warning: a local graph exploded (offset: 334973738, length: 57244) Warning: a local graph exploded (offset: 334973738, length: 57244) Returning from initFromVector Wrote 376924113 bytes to primary GFM file: ../output/10-hisat-deseq2/GCF_031168955.1.index.5.ht2 Wrote 141646948 bytes to secondary GFM file: ../output/10-hisat-deseq2/GCF_031168955.1.index.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HGFM constructor Headers: len: 555215489 gbwtLen: 558453710 nodes: 558228770 sz: 277607745 gbwtSz: 279226856 lineRate: 7 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 34889299 offsSz: 139557196 lineSz: 128 sideSz: 128 sideGbwtSz: 104 sideGbwtLen: 208 numSides: 2684874 numLines: 2684874 gbwtTotLen: 343663872 gbwtTotSz: 343663872 reverse: 0 linearFM: No Total time for call to driver() for forward index: 00:08:45