Settings: Output files: "../output/17-Peve-lncRNA/genome.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/17-Peve-lncRNA/genome.fasta 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: 00:00:07 Time to read SNPs and splice sites: 00:00:03 Generation 0 (563213590 -> 563213590 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 1 (563378013 -> 563378013 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 2 (563706870 -> 563706870 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 3 (564365043 -> 564365043 nodes, 0 ranks) BUILT FROM_INDEX: 0 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 RESIZE NODES: 2 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 1 25101437 2 22826067 1 15568505 6 17423205 7 24455176 3 23091748 6 19280822 2 24871191 38 19400016 2 17312135 7 16128289 7 15924710 7 15262924 2 14670488 38 23804235 3 20918073 7 15754205 6 13681367 3 16288665 6 13742495 2 17905748 37 13727106 2 14447650 1 11199572 6 17725684 2 15259365 5 10925620 2 14551403 1 11148642 5 13712190 1 12103843 1 12458732 1 25011448 2 1 16 1 128 2 FINISHED RECURSIVE SORTS: 2 SORT NODES: 2 MERGE, UPDATE RANK: 6 Generation 4 (565682760 -> 565154188 nodes, 343561961 ranks) ALLOCATE FROM_TABLE: 2 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 16856217 8 16859180 8 16851406 8 16854805 8 16847140 8 16843535 8 16846146 8 16850136 8 16842140 8 16845491 8 16851440 8 16845753 8 16840975 8 16845475 8 16845874 8 16834072 8 16838916 7 14733174 7 14733380 7 14730408 7 14733138 7 14731932 7 14730356 7 14728136 7 14727061 7 14732692 7 14730600 7 14727034 7 14729602 7 14732151 7 14731014 7 14729496 7 14727123 7 14726914 7 14724678 7 13616598 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 1 BUILD INDEX: 0 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 5 TOTAL TIME: 10 Generation 5 (565887731 -> 565377882 nodes, 475348256 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 16857174 8 16860188 8 16852310 8 16858232 8 16850666 8 16847771 8 16851683 8 16856745 8 16848102 8 16851714 8 16856826 8 16852130 8 16846671 8 16851306 8 16852892 8 16841843 8 16845518 7 14740493 7 14740134 7 14737295 7 14740094 7 14737389 7 14738434 7 14735781 7 14734193 7 14739396 7 14737746 7 14735756 7 14737726 7 14741589 7 14737819 7 14737542 7 14735491 7 14735922 7 14733035 7 13620276 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 1 BUILD INDEX: 0 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 2 TOTAL TIME: 5 Generation 6 (565866472 -> 565710385 nodes, 517855294 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 8 16861216 8 16863985 8 16856284 8 16866347 8 16856985 8 16854663 8 16860203 8 16866581 8 16856429 8 16861594 8 16865796 8 16861871 8 16854407 8 16860765 8 16863504 8 16853056 8 16854935 7 14751354 7 14749475 7 14746949 7 14749086 7 14745545 7 14749419 7 14746583 7 14744165 7 14749342 7 14747808 7 14747579 7 14747813 7 14754462 7 14747072 7 14748682 7 14748161 7 14748721 7 14744249 7 13625299 FINISHED RECURSIVE SORTS: 0 BUILD TABLE: 1 BUILD INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 MERGEUPDATERANK: 2 TOTAL TIME: 5 Generation 7 (566231379 -> 566096697 nodes, 535893212 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 16865139 8 16868168 8 16861438 8 16876380 8 16863555 8 16861306 8 16870032 8 16877586 8 16866356 8 16873519 8 16876283 8 16872720 8 16862151 8 16872491 8 16876384 8 16867412 8 16866174 7 14763238 7 14759706 7 14757364 7 14758072 7 14756059 7 14761749 7 14758535 7 14757097 7 14761873 7 14759438 7 14761200 7 14759133 7 14770846 7 14758083 7 14760806 7 14763895 7 14763927 7 14758201 7 13630381 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 1 BUILD INDEX: 0 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 MERGEUPDATERANK: 2 TOTAL TIME: 4 Generation 8 (566737555 -> 566626311 nodes, 544184936 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 16871297 8 16872944 8 16867954 8 16890190 8 16871917 8 16870389 8 16885697 8 16891928 8 16879940 8 16887803 8 16890585 8 16887718 8 16872660 8 16888165 8 16895400 8 16888202 8 16882080 7 14778465 7 14773495 7 14771469 7 14771431 7 14771311 7 14779174 7 14775359 7 14776309 7 14778188 7 14773979 7 14778685 7 14774210 7 14793188 7 14774833 7 14777213 7 14786573 7 14783663 7 14776999 7 13636898 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 1 BUILD INDEX: 0 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 MERGEUPDATERANK: 2 TOTAL TIME: 4 Generation 9 (567498592 -> 567287409 nodes, 552084332 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 16879564 8 16878569 8 16875744 8 16908472 8 16882492 8 16883068 8 16905333 8 16907888 8 16896866 8 16903239 8 16904929 8 16906662 8 16886627 8 16907428 8 16917148 8 16914371 8 16901221 7 14795759 7 14791130 7 14787041 7 14787756 7 14790334 7 14802819 7 14797459 7 14801087 7 14797538 7 14791452 7 14799139 7 14794397 7 14822353 7 14798638 7 14796746 7 14817625 7 14809340 7 14802695 7 13644480 FINISHED RECURSIVE SORTS: 0 BUILD TABLE: 0 BUILD INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 MERGEUPDATERANK: 1 TOTAL TIME: 3 Generation 10 (568295252 -> 567864082 nodes, 559547573 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 16886404 8 16882480 8 16886066 8 16921645 8 16890116 8 16895908 8 16922686 8 16917760 8 16909909 8 16914608 8 16916952 8 16921835 8 16900182 8 16924991 8 16929848 8 16940861 8 16921621 7 14811292 7 14807768 7 14798220 7 14806419 7 14806718 7 14824319 7 14819894 7 14828541 7 14813483 7 14807258 7 14815903 7 14813026 7 14843144 7 14821848 7 14811473 7 14843366 7 14832594 7 14823037 7 13651907 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 1 BUILD INDEX: 0 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 1 TOTAL TIME: 4 Generation 11 (568671556 -> 568070676 nodes, 564917914 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 16889661 8 16885100 8 16892614 8 16924893 8 16889240 8 16899696 8 16935083 8 16916671 8 16918607 8 16913973 8 16920394 8 16928340 8 16904354 8 16934022 8 16937599 8 16956929 8 16931015 7 14818986 7 14811979 7 14806499 7 14819010 7 14811128 7 14837455 7 14827087 7 14830029 7 14819861 7 14806836 7 14822792 7 14823368 7 14843362 7 14837767 7 14813655 7 14849515 7 14837174 7 14823234 7 13652748 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 1 BUILD INDEX: 0 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 MERGEUPDATERANK: 1 TOTAL TIME: 3 Generation 12 (568384495 -> 567974613 nodes, 567500869 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 16890932 8 16884707 8 16894137 8 16920300 8 16885748 8 16890783 8 16937085 8 16914589 8 16919458 8 16910798 8 16921240 8 16930235 8 16904264 8 16939410 8 16930558 8 16953189 8 16932952 7 14815939 7 14806774 7 14811720 7 14819355 7 14805670 7 14835435 7 14821955 7 14816783 7 14814120 7 14807244 7 14821072 7 14820176 7 14828646 7 14841049 7 14808017 7 14845196 7 14828322 7 14815109 7 13651646 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 1 BUILD INDEX: 0 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 0 MERGEUPDATERANK: 1 TOTAL TIME: 2 Generation 13 (568010184 -> 567937916 nodes, 567927833 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 8 16890794 8 16884082 8 16894137 8 16915690 8 16883278 8 16889144 8 16940075 8 16911411 8 16915897 8 16910112 8 16921130 8 16930877 8 16902568 8 16941487 8 16928785 8 16950375 8 16925262 7 14816387 7 14804622 7 14811955 7 14819467 7 14805310 7 14834522 7 14821955 7 14812566 7 14813949 7 14808159 7 14817969 7 14820096 7 14827390 7 14845804 7 14805507 7 14845262 7 14826228 7 14814018 7 13651646 FINISHED RECURSIVE SORTS: 0 BUILD TABLE: 1 BUILD INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 0 MERGEUPDATERANK: 1 TOTAL TIME: 3 Generation 14 (567937917 -> 567935208 nodes, 567935208 ranks) COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 16890794 8 16884082 8 16894137 8 16915690 8 16883278 8 16889144 8 16940075 8 16911411 8 16915897 8 16910112 8 16921130 8 16928707 8 16902568 8 16941487 8 16928785 8 16950375 8 16925068 7 14816387 7 14804622 7 14811955 7 14819467 7 14805310 7 14834522 7 14821955 7 14812566 7 14813949 7 14808159 7 14817969 7 14820096 7 14827390 7 14845804 7 14805507 7 14845262 7 14825884 7 14814018 7 13651646 FINISHED RECURSIVE SORTS: 1 Generating edges... NODE.TO -> GENOME POS: 1 BUILD FROM_INDEX 0 COUNTED NEW EDGES: 0 MADE NEW EDGES: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 6 4885324 6 4955212 6 5004369 6 4809539 6 5251881 7 5274804 7 5029332 7 5330078 7 5096791 7 5397695 7 5049673 7 5165723 7 4817557 8 5077139 8 4994943 9 4976038 8 4851199 8 4669706 8 4731512 8 5181635 8 5092571 8 5077911 7 4516101 8 4987014 8 4913213 8 4887785 8 4831544 8 4716574 8 4364111 9 4444438 8 4345726 8 4273692 8 4301603 9 4250216 8 4098660 7 3695522 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 3327635 8 3330143 7 3090421 8 3068607 8 3528167 7 3310880 7 3379681 6 3073577 7 3143318 7 3230525 7 3175883 8 3363931 7 3069147 8 3433348 6 3095872 8 3383417 8 3448181 7 3039731 8 2933669 9 3036851 9 3118978 9 3022412 10 3031775 9 3117901 9 3075073 8 3130691 8 2855748 7 3080075 7 3112067 6 2731633 6 2779248 7 2938761 7 2710638 7 2922287 7 2647507 6 2115697 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 3412977 8 3150979 8 3252536 9 3430343 8 3306570 8 3356673 8 3489855 8 3026509 8 3249269 9 3283558 8 3339088 8 3201579 8 3343078 7 3160868 7 3192811 7 3081302 7 3009833 7 3073907 7 3024612 7 2948747 7 3151474 7 3244819 6 2920587 7 2973733 8 3170612 7 2880221 7 2890874 8 3229866 8 3000979 7 2783452 7 2767599 8 2992114 8 2878180 8 2907533 7 2569507 6 2195065 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 11 4858470 11 4902259 11 5291707 10 5090343 11 4932753 11 4958124 10 5075825 9 5214079 8 4979397 8 5053053 8 4887380 8 5060051 8 4941878 8 5078182 7 4708787 7 4875456 7 4924347 8 5213995 7 4812985 7 4763511 7 4979502 6 4571374 7 5018862 7 5021597 6 4642373 6 4579134 6 4546280 6 4454375 7 4981494 7 5032840 6 4891100 5 4266685 5 4278638 5 4122892 5 4126768 5 3874154 FINISHED RECURSIVE SORTS: 0 SORTED NEW EDGES: 2 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 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 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 14287080 FINISHED RECURSIVE SORTS: 1 RE-SORTED NODES: 2 PROCESS EDGES: 1 REMOVE Y: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 16778215 8 16778597 8 16779226 8 16778444 8 16788180 8 16783057 8 16796015 8 16789031 8 16779088 8 16779114 8 16779877 8 16786786 8 16784164 8 16793890 8 16780728 8 16788052 8 16793736 8 16780649 8 16781629 7 14682658 7 14684960 7 14686537 7 14682673 7 14683522 7 14681116 7 14682579 7 14680850 7 14681601 7 14681060 7 14681134 7 14681215 7 14681127 7 14681696 7 14681701 7 14681462 7 14288297 FINISHED RECURSIVE SORTS: 1 SORT, Make index: 2 TOTAL: 9 Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 173346831 fchr[G]: 284200306 fchr[T]: 395092015 fchr[$]: 568102665 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 354684900 bytes to primary GFM file: ../output/17-Peve-lncRNA/genome.index.1.ht2 Wrote 141983808 bytes to secondary GFM file: ../output/17-Peve-lncRNA/genome.index.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Warning: a local graph exploded (offset: 107984333, length: 57219) Warning: a local graph exploded (offset: 147351179, length: 57344) Warning: a local graph exploded (offset: 172269137, length: 55417) Warning: a local graph exploded (offset: 231359163, length: 56828) Warning: a local graph exploded (offset: 260213041, length: 56851) Warning: a local graph exploded (offset: 321480042, length: 57038) Warning: a local graph exploded (offset: 321480042, length: 57038) Warning: a local graph exploded (offset: 439634616, length: 56791) Warning: a local graph exploded (offset: 468707454, length: 57343) Warning: a local graph exploded (offset: 481225062, length: 53449) Warning: a local graph exploded (offset: 481225062, length: 53449) Returning from initFromVector Wrote 438681801 bytes to primary GFM file: ../output/17-Peve-lncRNA/genome.index.5.ht2 Wrote 143271634 bytes to secondary GFM file: ../output/17-Peve-lncRNA/genome.index.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HGFM constructor Headers: len: 563049165 gbwtLen: 568102666 nodes: 567935207 sz: 281524583 gbwtSz: 284051334 lineRate: 7 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 35495951 offsSz: 141983804 lineSz: 128 sideSz: 128 sideGbwtSz: 104 sideGbwtLen: 208 numSides: 2731263 numLines: 2731263 gbwtTotLen: 349601664 gbwtTotSz: 349601664 reverse: 0 linearFM: No Total time for call to driver() for forward index: 00:06:45