Settings: Output files: "../output/25-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/25-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: 00:00:02 Time to read SNPs and splice sites: 00:00:02 Generation 0 (518464064 -> 518464064 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 1 (518614210 -> 518614210 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 2 (518914510 -> 518914510 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 3 (519515646 -> 519515646 nodes, 0 ranks) BUILT FROM_INDEX: 1 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 3 43947945 9 43487740 13 40256119 40 44010525 10 36566456 15 34759206 40 34809757 10 35711026 15 38732952 40 34357309 9 41285188 8 35060114 7 35400066 147 22336955 FINISHED RECURSIVE SORTS: 3 SORT NODES: 3 MERGE, UPDATE RANK: 5 Generation 4 (520721358 -> 520154430 nodes, 264742891 ranks) ALLOCATE FROM_TABLE: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37885761 36 37885026 36 37908429 36 37878687 36 37860076 35 36823093 35 36827366 35 36848510 35 36795415 35 36841081 35 36859459 35 36861649 35 36795471 35 36084407 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 2 BUILD INDEX: 0 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 5 TOTAL TIME: 10 Generation 5 (520656422 -> 520270430 nodes, 357421480 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37895524 36 37891008 36 37917248 36 37884644 36 37869907 35 36833869 35 36833374 35 36858121 35 36808242 35 36849222 35 36867287 35 36866718 35 36804985 35 36090281 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 1 BUILD INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 4 TOTAL TIME: 7 Generation 6 (520563564 -> 520465205 nodes, 408601196 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37911777 36 37902326 36 37932163 36 37895711 36 37885009 35 36850064 35 36844249 35 36873267 35 36825331 35 36863199 35 36881861 35 36878545 35 36819832 35 36101871 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 1 BUILD INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 2 TOTAL TIME: 6 Generation 7 (520751259 -> 520646504 nodes, 447241210 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 0 36 37927726 36 37913375 36 37945302 36 37906472 36 37897723 35 36864447 35 36853793 35 36888376 35 36840248 35 36875950 35 36895299 35 36889513 35 36834121 35 36114159 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 2 BUILD INDEX: 0 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 2 TOTAL TIME: 6 Generation 8 (520898308 -> 520805607 nodes, 472837373 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 36 37942545 36 37922799 36 37956318 36 37915942 36 37909395 35 36877038 35 36861899 35 36903227 35 36852892 35 36884885 35 36906628 35 36897311 35 36846181 35 36128547 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 2 BUILD INDEX: 0 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 1 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 1 TOTAL TIME: 5 Generation 9 (521038890 -> 520962281 nodes, 489429515 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 36 37954843 36 37933731 36 37965560 36 37927783 36 37918269 35 36890812 35 36866895 35 36920327 35 36865677 35 36893507 35 36915160 35 36903323 35 36857075 35 36149319 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 2 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: 5 Generation 10 (521216790 -> 521145128 nodes, 500447506 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 0 36 37963382 36 37948278 36 37973105 36 37940682 36 37930082 35 36903931 35 36869803 35 36945472 35 36875305 35 36900086 35 36925660 35 36911433 35 36872960 35 36184949 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 2 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: 5 Generation 11 (521452029 -> 521368817 nodes, 508241068 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37970393 36 37971973 36 37977900 36 37962146 36 37947086 35 36910484 35 36870340 35 36981421 35 36882935 35 36907297 35 36936462 35 36919191 35 36892810 35 36238379 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 1 BUILD INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 1 TOTAL TIME: 4 Generation 12 (521781777 -> 521668059 nodes, 513842279 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37974470 36 38006509 36 37986690 36 37994793 36 37973658 35 36920616 35 36872797 35 37039509 35 36892550 35 36916354 35 36940766 35 36927032 35 36904873 35 36317442 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 1 BUILD INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 1 TOTAL TIME: 4 Generation 13 (522161938 -> 521997960 nodes, 517764179 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37977332 36 38038412 36 37995140 36 38039549 36 38001424 35 36930358 35 36878330 35 37146455 35 36902704 35 36923047 35 36946292 35 36928354 35 36898312 35 36392251 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 2 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: 4 Generation 14 (522528028 -> 522346221 nodes, 520735761 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37977203 36 38058975 36 38003332 36 38071131 36 38020866 35 36937242 36 37925123 35 37323228 35 36909351 35 36926003 35 36941473 35 36937762 35 36900160 34 35414372 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 2 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: 4 Generation 15 (522880049 -> 522624644 nodes, 522077441 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 36 37977125 36 38050134 36 38007528 36 38119921 36 38018651 36 37989439 35 36866755 35 37579440 35 36909351 35 36926003 35 36936216 35 36924273 35 36888369 34 35431439 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 2 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: 4 Generation 16 (523254062 -> 522863003 nodes, 522430433 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37977125 36 38050134 36 38007528 36 38108845 36 38018651 36 37989439 35 36866755 35 37828875 35 36909351 35 36926003 35 36936216 35 36924273 35 36888369 34 35431439 FINISHED RECURSIVE SORTS: 1 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: 1 TOTAL TIME: 4 Generation 17 (523600742 -> 523190679 nodes, 522823649 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37977125 36 38050134 36 38007528 36 38108845 36 38018651 36 37989439 36 37921389 34 37101917 35 36909351 35 36926003 35 36936216 35 36924273 35 36888369 34 35431439 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 2 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: 4 Generation 18 (524106071 -> 523739763 nodes, 523503818 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37977125 36 38050134 36 38007528 36 38108845 36 38018651 36 37989439 36 37921389 34 37651001 35 36909351 35 36926003 35 36936216 35 36924273 35 36888369 34 35431439 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 2 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: 4 Generation 19 (524491977 -> 524232346 nodes, 524232346 ranks) COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37977125 36 38050134 36 38007528 36 38108845 36 38018651 36 37989439 36 37921389 33 37089696 35 36906333 35 36925861 35 36941031 35 36918939 35 36888333 35 36489042 FINISHED RECURSIVE SORTS: 1 Generating edges... NODE.TO -> GENOME POS: 1 BUILD FROM_INDEX 0 COUNTED NEW EDGES: 1 MADE NEW EDGES: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 29 11763492 28 11496172 31 11698180 30 11415404 32 11490157 37 11611456 39 11642905 38 11292816 36 11412208 37 11431141 37 11232433 42 11426818 41 11220105 43 10948422 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 32 7420851 34 7499416 31 7441977 31 7302780 32 7338575 35 7330087 36 7331226 39 7301106 45 7390986 42 7270158 38 7288876 33 7258537 36 7318657 36 7143403 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 7469800 37 7398370 34 7445880 37 7401772 35 7394168 33 7380227 33 7365278 35 7238657 34 7249006 36 7242601 36 7223457 38 7236624 38 7137479 38 7030081 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 55 11568153 52 11507268 46 11480173 37 11544705 35 11393203 34 11432742 32 11386476 32 11624302 31 11466781 31 11230129 30 11295039 30 11225334 28 11506995 27 10790994 FINISHED RECURSIVE SORTS: 0 SORTED NEW EDGES: 2 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37748736 36 37748736 36 37748736 36 37748736 36 37748736 36 37748736 36 37748736 36 37748736 36 37748736 36 37748736 35 36700160 35 36700160 35 36700160 35 36644506 FINISHED RECURSIVE SORTS: 2 RE-SORTED NODES: 3 PROCESS EDGES: 0 REMOVE Y: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 36 37750832 36 37760345 36 37780631 36 37754992 36 37760672 36 37771978 36 37775816 36 37757161 36 37761546 36 37754272 35 36703680 35 36701910 35 36702560 35 36647644 FINISHED RECURSIVE SORTS: 1 SORT, Make index: 2 TOTAL: 11 Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 160081709 fchr[G]: 262718344 fchr[T]: 364931744 fchr[$]: 524384038 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 326897143 bytes to primary GFM file: ../output/25-lncRNA/genome.index.1.ht2 Wrote 131058092 bytes to secondary GFM file: ../output/25-lncRNA/genome.index.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Warning: a local graph exploded (offset: 13925001, length: 57344) Warning: a local graph exploded (offset: 38659720, length: 57344) Warning: a local graph exploded (offset: 38603400, length: 57344) Warning: a local graph exploded (offset: 41948817, length: 57344) Warning: a local graph exploded (offset: 115973349, length: 57344) Warning: a local graph exploded (offset: 125396706, length: 57344) Warning: a local graph exploded (offset: 132961805, length: 57344) Warning: a local graph exploded (offset: 132961805, length: 57344) Warning: a local graph exploded (offset: 169175565, length: 57344) Warning: a local graph exploded (offset: 171282211, length: 57344) Warning: a local graph exploded (offset: 184461091, length: 57344) Warning: a local graph exploded (offset: 209498906, length: 57344) Warning: a local graph exploded (offset: 209498906, length: 57344) Warning: a local graph exploded (offset: 219411226, length: 57344) Warning: a local graph exploded (offset: 219411226, length: 57344) Warning: a local graph exploded (offset: 219411226, length: 57344) Warning: a local graph exploded (offset: 219411226, length: 57344) Warning: a local graph exploded (offset: 302771998, length: 57344) Warning: a local graph exploded (offset: 302771998, length: 57344) Warning: a local graph exploded (offset: 358471409, length: 57344) Warning: a local graph exploded (offset: 358471409, length: 57344) Warning: a local graph exploded (offset: 358471409, length: 57344) Warning: a local graph exploded (offset: 392037709, length: 57344) Warning: a local graph exploded (offset: 515228365, length: 56507) Returning from initFromVector Wrote 350535931 bytes to primary GFM file: ../output/25-lncRNA/genome.index.5.ht2 Wrote 132185422 bytes to secondary GFM file: ../output/25-lncRNA/genome.index.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HGFM constructor Headers: len: 518313916 gbwtLen: 524384039 nodes: 524232345 sz: 259156958 gbwtSz: 262192020 lineRate: 7 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 32764522 offsSz: 131058088 lineSz: 128 sideSz: 128 sideGbwtSz: 104 sideGbwtLen: 208 numSides: 2521078 numLines: 2521078 gbwtTotLen: 322697984 gbwtTotSz: 322697984 reverse: 0 linearFM: No Total time for call to driver() for forward index: 00:05:08