Settings: Output files: "../output/12-Peve-lncRNA-discovery/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/12-Peve-lncRNA-discovery/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: 00:00:03 Time to read SNPs and splice sites: 00:00:02 Generation 0 (563213590 -> 563213590 nodes, 0 ranks) COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 7 RESIZED NODES: 0 MADE NEW NODES: 1 Generation 1 (563378013 -> 563378013 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 2 (563706870 -> 563706870 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 5 RESIZED NODES: 0 MADE NEW NODES: 1 Generation 3 (564365043 -> 564365043 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 1 25101437 2 22826067 1 15568505 6 17423205 2 14318724 6 17006562 2 16221638 6 19280822 2 24871191 37 12530767 2 14856523 6 16742494 3 15646805 7 12404222 6 11847263 2 14670488 1 11677647 37 12126588 2 12865874 6 15208612 3 15457901 6 11593032 2 11516891 6 13742495 2 17905748 37 13727106 2 14447650 1 11199572 5 10905221 2 11965141 1 10114687 5 10925620 2 14551403 1 11148642 5 13712190 1 12103843 1 12458732 1 25011448 2 1 16 1 37 1 91 1 FINISHED RECURSIVE SORTS: 4 SORT NODES: 7 MERGE, UPDATE RANK: 9 Generation 4 (565682760 -> 565154188 nodes, 343561961 ranks) ALLOCATE FROM_TABLE: 15 COUNT NUMBER IN EACH BIN: 4 FINISHED FIRST ROUND: 4 7 14749095 7 14753029 7 14746584 7 14748743 7 14738876 7 14742158 7 14738749 7 14741195 7 14745117 7 14735515 7 14740500 7 14743328 7 14739940 7 14742677 7 14733043 7 14741290 7 14740196 6 12631419 6 12624342 6 12626922 6 12629157 6 12628048 6 12626945 6 12627476 6 12626384 6 12628984 6 12625071 6 12624442 6 12622646 6 12629719 6 12624615 6 12622101 6 12627050 6 12626350 6 12626659 6 12626526 6 12625542 6 12623503 6 12622864 6 12622963 6 12621218 6 11513207 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 9 BUILD INDEX: 2 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 7 RESIZED NODES: 0 MADE NEW NODES: 4 MERGEUPDATERANK: 7 TOTAL TIME: 45 Generation 5 (565887731 -> 565377882 nodes, 475348256 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 7 14749531 7 14754264 7 14747345 7 14750733 7 14742802 7 14744872 7 14741953 7 14746524 7 14751142 7 14741044 7 14745418 7 14747827 7 14746113 7 14746998 7 14738659 7 14746293 7 14746377 6 12637567 6 12628865 6 12632332 6 12635605 6 12633760 6 12633057 6 12633311 6 12631435 6 12634634 6 12632375 6 12630555 6 12629046 6 12635789 6 12630245 6 12628734 6 12634175 6 12633527 6 12634890 6 12632200 6 12632285 6 12630403 6 12630749 6 12630346 6 12628031 6 11516071 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 5 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 4 TOTAL TIME: 19 Generation 6 (565866472 -> 565710385 nodes, 517855294 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 4 7 14752760 7 14757941 7 14750716 7 14756132 7 14749913 7 14749613 7 14748302 7 14754306 7 14760164 7 14748262 7 14753761 7 14755239 7 14755458 7 14754128 7 14746009 7 14754422 7 14755580 6 12647061 6 12634867 6 12640201 6 12645140 6 12641683 6 12641834 6 12640993 6 12638165 6 12643179 6 12642057 6 12639146 6 12637808 6 12644866 6 12638471 6 12636983 6 12644023 6 12642897 6 12646121 6 12640036 6 12641721 6 12640013 6 12642524 6 12640354 6 12637667 6 11519869 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 6 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 3 TOTAL TIME: 18 Generation 7 (566231379 -> 566096697 nodes, 535893212 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 3 7 14756044 7 14761726 7 14754992 7 14762525 7 14758075 7 14754948 7 14754804 7 14762904 7 14770023 7 14756748 7 14763734 7 14764589 7 14766277 7 14761935 7 14753217 7 14764583 7 14766767 6 12659144 6 12642480 6 12649330 6 12655487 6 12650546 6 12650831 6 12649463 6 12645656 6 12654035 6 12652439 6 12648515 6 12649317 6 12656253 6 12648314 6 12646244 6 12655193 6 12653923 6 12660343 6 12649159 6 12652128 6 12651525 6 12656710 6 12653324 6 12649045 6 11523402 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 6 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 3 TOTAL TIME: 18 Generation 8 (566737555 -> 566626311 nodes, 544184936 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 4 7 14761052 7 14766957 7 14759908 7 14770238 7 14769604 7 14761836 7 14764323 7 14776470 7 14782462 7 14768511 7 14776831 7 14776320 7 14780845 7 14773013 7 14762565 7 14778252 7 14783188 6 12677056 6 12653576 6 12660939 6 12669388 6 12662713 6 12662950 6 12660434 6 12657590 6 12669887 6 12666979 6 12661686 6 12666659 6 12671355 6 12661019 6 12657208 6 12670038 6 12668829 6 12679451 6 12662929 6 12666570 6 12668016 6 12676561 6 12671011 6 12663304 6 11527788 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 6 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 2 TOTAL TIME: 18 Generation 9 (567498592 -> 567287409 nodes, 552084332 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 4 7 14767328 7 14773922 7 14765729 7 14780402 7 14784610 7 14770013 7 14777769 7 14793469 7 14796120 7 14782701 7 14791630 7 14789852 7 14796064 7 14787222 7 14775913 7 14794137 7 14801249 6 12698981 6 12667999 6 12675092 6 12685178 6 12677884 6 12676850 6 12673627 6 12672225 6 12691459 6 12685528 6 12678966 6 12690274 6 12689018 6 12676519 6 12669157 6 12687328 6 12689388 6 12704282 6 12682671 6 12685186 6 12688405 6 12703658 6 12694000 6 12681842 6 11533762 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 6 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 2 TOTAL TIME: 17 Generation 10 (568295252 -> 567864082 nodes, 559547573 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 4 7 14772382 7 14779578 7 14772545 7 14790118 7 14795292 7 14775974 7 14790024 7 14809392 7 14803449 7 14793765 7 14804284 7 14801857 7 14806471 7 14800052 7 14788318 7 14808041 7 14809975 6 12719446 6 12683963 6 12689382 6 12700856 6 12692102 6 12684564 6 12690423 6 12686394 6 12709614 6 12703387 6 12696854 6 12716551 6 12703863 6 12689515 6 12680006 6 12701784 6 12707187 6 12722449 6 12703601 6 12697313 6 12706601 6 12729812 6 12710609 6 12695380 6 11540909 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 6 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 2 TOTAL TIME: 18 Generation 11 (568671556 -> 568070676 nodes, 564917914 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 4 7 14774036 7 14783433 7 14778444 7 14793135 7 14796682 7 14774974 7 14795429 7 14820154 7 14800218 7 14800601 7 14806907 7 14808553 7 14806400 7 14806730 7 14793683 7 14813269 7 14816729 6 12729004 6 12694452 6 12695754 6 12708590 6 12697371 6 12687096 6 12703707 6 12694238 6 12715038 6 12712421 6 12703287 6 12717678 6 12711102 6 12687179 6 12686010 6 12704904 6 12717367 6 12722008 6 12717434 6 12698585 6 12711576 6 12742313 6 12709834 6 12692961 6 11541390 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 6 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 2 TOTAL TIME: 17 Generation 12 (568384495 -> 567974613 nodes, 567500869 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 4 7 14775060 7 14783287 7 14782085 7 14791473 7 14790220 7 14772234 7 14785703 7 14823630 7 14797938 7 14801151 7 14801538 7 14813551 7 14805743 7 14807965 7 14793176 7 14818932 7 14812930 6 12724791 6 12690895 6 12697932 6 12706090 6 12692786 6 12689274 6 12707399 6 12694131 6 12705988 6 12713757 6 12697574 6 12707714 6 12702248 6 12683061 6 12692933 6 12698797 6 12714344 6 12708944 6 12720720 6 12690912 6 12712909 6 12736237 6 12701806 6 12686136 6 11540619 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 13 (568010184 -> 567937916 nodes, 567927833 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 4 7 14775060 7 14782524 7 14782085 7 14788868 7 14785746 7 14772233 7 14784064 7 14826620 7 14797428 7 14794996 7 14800829 7 14813390 7 14806354 7 14806997 7 14792141 7 14821347 7 14811157 6 12722589 6 12687318 6 12693207 6 12706538 6 12690634 6 12689273 6 12707747 6 12693855 6 12704991 6 12713757 6 12697574 6 12703497 6 12702077 6 12683061 6 12691671 6 12697790 6 12714345 6 12707688 6 12724459 6 12689418 6 12712909 6 12734209 6 12701904 6 12684947 6 11540619 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: 3 MERGEUPDATERANK: 2 TOTAL TIME: 13 Generation 14 (567937917 -> 567935208 nodes, 567935208 ranks) COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 4 7 14775060 7 14782524 7 14782085 7 14788868 7 14785746 7 14772233 7 14784064 7 14826620 7 14797428 7 14794996 7 14800829 7 14813390 7 14806354 7 14804827 7 14792141 7 14821347 7 14811157 6 12722589 6 12687124 6 12693207 6 12706538 6 12690634 6 12689273 6 12707747 6 12693855 6 12704991 6 12713757 6 12697574 6 12703497 6 12702077 6 12683061 6 12691671 6 12697790 6 12714345 6 12707688 6 12724459 6 12689418 6 12712909 6 12733865 6 12701904 6 12684947 6 11540619 FINISHED RECURSIVE SORTS: 2 Generating edges... NODE.TO -> GENOME POS: 2 BUILD FROM_INDEX 2 COUNTED NEW EDGES: 1 MADE NEW EDGES: 6 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 6 4885324 5 4140323 5 4187803 6 4786644 5 4294205 5 4225653 6 4347706 6 4342803 6 4578137 6 4365460 6 4399144 6 4702812 6 4300998 6 4375501 6 4135465 7 4420563 7 4422813 7 3952902 7 4089367 7 4244861 7 4071041 7 4098990 6 3956012 7 4486769 7 4394782 7 4436373 6 3836481 7 4352863 7 4305165 7 4276142 6 3793150 7 3900308 7 4169698 7 3636414 8 4029107 7 3785359 7 3758596 7 3622621 7 3567801 7 3305975 6 3198424 6 3166276 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 7 2890650 7 2934614 7 3031129 7 2855684 7 2762901 6 2816906 6 2794825 6 2948825 6 3073577 6 2763944 6 2689242 6 2733532 6 2735366 7 2860647 6 2615074 6 2564450 5 2590811 6 2665369 7 2913970 6 2687733 6 2563215 7 2616590 8 2654971 8 2608047 7 2647234 8 2467403 8 2505878 8 2761463 7 2443465 7 2622918 7 2506645 7 2715615 6 2775916 6 2610334 5 2310394 5 2311107 6 2652831 7 2615073 6 2509147 6 2371513 5 1925958 5 1728509 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 7 2972403 7 2852119 7 2844267 8 2974440 7 2786983 7 2899820 7 3018303 6 2587463 7 2736932 7 2729934 7 2730027 7 2645948 7 2910943 7 2810354 6 2602592 7 2945479 6 2834399 6 2732698 6 2549145 6 2542542 6 2654944 6 2607708 6 2519381 6 2664474 6 2746251 5 2568254 6 2617138 6 2540766 7 2734996 6 2508786 6 2511846 7 2706970 6 2444322 7 2652896 6 2396188 6 2345281 6 2330714 7 2605229 7 2371023 6 2298202 7 2540324 5 1819225 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 10 4450009 10 4451603 9 4166550 8 4129045 9 4400277 10 4267643 9 4168529 8 4121886 8 4414678 7 4140721 7 4374345 7 4504471 7 4276947 7 4436737 7 4268252 7 4409593 6 4024226 6 4170732 6 4016472 6 4359517 7 4493853 6 4131268 6 3942972 6 4471405 6 4220655 6 4508823 6 4356151 6 4253614 5 3925316 5 3801177 6 4528809 5 3899514 6 4186196 6 4197345 5 3817298 5 4054884 5 4266685 4 3436867 4 3302851 4 3310680 4 3265591 4 3086463 FINISHED RECURSIVE SORTS: 0 SORTED NEW EDGES: 7 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 2 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 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12582912 6 12189928 FINISHED RECURSIVE SORTS: 1 RE-SORTED NODES: 10 PROCESS EDGES: 3 REMOVE Y: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 7 14680881 7 14681063 7 14681890 7 14681416 7 14682184 7 14690037 7 14687106 7 14697157 7 14691655 7 14681689 7 14681717 7 14681687 7 14683370 7 14689341 7 14686371 7 14696120 7 14682968 7 14687215 7 14695356 6 12589671 6 12585492 6 12586579 6 12585239 6 12585909 6 12587555 6 12588008 6 12585212 6 12585940 6 12583872 6 12584946 6 12583971 6 12584216 6 12583706 6 12583837 6 12583792 6 12583900 6 12583882 6 12584138 6 12584075 6 12584586 6 12583978 6 12190939 FINISHED RECURSIVE SORTS: 1 SORT, Make index: 8 TOTAL: 40 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/12-Peve-lncRNA-discovery/genome.index.1.ht2 Wrote 141983808 bytes to secondary GFM file: ../output/12-Peve-lncRNA-discovery/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/12-Peve-lncRNA-discovery/genome.index.5.ht2 Wrote 143271634 bytes to secondary GFM file: ../output/12-Peve-lncRNA-discovery/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: 00:16:01