Settings: Output files: "../output/13-Hisat/PNRI_Mtr1.1.1.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_036588685.1/GCF_036588685.1_PNRI_Mtr1.1.1.hap1_genomic.fna Reading reference sizes Time reading reference sizes: 00:00:11 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:05 Time to read SNPs and splice sites: 00:00:01 Generation 0 (1298721918 -> 1298721918 nodes, 0 ranks) COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 15 RESIZED NODES: 0 MADE NEW NODES: 6 Generation 1 (1298953952 -> 1298953952 nodes, 0 ranks) COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 15 RESIZED NODES: 0 MADE NEW NODES: 6 Generation 2 (1299418172 -> 1299418172 nodes, 0 ranks) COUNTED NEW NODES: 2 COUNTED TEMP NODES: 0 RESIZED NODES: 14 RESIZED NODES: 0 MADE NEW NODES: 6 Generation 3 (1300346954 -> 1300346954 nodes, 0 ranks) BUILT FROM_INDEX: 5 COUNTED NEW NODES: 2 COUNTED TEMP NODES: 0 RESIZED NODES: 14 RESIZED NODES: 0 MADE NEW NODES: 7 RESIZE NODES: 36 COUNT NUMBER IN EACH BIN: 9 FINISHED FIRST ROUND: 8 1 68122407 2 49443133 1 47679866 6 44158602 7 50321172 3 41645192 5 43732488 2 47595013 1 47646000 38 44014491 2 41434640 8 37860373 13 40458101 3 47124709 38 38180760 7 42699506 9 37213511 7 40640603 3 52134178 37 40820854 2 36830830 1 43686725 6 38940222 7 56606071 3 58180854 5 40810680 1 25246422 1 30935202 1 68044371 18 1 30 1 98 1 FINISHED RECURSIVE SORTS: 7 SORT NODES: 24 MERGE, UPDATE RANK: 23 Generation 4 (1302206979 -> 1301590605 nodes, 487449694 ranks) ALLOCATE FROM_TABLE: 39 COUNT NUMBER IN EACH BIN: 15 FINISHED FIRST ROUND: 14 10 42076377 10 42061849 10 42106435 10 42087523 10 42062783 10 42059740 10 42102978 10 42075462 10 42059858 10 42045093 10 42007797 10 42003668 10 42045767 10 42051350 10 42032320 10 42085232 10 42043172 10 42016276 10 42053687 10 42012621 10 42042431 10 42046820 9 37815353 9 37816647 9 37834196 9 37813085 9 37806522 9 37839079 9 37832230 9 37799418 9 37813369 9 36041467 FINISHED RECURSIVE SORTS: 5 BUILD TABLE: 34 BUILD INDEX: 5 COUNTED NEW NODES: 8 COUNTED TEMP NODES: 0 RESIZED NODES: 19 RESIZED NODES: 0 MADE NEW NODES: 23 MERGEUPDATERANK: 23 TOTAL TIME: 151 Generation 5 (1302925850 -> 1301546250 nodes, 950014088 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 16 10 42070172 10 42056499 10 42098445 10 42080522 10 42057508 10 42055706 10 42094557 10 42069762 10 42057853 10 42043656 10 42007907 10 42009901 10 42043423 10 42049326 10 42033114 10 42079611 10 42043256 10 42017335 10 42050812 10 42014566 10 42039632 10 42044131 9 37815833 9 37820504 9 37833340 9 37814608 9 37807669 9 37838379 9 37830631 9 37805090 9 37818279 9 36044223 FINISHED RECURSIVE SORTS: 5 BUILD TABLE: 23 BUILD INDEX: 4 COUNTED NEW NODES: 4 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 12 MERGEUPDATERANK: 13 TOTAL TIME: 56 Generation 6 (1301810123 -> 1301710602 nodes, 1082922894 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 16 10 42073355 10 42059280 10 42102089 10 42083723 10 42060908 10 42059976 10 42097675 10 42072998 10 42063606 10 42049133 10 42011755 10 42020075 10 42048337 10 42054101 10 42039980 10 42083962 10 42049293 10 42023113 10 42055434 10 42020484 10 42042887 10 42048336 9 37820411 9 37828741 9 37838847 9 37819273 9 37812887 9 37843706 9 37834991 9 37813901 9 37827225 9 36050120 FINISHED RECURSIVE SORTS: 5 BUILD TABLE: 23 BUILD INDEX: 4 COUNTED NEW NODES: 4 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 11 MERGEUPDATERANK: 9 TOTAL TIME: 51 Generation 7 (1301942920 -> 1301852483 nodes, 1169584571 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 17 10 42075993 10 42061397 10 42104714 10 42086733 10 42063726 10 42063811 10 42100186 10 42075829 10 42067898 10 42053196 10 42015728 10 42028745 10 42052625 10 42058275 10 42047194 10 42087346 10 42054526 10 42027967 10 42059915 10 42025005 10 42045868 10 42052762 9 37824840 9 37835292 9 37844646 9 37822622 9 37817281 9 37847642 9 37838465 9 37821345 9 37834912 9 36055999 FINISHED RECURSIVE SORTS: 5 BUILD TABLE: 24 BUILD INDEX: 4 COUNTED NEW NODES: 3 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 12 MERGEUPDATERANK: 8 TOTAL TIME: 51 Generation 8 (1302037321 -> 1301955399 nodes, 1219564742 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 16 10 42078222 10 42062802 10 42106763 10 42088672 10 42065089 10 42065832 10 42102545 10 42078235 10 42071709 10 42056091 10 42019490 10 42033858 10 42056689 10 42062504 10 42051175 10 42090721 10 42057393 10 42030948 10 42062599 10 42026891 10 42048402 10 42056362 9 37828055 9 37840892 9 37850820 9 37824099 9 37820507 9 37850651 9 37840169 9 37825802 9 37841280 9 36060132 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 24 BUILD INDEX: 4 COUNTED NEW NODES: 3 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 12 MERGEUPDATERANK: 7 TOTAL TIME: 50 Generation 9 (1302091192 -> 1302028356 nodes, 1247252875 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 16 10 42079707 10 42063030 10 42108203 10 42090449 10 42065825 10 42066976 10 42104687 10 42080111 10 42074592 10 42058900 10 42023251 10 42035760 10 42059678 10 42066434 10 42051664 10 42094466 10 42059350 10 42033281 10 42063677 10 42028373 10 42050728 10 42059041 9 37831666 9 37843937 9 37856418 9 37824018 9 37822387 9 37854183 9 37841451 9 37827994 9 37844852 9 36063267 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 24 BUILD INDEX: 4 COUNTED NEW NODES: 3 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 13 MERGEUPDATERANK: 6 TOTAL TIME: 50 Generation 10 (1302126859 -> 1302075217 nodes, 1265659493 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 17 10 42081166 10 42062521 10 42108894 10 42090944 10 42065809 10 42068277 10 42107410 10 42080970 10 42077379 10 42061000 10 42025742 10 42036111 10 42060709 10 42069105 10 42051788 10 42098611 10 42059932 10 42035511 10 42064381 10 42029114 10 42051583 10 42060767 9 37833264 9 37846277 9 37857622 9 37824069 9 37822634 9 37857119 9 37842749 9 37830575 9 37847698 9 36065486 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 25 BUILD INDEX: 4 COUNTED NEW NODES: 3 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 12 MERGEUPDATERANK: 7 TOTAL TIME: 51 Generation 11 (1302149304 -> 1302104404 nodes, 1280791094 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 16 10 42083147 10 42062196 10 42108864 10 42091661 10 42065770 10 42069301 10 42109215 10 42083491 10 42081486 10 42061780 10 42027468 10 42034501 10 42062190 10 42071243 10 42051243 10 42099671 10 42061799 10 42037801 10 42065120 10 42029196 10 42050992 10 42061450 9 37832396 9 37848681 9 37856190 9 37823936 9 37823744 9 37858373 9 37842192 9 37832443 9 37848548 9 36068316 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 24 BUILD INDEX: 4 COUNTED NEW NODES: 3 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 14 MERGEUPDATERANK: 6 TOTAL TIME: 51 Generation 12 (1302174016 -> 1302142167 nodes, 1292129550 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 17 10 42083673 10 42062196 10 42108550 10 42092470 10 42065197 10 42071349 10 42109680 10 42084194 10 42089678 10 42067283 10 42026877 10 42034490 10 42064050 10 42070771 10 42051243 10 42101960 10 42063847 10 42038455 10 42065969 10 42029196 10 42050917 10 42061911 9 37834444 9 37850018 9 37856445 9 37823724 9 37827502 9 37858381 9 37841769 9 37834491 9 37850430 9 36071007 FINISHED RECURSIVE SORTS: 5 BUILD TABLE: 24 BUILD INDEX: 4 COUNTED NEW NODES: 3 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 14 MERGEUPDATERANK: 6 TOTAL TIME: 51 Generation 13 (1302210485 -> 1302175988 nodes, 1299884838 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 17 10 42081006 10 42062196 10 42108550 10 42092470 10 42065197 10 42075445 10 42109680 10 42084194 10 42100007 10 42075475 10 42028634 10 42034490 10 42062078 10 42070771 10 42050260 10 42102771 10 42064073 10 42037005 10 42068358 10 42029196 10 42050917 10 42061223 9 37838540 9 37854114 9 37856445 9 37823724 9 37829510 9 37858094 9 37841769 9 37833571 9 37853162 9 36073063 FINISHED RECURSIVE SORTS: 5 BUILD TABLE: 24 BUILD INDEX: 4 COUNTED NEW NODES: 4 COUNTED TEMP NODES: 0 RESIZED NODES: 17 RESIZED NODES: 0 MADE NEW NODES: 7 MERGEUPDATERANK: 5 TOTAL TIME: 61 Generation 14 (1302214537 -> 1302181908 nodes, 1302060416 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 17 10 42080449 10 42062196 10 42108550 10 42092470 10 42065197 10 42077432 10 42109680 10 42079422 10 42105078 10 42086686 10 42028634 10 42034490 10 42057828 10 42070771 10 42050260 10 42101869 10 42064073 10 42033072 10 42068358 10 42029196 10 42050917 10 42061223 9 37839157 9 37857323 9 37856445 9 37823724 9 37829510 9 37858094 9 37841769 9 37830407 9 37854565 9 36073063 FINISHED RECURSIVE SORTS: 6 BUILD TABLE: 25 BUILD INDEX: 4 COUNTED NEW NODES: 4 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 15 MERGEUPDATERANK: 6 TOTAL TIME: 54 Generation 15 (1302181917 -> 1302174714 nodes, 1302174714 ranks) COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 16 10 42080449 10 42062196 10 42108550 10 42092470 10 42065197 10 42077432 10 42106393 10 42079422 10 42104568 10 42083289 10 42028634 10 42034490 10 42057828 10 42070771 10 42050260 10 42101869 10 42064073 10 42033072 10 42068358 10 42029196 10 42050917 10 42061223 9 37839157 9 37857323 9 37856445 9 37823724 9 37829510 9 37858094 9 37841769 9 37830407 9 37854565 9 36073063 FINISHED RECURSIVE SORTS: 5 Generating edges... NODE.TO -> GENOME POS: 8 BUILD FROM_INDEX 5 COUNTED NEW EDGES: 6 MADE NEW EDGES: 18 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 2 9 15135740 9 15393131 9 15405107 8 14618183 9 14778215 10 14909448 9 13688008 9 13907982 10 14610982 10 14547854 10 14414274 10 14711655 9 13959871 9 13533984 10 13850629 10 13399199 10 13653954 10 13300324 11 14094929 11 13751201 12 13902940 9 13086672 9 13379665 9 13889833 10 13769455 11 13618936 9 12195315 10 13127537 11 13067518 10 11676416 10 12402987 9 10636853 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 1 9 7028001 9 7121784 9 7049449 9 7099484 9 6739445 9 6880572 8 6968569 7 6652656 8 6570772 9 6982404 8 7001243 8 6742814 9 6916841 10 6891794 9 6567310 8 6706343 9 6986896 9 6761609 14 6607717 13 6506217 13 6298131 13 6307786 11 6185759 11 6388879 12 6637422 10 6501146 9 6329234 9 6275010 11 6380508 10 6042596 10 5858323 9 4931047 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 1 10 6706461 11 7082953 11 7125156 11 7094509 9 6975534 10 6678279 11 6926011 11 6819774 11 6889376 11 6586715 11 6737657 10 6471734 10 6536956 10 6515597 11 7104033 9 6745934 9 6616650 9 7510683 9 6849276 9 6686861 10 6817588 9 6599612 9 6383753 9 6761229 8 6336488 10 6547649 9 5898340 9 5925719 9 5937291 9 6110532 9 5937413 8 4981818 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 2 13 13799476 14 14407074 14 14413659 12 14331617 13 14289026 12 14561995 10 13630658 11 13716769 11 14896049 11 14706276 11 14349104 10 13533833 10 14437145 9 14170726 9 14913415 9 15010975 9 14032709 8 14546312 8 14446428 9 13680226 10 13957167 10 13865952 9 13868020 9 13999049 9 13603007 9 13614580 7 12011237 7 12278296 7 12355559 7 12039553 7 11801271 7 10906526 FINISHED RECURSIVE SORTS: 1 SORTED NEW EDGES: 23 COUNT NUMBER IN EACH BIN: 8 FINISHED FIRST ROUND: 9 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 10 41943040 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 37748736 9 35494906 FINISHED RECURSIVE SORTS: 6 RE-SORTED NODES: 36 PROCESS EDGES: 9 REMOVE Y: 3 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 2 10 41944437 10 41944977 10 41945769 10 41944919 10 41957086 10 41954617 10 41977393 10 41947947 10 41946249 10 41946386 10 41946733 10 41957233 10 41954403 10 41963435 10 41965766 10 41962190 10 41951291 10 41950329 10 41955279 10 41948404 10 41946675 10 41947298 10 41945470 9 37751016 9 37750149 9 37750457 9 37750571 9 37750348 9 37751498 9 37751561 9 37750951 9 35496992 FINISHED RECURSIVE SORTS: 3 SORT, Make index: 27 TOTAL: 135 Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 440418797 fchr[G]: 651336558 fchr[T]: 862234139 fchr[$]: 1302407828 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 805776293 bytes to primary GFM file: ../output/13-Hisat/PNRI_Mtr1.1.1.index.1.ht2 Wrote 325543684 bytes to secondary GFM file: ../output/13-Hisat/PNRI_Mtr1.1.1.index.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Warning: a local graph exploded (offset: 351191866, length: 57344) Warning: a local graph exploded (offset: 384697738, length: 57344) Warning: a local graph exploded (offset: 384697738, length: 57344) Warning: a local graph exploded (offset: 384697738, length: 57344) Warning: a local graph exploded (offset: 384697738, length: 57344) Warning: a local graph exploded (offset: 453704004, length: 57144) Warning: a local graph exploded (offset: 646724453, length: 57344) Warning: a local graph exploded (offset: 680878061, length: 57344) Warning: a local graph exploded (offset: 934504236, length: 57344) Warning: a local graph exploded (offset: 934504236, length: 57344) Warning: a local graph exploded (offset: 934504236, length: 57344) Warning: a local graph exploded (offset: 1106416590, length: 57344) Returning from initFromVector Wrote 849453561 bytes to primary GFM file: ../output/13-Hisat/PNRI_Mtr1.1.1.index.5.ht2 Wrote 330839076 bytes to secondary GFM file: ../output/13-Hisat/PNRI_Mtr1.1.1.index.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HGFM constructor Headers: len: 1298484359 gbwtLen: 1302407829 nodes: 1302174713 sz: 649242180 gbwtSz: 651203915 lineRate: 7 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 81385920 offsSz: 325543680 lineSz: 128 sideSz: 128 sideGbwtSz: 104 sideGbwtLen: 208 numSides: 6261577 numLines: 6261577 gbwtTotLen: 801481856 gbwtTotSz: 801481856 reverse: 0 linearFM: No Total time for call to driver() for forward index: 00:29:51