Settings: Output files: "../output/hisat/GCF_026571515.1_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_202404/data/GCF_026571515.1/GCF_026571515.1_ASM2657151v2_genomic.fna 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: 00:00:06 Time to read SNPs and splice sites: 00:00:21 Generation 0 (1408401826 -> 1408401826 nodes, 0 ranks) COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 16 RESIZED NODES: 0 MADE NEW NODES: 9 Generation 1 (1408658958 -> 1408658958 nodes, 0 ranks) COUNTED NEW NODES: 2 COUNTED TEMP NODES: 0 RESIZED NODES: 17 RESIZED NODES: 0 MADE NEW NODES: 8 Generation 2 (1409173290 -> 1409173290 nodes, 0 ranks) COUNTED NEW NODES: 2 COUNTED TEMP NODES: 0 RESIZED NODES: 16 RESIZED NODES: 0 MADE NEW NODES: 9 Generation 3 (1410202191 -> 1410202191 nodes, 0 ranks) BUILT FROM_INDEX: 5 COUNTED NEW NODES: 2 COUNTED TEMP NODES: 0 RESIZED NODES: 17 RESIZED NODES: 0 MADE NEW NODES: 8 RESIZE NODES: 42 COUNT NUMBER IN EACH BIN: 11 FINISHED FIRST ROUND: 9 1 74657676 2 53626536 1 53137165 6 45744227 7 53303224 3 45543214 5 48497547 2 51027778 1 53153919 37 32296464 3 59315109 8 40393323 13 43980534 3 51425515 37 27379700 3 44235546 7 27443230 7 30904392 7 42644036 2 27270631 1 27481310 37 47071411 2 38465506 1 48516267 5 29227054 3 42448860 5 29227298 2 29290114 1 33122780 5 47083731 1 27386859 1 32316559 1 74644562 0 0 0 0 0 0 2 1 16 1 19 1 109 1 FINISHED RECURSIVE SORTS: 10 SORT NODES: 30 MERGE, UPDATE RANK: 25 Generation 4 (1412262081 -> 1411586857 nodes, 564861282 ranks) ALLOCATE FROM_TABLE: 39 COUNT NUMBER IN EACH BIN: 16 FINISHED FIRST ROUND: 16 9 37843873 9 37837860 9 37843763 9 37839905 9 37842235 9 37851376 9 37837217 9 37845379 9 37838842 9 37834474 9 37834842 9 37835937 9 37843567 9 37843592 9 37837055 9 37841790 8 33635185 8 33633956 8 33635548 8 33643490 8 33636379 8 33635640 8 33646557 8 33633513 8 33641391 8 33633257 8 33633875 8 33634985 8 33632041 8 33634193 8 33632362 8 33633765 8 33646193 8 33636319 8 33636814 8 33636497 8 33641523 8 33628767 8 33635047 8 32497853 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 38 BUILD INDEX: 5 COUNTED NEW NODES: 9 COUNTED TEMP NODES: 0 RESIZED NODES: 21 RESIZED NODES: 0 MADE NEW NODES: 26 MERGEUPDATERANK: 25 TOTAL TIME: 163 Generation 5 (1413083136 -> 1411613717 nodes, 1143307682 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 3 FINISHED FIRST ROUND: 18 9 37845367 9 37836637 9 37844197 9 37841772 9 37844236 9 37852095 9 37837283 9 37846505 9 37840242 9 37835788 9 37835876 9 37836601 9 37843404 9 37844758 9 37838033 9 37843184 8 33635754 8 33635214 8 33636299 8 33642992 8 33636784 8 33636184 8 33646314 8 33634698 8 33640700 8 33633736 8 33634156 8 33635080 8 33633265 8 33634956 8 33633875 8 33634284 8 33645699 8 33638117 8 33637570 8 33636432 8 33641865 8 33629975 8 33635536 8 32498254 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 27 BUILD INDEX: 5 COUNTED NEW NODES: 4 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 14 MERGEUPDATERANK: 12 TOTAL TIME: 62 Generation 6 (1411979270 -> 1411803769 nodes, 1277246914 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 3 FINISHED FIRST ROUND: 19 9 37851140 9 37840231 9 37849702 9 37847832 9 37849815 9 37857694 9 37841425 9 37851599 9 37845592 9 37840659 9 37840482 9 37841466 9 37847966 9 37850613 9 37843168 9 37848632 8 33640838 8 33640063 8 33640546 8 33646410 8 33640969 8 33640687 8 33650692 8 33639825 8 33645120 8 33638156 8 33638556 8 33639244 8 33637725 8 33638521 8 33638971 8 33638680 8 33650085 8 33643187 8 33642819 8 33640838 8 33645756 8 33635093 8 33640151 8 32502821 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 28 BUILD INDEX: 5 COUNTED NEW NODES: 4 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 14 MERGEUPDATERANK: 9 TOTAL TIME: 60 Generation 7 (1412056979 -> 1411931561 nodes, 1360952812 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 20 9 37854584 9 37842557 9 37853400 9 37851779 9 37853384 9 37860620 9 37844360 9 37855581 9 37848963 9 37843938 9 37844084 9 37844507 9 37851085 9 37854386 9 37847041 9 37851610 8 33644984 8 33643653 8 33642583 8 33648599 8 33643745 8 33644064 8 33653176 8 33643363 8 33648636 8 33641838 8 33641467 8 33641437 8 33640691 8 33640499 8 33642507 8 33641524 8 33653119 8 33646396 8 33646552 8 33643740 8 33648270 8 33639318 8 33643167 8 32506354 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 28 BUILD INDEX: 5 COUNTED NEW NODES: 4 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 14 MERGEUPDATERANK: 8 TOTAL TIME: 59 Generation 8 (1412060157 -> 1411977442 nodes, 1399607980 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 20 9 37855750 9 37842891 9 37854630 9 37853760 9 37854870 9 37861707 9 37844713 9 37856824 9 37850226 9 37844585 9 37845466 9 37845365 9 37852779 9 37855972 9 37848967 9 37852377 8 33646232 8 33644010 8 33643387 8 33649968 8 33644491 8 33645330 8 33654274 8 33644616 8 33649596 8 33643588 8 33642228 8 33641774 8 33641456 8 33641654 8 33643385 8 33642711 8 33653246 8 33647757 8 33648379 8 33645350 8 33649524 8 33641089 8 33644372 8 32508143 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 28 BUILD INDEX: 5 COUNTED NEW NODES: 4 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 16 MERGEUPDATERANK: 7 TOTAL TIME: 60 Generation 9 (1412019149 -> 1411979057 nodes, 1410398060 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 20 9 37855368 9 37842812 9 37854680 9 37854193 9 37855992 9 37861692 9 37844507 9 37856464 9 37850418 9 37844147 9 37845775 9 37845229 9 37852988 9 37856139 9 37849975 9 37852271 8 33646314 8 33643618 8 33643604 8 33650360 8 33643651 8 33645464 8 33653373 8 33644672 8 33650039 8 33643897 8 33641727 8 33641866 8 33641164 8 33641259 8 33642859 8 33643187 8 33652766 8 33648085 8 33649361 8 33646001 8 33648958 8 33641034 8 33645063 8 32508085 FINISHED RECURSIVE SORTS: 7 BUILD TABLE: 29 BUILD INDEX: 4 COUNTED NEW NODES: 5 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 18 MERGEUPDATERANK: 6 TOTAL TIME: 62 Generation 10 (1411988434 -> 1411979278 nodes, 1411877440 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 3 FINISHED FIRST ROUND: 20 9 37855174 9 37842923 9 37854377 9 37854069 9 37857467 9 37861669 9 37844295 9 37856407 9 37850248 9 37844092 9 37845774 9 37845183 9 37853351 9 37856311 9 37850171 9 37852234 8 33646693 8 33643618 8 33643590 8 33650365 8 33643651 8 33645313 8 33653197 8 33644865 8 33650210 8 33643489 8 33641727 8 33641697 8 33640709 8 33641177 8 33642755 8 33643815 8 33652695 8 33648404 8 33649183 8 33646208 8 33648933 8 33640699 8 33644605 8 32507935 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 29 BUILD INDEX: 5 COUNTED NEW NODES: 4 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 18 MERGEUPDATERANK: 6 TOTAL TIME: 62 Generation 11 (1411980162 -> 1411979412 nodes, 1411971880 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 3 FINISHED FIRST ROUND: 20 9 37855174 9 37842923 9 37854340 9 37854048 9 37857417 9 37861669 9 37844295 9 37856407 9 37850248 9 37844092 9 37845520 9 37845183 9 37853351 9 37856311 9 37849928 9 37852234 8 33647226 8 33643618 8 33643590 8 33650365 8 33643651 8 33645313 8 33653197 8 33644865 8 33650210 8 33643489 8 33641727 8 33641697 8 33640709 8 33641177 8 33642755 8 33644114 8 33652695 8 33648404 8 33649183 8 33646208 8 33648933 8 33640699 8 33644590 8 32507857 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 29 BUILD INDEX: 5 COUNTED NEW NODES: 5 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 18 MERGEUPDATERANK: 6 TOTAL TIME: 63 Generation 12 (1411979412 -> 1411979412 nodes, 1411978977 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 3 FINISHED FIRST ROUND: 20 9 37855174 9 37842923 9 37854340 9 37854048 9 37857417 9 37861669 9 37844295 9 37856407 9 37850248 9 37844092 9 37845520 9 37845183 9 37853351 9 37856311 9 37849928 9 37852234 8 33647226 8 33643618 8 33643590 8 33650365 8 33643651 8 33645313 8 33653197 8 33644865 8 33650210 8 33643489 8 33641727 8 33641697 8 33640709 8 33641177 8 33642755 8 33644114 8 33652695 8 33648404 8 33649183 8 33646208 8 33648933 8 33640699 8 33644590 8 32507857 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 29 BUILD INDEX: 5 COUNTED NEW NODES: 5 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 18 MERGEUPDATERANK: 6 TOTAL TIME: 63 Generation 13 (1411979412 -> 1411979412 nodes, 1411979412 ranks) COUNT NUMBER IN EACH BIN: 3 FINISHED FIRST ROUND: 18 9 37855174 9 37842923 9 37854340 9 37854048 9 37857417 9 37861669 9 37844295 9 37856407 9 37850248 9 37844092 9 37845520 9 37845183 9 37853351 9 37856311 9 37849928 9 37852234 8 33647226 8 33643618 8 33643590 8 33650365 8 33643651 8 33645313 8 33653197 8 33644865 8 33650210 8 33643489 8 33641727 8 33641697 8 33640709 8 33641177 8 33642755 8 33644114 8 33652695 8 33648404 8 33649183 8 33646208 8 33648933 8 33640699 8 33644590 8 32507857 FINISHED RECURSIVE SORTS: 6 Generating edges... NODE.TO -> GENOME POS: 9 BUILD FROM_INDEX 6 COUNTED NEW EDGES: 8 MADE NEW EDGES: 24 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 2 8 13111408 8 13484126 7 12051673 7 12106133 7 13036538 7 12177049 8 12246324 9 13275919 8 12480214 8 13059634 8 12666894 9 12864419 8 12210468 9 12742099 9 12933340 8 11958569 8 12200915 9 11803251 9 12137072 9 11949624 9 12365454 9 11827953 9 11470647 10 12579818 10 12321378 10 11917466 8 11141004 8 12245679 8 11491107 7 11303308 8 11124418 9 11008872 9 11794646 8 10878816 8 11095745 10 12057511 10 11491365 9 11068355 8 10130192 7 8880622 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 1 8 5977907 8 5934495 8 5904286 8 6160059 8 5927890 8 5849872 8 6180649 7 5719807 6 5699212 6 5767750 8 6417333 8 5965586 7 6022242 7 6108558 7 6080193 8 5594424 9 6015169 9 6009989 7 6277340 7 6125022 8 5917668 8 6084296 12 5656696 11 5355326 10 5757328 11 5415424 11 5394963 11 5342858 9 5548855 11 5512781 10 5431930 9 5785096 8 5400574 7 5250350 8 5274047 9 5088836 8 5076891 8 5112012 8 4779500 8 4471538 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 9 6209177 9 6026684 9 5705913 10 5807698 10 6268142 8 6157193 9 5903513 9 5812492 10 5879194 10 6016539 10 5766937 11 5974994 9 6156536 8 5716826 8 5815081 8 6057641 8 5992943 8 5833283 9 6130277 8 5834205 8 5476250 7 5709629 6 5537084 8 5817350 8 5990644 9 5845833 8 5571035 8 5747622 9 5759192 8 5823964 7 5598818 8 5353307 8 5364558 8 5101368 8 4995399 8 5160819 9 5505587 8 5045169 7 4565748 7 4318656 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 2 11 12220132 11 12017152 12 12689624 11 12074902 10 12053138 11 12555828 12 12248968 9 11991185 9 11930310 10 12579270 9 12782858 9 12378341 10 13057295 10 12637410 10 12676972 9 12474271 8 11888377 7 12224887 7 11771239 8 12949125 8 11824572 7 11971808 7 12286254 7 13116399 8 12292757 8 11931660 9 12474079 8 12199775 7 11142710 8 12644092 7 11017711 8 11570723 8 11774655 7 12521067 6 10482194 6 11146012 7 11965492 6 10082380 6 9901301 6 9252538 FINISHED RECURSIVE SORTS: 1 SORTED NEW EDGES: 26 COUNT NUMBER IN EACH BIN: 11 FINISHED FIRST ROUND: 10 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 33554432 8 32053396 FINISHED RECURSIVE SORTS: 7 RE-SORTED NODES: 43 PROCESS EDGES: 11 REMOVE Y: 3 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 3 9 37749798 9 37750235 9 37751159 9 37751006 9 37750396 9 37763003 9 37757133 9 37781711 9 37761652 9 37751210 9 37752009 9 37751300 9 37751498 9 37756146 9 37763980 9 37765789 9 37764578 8 33572963 8 33577323 8 33559733 8 33562691 8 33558828 8 33564301 8 33563467 8 33559241 8 33558024 8 33555120 8 33559547 8 33555827 8 33555264 8 33556993 8 33555985 8 33555930 8 33556134 8 33555766 8 33556403 8 33556818 8 33557039 8 33556472 8 32055069 FINISHED RECURSIVE SORTS: 4 SORT, Make index: 34 TOTAL: 164 Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 478690025 fchr[G]: 706084777 fchr[T]: 933438077 fchr[$]: 1412237540 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 875699261 bytes to primary GFM file: ../output/hisat/GCF_026571515.1_index.1.ht2 Wrote 352994860 bytes to secondary GFM file: ../output/hisat/GCF_026571515.1_index.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Returning from initFromVector Wrote 966833633 bytes to primary GFM file: ../output/hisat/GCF_026571515.1_index.5.ht2 Wrote 356964426 bytes to secondary GFM file: ../output/hisat/GCF_026571515.1_index.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HGFM constructor Headers: len: 1408138905 gbwtLen: 1412237541 nodes: 1411979411 sz: 704069453 gbwtSz: 706118771 lineRate: 7 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 88248714 offsSz: 352994856 lineSz: 128 sideSz: 128 sideGbwtSz: 104 sideGbwtLen: 208 numSides: 6789604 numLines: 6789604 gbwtTotLen: 869069312 gbwtTotSz: 869069312 reverse: 0 linearFM: No Total time for call to driver() for forward index: 00:42:23