Settings: Output files: "../output/17-Ptuh-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-Ptuh-lncRNA/genome.fasta Reading reference sizes Time reading reference sizes: 00:00:02 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 Time to read SNPs and splice sites: 00:00:02 Generation 0 (376743094 -> 376743094 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 1 (376906272 -> 376906272 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 2 (377232638 -> 377232638 nodes, 0 ranks) COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 3 (377885652 -> 377885652 nodes, 0 ranks) BUILT FROM_INDEX: 0 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 0 RESIZE NODES: 2 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 1 16480325 3 26372907 8 20997567 7 16280846 7 19806861 2 17456072 39 18547385 8 16067487 9 14961925 7 14507364 38 16575105 3 14590596 8 14114153 8 13965493 8 20989359 38 14300112 7 19984457 3 15147003 6 12636982 2 12508902 6 17781152 1 8603410 1 16518930 146 4 FINISHED RECURSIVE SORTS: 2 SORT NODES: 2 MERGE, UPDATE RANK: 4 Generation 4 (379194397 -> 378534816 nodes, 240705876 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 15820604 15 15836120 15 15825758 15 15825422 15 15820521 15 15789516 15 15818026 15 15823204 15 15809748 15 15796782 15 15778237 15 15839927 15 15783766 15 15821924 15 15809530 15 15818415 15 15808563 15 15797806 15 15797033 15 15812131 15 15838087 15 15815402 15 15806323 15 14841971 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: 1 MERGEUPDATERANK: 3 TOTAL TIME: 5 Generation 5 (378979682 -> 378592021 nodes, 307454446 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 15822719 15 15837507 15 15826303 15 15829074 15 15822473 15 15792598 15 15819134 15 15824664 15 15811782 15 15799716 15 15781685 15 15841754 15 15786630 15 15822455 15 15811482 15 15819489 15 15810609 15 15801855 15 15801607 15 15814315 15 15839179 15 15817626 15 15808545 15 14848820 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: 1 MERGEUPDATERANK: 1 TOTAL TIME: 3 Generation 6 (378799003 -> 378727505 nodes, 334740479 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 0 15 15829598 15 15842323 15 15830514 15 15836011 15 15827473 15 15797933 15 15824625 15 15829970 15 15816499 15 15805308 15 15787314 15 15846892 15 15792132 15 15826991 15 15816768 15 15824219 15 15815095 15 15808786 15 15808938 15 15820478 15 15844807 15 15822706 15 15814224 15 14857901 FINISHED RECURSIVE SORTS: 0 BUILD TABLE: 1 BUILD INDEX: 0 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 0 MERGEUPDATERANK: 1 TOTAL TIME: 3 Generation 7 (378918238 -> 378844707 nodes, 353899401 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 15836902 15 15846215 15 15833117 15 15841862 15 15831233 15 15802789 15 15829781 15 15834851 15 15820176 15 15809725 15 15791766 15 15850618 15 15797398 15 15830803 15 15820985 15 15828480 15 15818443 15 15814121 15 15815820 15 15826174 15 15849595 15 15827581 15 15818803 15 14867469 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: 1 MERGEUPDATERANK: 1 TOTAL TIME: 3 Generation 8 (379004130 -> 378942311 nodes, 364949704 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 15843117 15 15849229 15 15835013 15 15846217 15 15833923 15 15806545 15 15833414 15 15837544 15 15823842 15 15812475 15 15794833 15 15852763 15 15803593 15 15834737 15 15824152 15 15832000 15 15821957 15 15818725 15 15821365 15 15830404 15 15854772 15 15831535 15 15823510 15 14876646 FINISHED RECURSIVE SORTS: 0 BUILD TABLE: 0 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: 2 Generation 9 (379070273 -> 379023413 nodes, 370753253 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 15847114 15 15851330 15 15837089 15 15849111 15 15836805 15 15809421 15 15833971 15 15839979 15 15827632 15 15813893 15 15796572 15 15854573 15 15810862 15 15836648 15 15825876 15 15833737 15 15825282 15 15821444 15 15824968 15 15834352 15 15858904 15 15835078 15 15830587 15 14888185 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 10 (379138588 -> 379094553 nodes, 374045257 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 15849630 15 15852461 15 15839158 15 15849903 15 15837467 15 15811944 15 15834757 15 15842910 15 15830131 15 15814372 15 15797229 15 15855723 15 15816584 15 15837764 15 15826991 15 15836026 15 15826806 15 15823392 15 15827552 15 15836891 15 15864022 15 15838896 15 15839143 15 14904801 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: 1 MERGEUPDATERANK: 0 TOTAL TIME: 2 Generation 11 (379197024 -> 379150175 nodes, 376054726 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 15849657 15 15851569 15 15842214 15 15849312 15 15837371 15 15813464 15 15834934 15 15843930 15 15830994 15 15816530 15 15798334 15 15856196 15 15819013 15 15838088 15 15826038 15 15836063 15 15829113 15 15827131 15 15829326 15 15839727 15 15869384 15 15841797 15 15846073 15 14923917 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 (379238581 -> 379187140 nodes, 377436170 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 15849704 15 15850092 15 15844927 15 15849312 15 15837371 15 15815512 15 15833787 15 15843319 15 15831290 15 15818578 15 15798650 15 15856416 15 15816975 15 15838088 15 15826029 15 15834860 15 15831312 15 15833048 15 15831508 15 15843653 15 15874362 15 15842113 15 15853185 15 14933049 FINISHED RECURSIVE SORTS: 0 BUILD TABLE: 0 BUILD INDEX: 0 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 0 MERGEUPDATERANK: 1 TOTAL TIME: 2 Generation 13 (379279715 -> 379232727 nodes, 378492635 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 15849117 15 15850092 15 15845913 15 15849312 15 15837371 15 15815650 15 15833745 15 15843319 15 15827557 15 15822674 15 15798650 15 15856416 15 15814099 15 15838088 15 15826029 15 15834860 15 15834717 15 15843359 15 15832263 15 15849372 15 15881492 15 15845096 15 15856585 15 14946951 FINISHED RECURSIVE SORTS: 0 BUILD TABLE: 0 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: 2 Generation 14 (379304138 -> 379248130 nodes, 379116739 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 15845597 15 15850092 15 15845913 15 15849312 15 15837371 15 15811428 15 15833745 15 15843319 15 15826941 15 15830866 15 15798650 15 15856416 15 15814099 15 15838088 15 15826029 15 15834860 15 15834717 15 15851376 15 15832143 15 15857564 15 15881492 15 15841582 15 15849248 15 14957282 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 15 (379273989 -> 379258951 nodes, 379258951 ranks) COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 15845597 15 15850092 15 15845913 15 15849312 15 15837371 15 15811428 15 15833745 15 15843319 15 15826941 15 15831596 15 15798650 15 15856416 15 15814099 15 15838088 15 15826029 15 15834860 15 15834717 15 15858880 15 15827425 15 15865068 15 15881492 15 15841582 15 15846763 15 14959568 FINISHED RECURSIVE SORTS: 0 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 13 5145698 13 5209447 12 4971812 13 4970724 13 4877756 13 4879699 13 4959696 14 4997234 14 4895059 16 5016287 16 4836997 17 5031595 16 4864028 15 5029532 15 4878030 14 4795112 16 5027465 16 4977115 16 4817515 18 4869154 17 4633311 17 4596500 19 4821801 16 4365134 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 15 3111634 14 3066522 15 3092346 13 3037703 13 3081077 12 3048241 14 3100037 14 3179284 15 3079689 15 2979297 15 3060897 15 3038285 16 2985406 19 2950944 19 2957967 20 2988169 18 3054934 17 2997902 14 3133981 13 2887471 13 2909073 15 2938340 14 2906533 14 2617750 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 14 3120163 15 3096982 16 3098963 16 3113109 14 3224005 15 3136592 15 3039712 16 3067324 16 3110024 15 3127243 14 3023216 15 3106668 14 2935184 15 2958436 15 3125433 15 3040753 15 3000679 14 2854105 16 2928898 16 2865514 15 2913952 15 2781333 16 2827017 15 2697145 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 22 4992917 22 5029731 21 5067838 23 4963491 20 5123038 16 5076166 15 5031528 15 5071845 15 5102054 15 5094208 14 4951268 13 4800999 14 4933004 13 4963961 13 4931507 13 4767397 13 4858477 13 4961220 13 4834722 13 4644695 12 4705053 11 4659037 12 4767822 11 4228802 FINISHED RECURSIVE SORTS: 0 SORTED NEW EDGES: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 16 16777216 16 16777216 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15728640 15 15403079 FINISHED RECURSIVE SORTS: 1 RE-SORTED NODES: 2 PROCESS EDGES: 0 REMOVE Y: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 16 16778157 16 16779732 15 15730735 15 15740848 15 15759435 15 15734741 15 15730547 15 15731897 15 15741153 15 15749923 15 15736734 15 15751477 15 15733208 15 15733867 15 15737978 15 15735122 15 15731434 15 15731133 15 15730236 15 15729698 15 15729851 15 15730205 15 15730703 15 15404600 FINISHED RECURSIVE SORTS: 1 SORT, Make index: 1 TOTAL: 7 Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 117466701 fchr[G]: 189670183 fchr[T]: 261862633 fchr[$]: 379423413 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 237697865 bytes to primary GFM file: ../output/17-Ptuh-lncRNA/genome.index.1.ht2 Wrote 94814744 bytes to secondary GFM file: ../output/17-Ptuh-lncRNA/genome.index.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Warning: a local graph exploded (offset: 322184488, length: 57344) Returning from initFromVector Wrote 256383163 bytes to primary GFM file: ../output/17-Ptuh-lncRNA/genome.index.5.ht2 Wrote 96078770 bytes to secondary GFM file: ../output/17-Ptuh-lncRNA/genome.index.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HGFM constructor Headers: len: 376579914 gbwtLen: 379423414 nodes: 379258950 sz: 188289957 gbwtSz: 189711708 lineRate: 7 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 23703685 offsSz: 94814740 lineSz: 128 sideSz: 128 sideGbwtSz: 104 sideGbwtLen: 208 numSides: 1824152 numLines: 1824152 gbwtTotLen: 233491456 gbwtTotSz: 233491456 reverse: 0 linearFM: No Total time for call to driver() for forward index: 00:02:46