Settings: Output files: "../output/10.1-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: 00:00:04 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:03 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: 1 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: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 5 RESIZED NODES: 0 MADE NEW NODES: 1 RESIZE NODES: 11 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 1 2 24138687 2 19085681 5 16481509 3 19849916 6 18692184 2 16408669 6 16914113 2 20547161 38 23460273 2 20211512 6 17978261 7 17082412 3 13675250 6 16410528 2 18642488 38 15900337 2 17476677 6 14700810 7 20157188 2 15523834 6 13932344 2 20523216 38 18716760 2 12560394 6 19801456 2 12163144 1 11206146 5 10001527 2 17149945 1 16377403 5 9505541 1 8800849 1 9912942 1 14822425 18 2 128 2 FINISHED RECURSIVE SORTS: 3 SORT NODES: 6 MERGE, UPDATE RANK: 8 Generation 4 (558811586 -> 557941980 nodes, 347556972 ranks) ALLOCATE FROM_TABLE: 18 COUNT NUMBER IN EACH BIN: 4 FINISHED FIRST ROUND: 3 8 16867423 8 16887309 8 16847432 8 16846472 8 16892998 8 16843176 8 16832204 8 16879086 8 16849847 8 16856378 8 16864304 8 16880375 8 16863026 7 14768469 7 14734496 7 14751469 7 14775503 7 14741123 7 14734230 7 14767432 7 14762669 7 14746462 7 14749109 7 14761291 7 14727289 7 14750784 7 14742209 7 14755430 7 14755160 7 14744307 7 14725768 7 14763634 7 14762472 7 14746438 7 14745657 7 14220549 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 9 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 4 MERGEUPDATERANK: 7 TOTAL TIME: 40 Generation 5 (558559987 -> 557905527 nodes, 447173183 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 8 16866322 8 16885340 8 16846959 8 16845711 8 16891328 8 16843370 8 16835758 8 16876869 8 16848695 8 16857277 8 16862258 8 16878054 8 16861633 7 14765508 7 14733706 7 14750410 7 14772311 7 14739949 7 14734116 7 14765339 7 14760329 7 14744169 7 14747715 7 14758756 7 14729011 7 14749233 7 14742614 7 14754738 7 14753032 7 14743619 7 14726117 7 14761304 7 14760953 7 14747597 7 14744461 7 14220966 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: 4 8 16870090 8 16887644 8 16850267 8 16848364 8 16894531 8 16847075 8 16841051 8 16879381 8 16851152 8 16861693 8 16864081 8 16879909 8 16865065 7 14767150 7 14735829 7 14752189 7 14773837 7 14741801 7 14737186 7 14766978 7 14761973 7 14745035 7 14749822 7 14759972 7 14733463 7 14750947 7 14745496 7 14757182 7 14754890 7 14746687 7 14728351 7 14762700 7 14763472 7 14751628 7 14746681 7 14224184 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 5 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 3 MERGEUPDATERANK: 4 TOTAL TIME: 14 Generation 7 (558138390 -> 558077038 nodes, 520901965 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 8 16874172 8 16889536 8 16853113 8 16851120 8 16896350 8 16850547 8 16844703 8 16880822 8 16852975 8 16864369 8 16865612 8 16881307 8 16868387 7 14768313 7 14737649 7 14753467 7 14775012 7 14743097 7 14739980 7 14768577 7 14763908 7 14745713 7 14751258 7 14761252 7 14737333 7 14752976 7 14748496 7 14759711 7 14756541 7 14749655 7 14730645 7 14763446 7 14765272 7 14755374 7 14749084 7 14227266 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: 3 MERGEUPDATERANK: 2 TOTAL TIME: 12 Generation 8 (558181901 -> 558131068 nodes, 539273927 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 3 8 16876159 8 16890817 8 16855933 8 16853297 8 16896702 8 16852254 8 16846412 8 16881547 8 16853891 8 16866124 8 16866292 8 16882528 8 16870846 7 14769187 7 14739499 7 14753937 7 14776384 7 14744227 7 14742769 7 14769015 7 14765930 7 14746283 7 14752581 7 14762296 7 14741129 7 14754273 7 14751765 7 14761245 7 14757176 7 14751415 7 14731281 7 14763926 7 14766143 7 14757324 7 14751165 7 14229316 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: 3 TOTAL TIME: 13 Generation 9 (558203646 -> 558163040 nodes, 549213118 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 4 8 16877137 8 16890711 8 16858701 8 16854697 8 16896513 8 16852906 8 16846600 8 16881697 8 16854810 8 16868254 8 16866430 8 16884106 8 16871942 7 14769888 7 14740646 7 14753983 7 14776730 7 14745010 7 14744667 7 14768740 7 14767921 7 14746415 7 14753808 7 14763023 7 14744528 7 14754824 7 14754689 7 14761405 7 14756950 7 14752134 7 14731895 7 14764116 7 14766232 7 14758086 7 14751948 7 14230898 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 5 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 3 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: 4 8 16877967 8 16890181 8 16861422 8 16856466 8 16896602 8 16853740 8 16846416 8 16882234 8 16856076 8 16871266 8 16866430 8 16885831 8 16873716 7 14769511 7 14741705 7 14753927 7 14777140 7 14745378 7 14744689 7 14768740 7 14770636 7 14746415 7 14754541 7 14763593 7 14746298 7 14755336 7 14756307 7 14761374 7 14756824 7 14752620 7 14732796 7 14764116 7 14765529 7 14758365 7 14752395 7 14234048 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 11 (558246671 -> 558220698 nodes, 556303271 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 3 8 16878906 8 16889826 8 16863689 8 16859204 8 16896602 8 16853899 8 16846474 8 16882821 8 16857380 8 16874708 8 16866430 8 16887669 8 16875047 7 14769511 7 14742787 7 14753636 7 14777544 7 14745768 7 14743321 7 14768571 7 14774625 7 14746415 7 14756589 7 14763315 7 14748436 7 14756360 7 14757661 7 14760794 7 14756824 7 14754427 7 14734844 7 14764116 7 14765529 7 14758100 7 14752491 7 14236379 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: 3 MERGEUPDATERANK: 2 TOTAL TIME: 13 Generation 12 (558257399 -> 558233138 nodes, 557538929 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 4 8 16879047 8 16889826 8 16864923 8 16860110 8 16896602 8 16853899 8 16846689 8 16882260 8 16857380 8 16874120 8 16866430 8 16887669 8 16876954 7 14769511 7 14742787 7 14753636 7 14777544 7 14745768 7 14743120 7 14768571 7 14779752 7 14746415 7 14757206 7 14763137 7 14745983 7 14758408 7 14757539 7 14760191 7 14756824 7 14756171 7 14737530 7 14764116 7 14765529 7 14758100 7 14752415 7 14236976 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 5 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 3 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 8 16879047 8 16889826 8 16863191 8 16860110 8 16896602 8 16853899 8 16846689 8 16882260 8 16857380 8 16870934 8 16866430 8 16887669 8 16879732 7 14769511 7 14742787 7 14753636 7 14777544 7 14745768 7 14743120 7 14768571 7 14777602 7 14746415 7 14757206 7 14763137 7 14745983 7 14758784 7 14757114 7 14760191 7 14756824 7 14756171 7 14737530 7 14764116 7 14765529 7 14758100 7 14752415 7 14236803 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 5 BUILD INDEX: 2 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: 1 FINISHED FIRST ROUND: 3 8 16879047 8 16889826 8 16862749 8 16860110 8 16896602 8 16853899 8 16846689 8 16882260 8 16857380 8 16870934 8 16866430 8 16887669 8 16883575 7 14769511 7 14741439 7 14753636 7 14777544 7 14745768 7 14743120 7 14768571 7 14777304 7 14746415 7 14757206 7 14763137 7 14744373 7 14758784 7 14757114 7 14760191 7 14756824 7 14756171 7 14737530 7 14764116 7 14765529 7 14758100 7 14752415 7 14236803 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: 3 MERGEUPDATERANK: 2 TOTAL TIME: 13 Generation 15 (558228771 -> 558228771 nodes, 558228771 ranks) COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 8 16879047 8 16889826 8 16862749 8 16860110 8 16896602 8 16853899 8 16846689 8 16882260 8 16857380 8 16870934 8 16866430 8 16887669 8 16883575 7 14769511 7 14741439 7 14753636 7 14777544 7 14745768 7 14743120 7 14768571 7 14777304 7 14746415 7 14757206 7 14763137 7 14744373 7 14758784 7 14757114 7 14760191 7 14756824 7 14756171 7 14737530 7 14764116 7 14765529 7 14758100 7 14752415 7 14236803 FINISHED RECURSIVE SORTS: 1 Generating edges... NODE.TO -> GENOME POS: 2 BUILD FROM_INDEX 2 COUNTED NEW EDGES: 1 MADE NEW EDGES: 6 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 0 6 4485735 6 4267918 6 4416036 9 4691177 8 4765767 9 4426291 9 4657927 7 4603061 7 4168880 8 4506410 4 4547733 5 4150689 7 4509743 7 4208559 9 4122920 8 4593749 10 4501673 9 4510440 7 4634473 5 4148310 7 4283798 7 4083313 7 4309070 7 4050144 8 4207420 10 3993507 7 4269572 7 4448953 7 3917753 8 3657113 9 4229166 7 3546514 9 3710325 7 3814561 7 3488606 7 3123459 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 3856907 8 3897119 7 4563347 3 3576846 6 3775526 6 3818915 6 3525140 6 3783130 6 3503357 7 3927808 7 3921625 7 3567908 9 3495743 8 3783616 6 3785618 6 3603854 7 3824722 7 3572136 6 3331484 7 3650181 14 3323156 10 3340927 11 3524616 12 3402563 12 3387327 9 3502868 9 3532627 6 3466649 5 3205176 4 3278276 7 3787829 6 3400945 8 3138769 7 2832168 7 2919724 7 2520796 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 9 3599214 8 3784053 11 3843215 8 3825504 6 4105061 7 4019276 7 3555077 9 3609305 9 3584343 11 3747416 8 3686631 9 3774995 8 3804269 7 3686700 9 3833126 8 3791327 7 3567571 7 3836432 7 3421464 6 3308573 7 3789554 5 3618465 7 3420264 7 3508622 10 3651450 7 3204851 8 3318638 7 3168452 8 3501130 7 3473262 6 3175555 3 3541698 5 3335169 7 3015174 6 2809351 6 2381344 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 0 10 4679415 10 4454848 12 4415483 12 4490507 11 4211453 8 4357514 9 4841247 10 4529999 9 4633226 8 4514621 8 4362336 9 4286642 7 4395404 6 4447291 7 4567008 7 4061441 7 4652721 7 4269368 6 3994134 7 4223586 7 4314044 6 4810984 5 4977010 4 4462890 5 3820162 7 4184446 6 3925433 7 4088036 8 4109078 7 3756960 8 3990760 8 3864224 5 3548817 5 3551769 5 3492979 4 2491179 FINISHED RECURSIVE SORTS: 0 SORTED NEW EDGES: 7 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 1 8 16777216 8 16777216 8 16777216 8 16777216 8 16777216 8 16777216 8 16777216 8 16777216 8 16777216 8 16777216 8 16777216 8 16777216 8 16777216 8 16777216 8 16777216 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 14680064 7 12969251 FINISHED RECURSIVE SORTS: 2 RE-SORTED NODES: 10 PROCESS EDGES: 3 REMOVE Y: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 16777936 8 16779087 8 16777947 8 16791868 8 16783717 8 16794016 8 16795705 8 16778844 8 16778857 8 16779077 8 16796968 8 16784538 8 16789731 8 16800511 8 16784095 7 14694057 7 14699352 7 14684667 7 14684923 7 14684103 7 14684597 7 14687849 7 14688882 7 14683808 7 14683201 7 14682267 7 14682121 7 14681032 7 14681786 7 14681354 7 14681324 7 14681527 7 14680929 7 14680995 7 14681798 7 12970241 FINISHED RECURSIVE SORTS: 2 SORT, Make index: 8 TOTAL: 40 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/10.1-hisat-deseq2/GCF_031168955.1.index.1.ht2 Wrote 139557200 bytes to secondary GFM file: ../output/10.1-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/10.1-hisat-deseq2/GCF_031168955.1.index.5.ht2 Wrote 141646948 bytes to secondary GFM file: ../output/10.1-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: 00:09:11