Settings: Output files: "../analyses/13-hisat-deseq2/GCA_032158295.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/GCA_032158295.1/GCA_032158295.1_ASM3215829v1_genomic.fna Reading reference sizes Time reading reference sizes: 00:00:06 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: 00:00:01 Generation 0 (483954537 -> 483954537 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 1 Generation 1 (484091882 -> 484091882 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 5 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 2 (484366576 -> 484366576 nodes, 0 ranks) COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 3 (484916235 -> 484916235 nodes, 0 ranks) BUILT FROM_INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 1 RESIZE NODES: 9 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 1 2 30461839 7 34010182 8 25353176 8 28486892 3 29592569 39 25936118 8 24724972 14 22977298 40 30623843 8 24180103 9 21554112 8 23800385 39 27569748 3 22015109 8 26667841 7 23702705 6 22603609 2 20890341 1 20868262 146 3 FINISHED RECURSIVE SORTS: 3 SORT NODES: 5 MERGE, UPDATE RANK: 7 Generation 4 (486019107 -> 485458925 nodes, 302048258 ranks) ALLOCATE FROM_TABLE: 9 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 1 24 25259494 24 25259198 23 24203135 23 24200532 23 24205677 23 24199119 23 24198193 23 24210261 23 24210701 23 24189689 23 24202010 23 24201233 23 24193325 23 24197978 23 24196814 23 24220640 23 24205117 23 24215314 23 24198163 23 23492332 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 4 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 3 MERGEUPDATERANK: 6 TOTAL TIME: 24 Generation 5 (485743916 -> 485449217 nodes, 413824412 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 24 25257445 24 25258670 23 24203968 23 24200300 23 24205100 23 24198027 23 24197265 23 24208392 23 24209124 23 24189325 23 24201477 23 24201138 23 24193584 23 24197473 23 24198241 23 24220722 23 24203530 23 24214988 23 24198116 23 23492332 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 4 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 3 TOTAL TIME: 10 Generation 6 (485531740 -> 485501772 nodes, 446361247 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 2 24 25258767 24 25261621 23 24208418 23 24203092 23 24208051 23 24200798 23 24199327 23 24210308 23 24211345 23 24191775 23 24204290 23 24203968 23 24196422 23 24199750 23 24203067 23 24223827 23 24204934 23 24218713 23 24200967 23 23492332 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 5 BUILD INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 3 TOTAL TIME: 11 Generation 7 (485581103 -> 485555156 nodes, 466019828 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 24 25259898 24 25265040 23 24212696 23 24206124 23 24211609 23 24204291 23 24200755 23 24212225 23 24213912 23 24194184 23 24207496 23 24207227 23 24198778 23 24201380 23 24208127 23 24227139 23 24206213 23 24222298 23 24203432 23 23492332 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 4 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 2 TOTAL TIME: 9 Generation 8 (485630748 -> 485608794 nodes, 475515427 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 24 25260757 24 25268632 23 24216433 23 24208954 23 24214643 23 24207877 23 24201815 23 24213690 23 24216960 23 24196942 23 24210675 23 24210787 23 24200777 23 24202683 23 24213407 23 24230923 23 24207842 23 24226504 23 24206161 23 23492332 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 5 BUILD INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 2 TOTAL TIME: 10 Generation 9 (485687999 -> 485665025 nodes, 480521691 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 24 25261754 24 25272402 23 24219008 23 24211853 23 24216721 23 24211736 23 24203532 23 24215644 23 24219814 23 24198479 23 24214440 23 24215710 23 24203210 23 24204453 23 24218574 23 24234516 23 24210212 23 24231276 23 24209359 23 23492332 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 4 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 2 TOTAL TIME: 9 Generation 10 (485743525 -> 485717598 nodes, 483506537 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 24 25262774 24 25276919 23 24219881 23 24213468 23 24218126 23 24217054 23 24204804 23 24217769 23 24219795 23 24198897 23 24218027 23 24219886 23 24205993 23 24206416 23 24225719 23 24239046 23 24212286 23 24235112 23 24213294 23 23492332 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 4 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 2 TOTAL TIME: 9 Generation 11 (485783162 -> 485752837 nodes, 484990294 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 24 25262649 24 25280133 23 24220801 23 24209911 23 24220846 23 24221976 23 24205140 23 24217031 23 24217586 23 24200447 23 24219128 23 24221718 23 24206091 23 24208719 23 24234370 23 24243289 23 24214157 23 24238616 23 24217897 23 23492332 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 5 BUILD INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 1 TOTAL TIME: 9 Generation 12 (485792697 -> 485766488 nodes, 485603335 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 2 24 25262649 24 25281971 23 24221752 23 24209680 23 24223283 23 24222789 23 24205168 23 24217031 23 24217365 23 24199549 23 24217818 23 24220704 23 24203944 23 24211175 23 24238466 23 24245141 23 24214771 23 24241417 23 24219483 23 23492332 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 5 BUILD INDEX: 1 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 2 TOTAL TIME: 10 Generation 13 (485772492 -> 485760846 nodes, 485753917 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 24 25261492 24 25281971 23 24221752 23 24209680 23 24224473 23 24221249 23 24202314 23 24217031 23 24217365 23 24199549 23 24217818 23 24220704 23 24203944 23 24211175 23 24237274 23 24245141 23 24214771 23 24241328 23 24219483 23 23492332 FINISHED RECURSIVE SORTS: 1 BUILD TABLE: 4 BUILD INDEX: 1 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 2 TOTAL TIME: 9 Generation 14 (485760846 -> 485760846 nodes, 485760846 ranks) COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 3 24 25261492 24 25281971 23 24221752 23 24209680 23 24224473 23 24221249 23 24202314 23 24217031 23 24217365 23 24199549 23 24217818 23 24220704 23 24203944 23 24211175 23 24237274 23 24245141 23 24214771 23 24241328 23 24219483 23 23492332 FINISHED RECURSIVE SORTS: 1 Generating edges... NODE.TO -> GENOME POS: 2 BUILD FROM_INDEX 1 COUNTED NEW EDGES: 1 MADE NEW EDGES: 4 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 18 7594701 19 7697957 19 7676760 22 7490868 21 7345954 20 7418388 21 7343946 21 7332465 23 7496852 25 7489530 24 7390166 24 7503604 25 7505873 26 7288178 24 7220609 25 7363683 27 7280247 26 7205370 27 7176445 27 7054232 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 21 4761563 20 4838062 20 4880398 19 4842786 18 4977808 19 4773406 19 4972381 22 4848824 22 4913268 17 4693724 21 4804073 27 4671176 34 4666755 36 4731323 30 4755957 25 4828883 21 4543685 22 4702803 24 4493598 27 4425180 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 27 4874761 27 4834236 25 4942730 22 4739993 26 4814044 27 4884505 24 4849318 23 4848483 23 4892114 23 4777707 21 4774135 19 4829128 19 4666597 22 4707511 20 4683510 23 4777035 23 4705335 22 4515875 25 4657818 23 4343165 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 35 7505180 30 7412507 34 7515213 31 7475383 26 7556276 26 7484301 26 7350220 24 7532182 20 7677140 20 7546335 21 7633170 18 7392894 18 7271327 22 7498961 20 7245052 21 7444910 21 7421324 17 7037417 17 6908457 17 6871305 FINISHED RECURSIVE SORTS: 1 SORTED NEW EDGES: 6 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 24 25165824 24 25165824 24 25165824 24 25165824 23 24117248 23 24117248 23 24117248 23 24117248 23 24117248 23 24117248 23 24117248 23 24117248 23 24117248 23 24117248 23 24117248 23 24117248 23 24117248 23 24117248 23 24117248 23 23338830 FINISHED RECURSIVE SORTS: 1 RE-SORTED NODES: 8 PROCESS EDGES: 2 REMOVE Y: 1 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 0 24 25166821 24 25167793 24 25176185 24 25189555 23 24123030 23 24119564 23 24127708 23 24126281 23 24132942 23 24138590 23 24124037 23 24123597 23 24125173 23 24121569 23 24119565 23 24118981 23 24118842 23 24118845 23 24119457 23 23340501 FINISHED RECURSIVE SORTS: 1 SORT, Make index: 7 TOTAL: 32 Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 147875828 fchr[G]: 243001481 fchr[T]: 338119481 fchr[$]: 485899035 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 303416084 bytes to primary GFM file: ../analyses/13-hisat-deseq2/GCA_032158295.index.1.ht2 Wrote 121440216 bytes to secondary GFM file: ../analyses/13-hisat-deseq2/GCA_032158295.index.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Warning: a local graph exploded (offset: 121194950, length: 57344) Warning: a local graph exploded (offset: 327235680, length: 57344) Returning from initFromVector Wrote 336934463 bytes to primary GFM file: ../analyses/13-hisat-deseq2/GCA_032158295.index.5.ht2 Wrote 123284342 bytes to secondary GFM file: ../analyses/13-hisat-deseq2/GCA_032158295.index.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HGFM constructor Headers: len: 483816647 gbwtLen: 485899036 nodes: 485760845 sz: 241908324 gbwtSz: 242949519 lineRate: 7 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 30360053 offsSz: 121440212 lineSz: 128 sideSz: 128 sideGbwtSz: 104 sideGbwtLen: 208 numSides: 2336054 numLines: 2336054 gbwtTotLen: 299014912 gbwtTotSz: 299014912 reverse: 0 linearFM: No Total time for call to driver() for forward index: 00:08:02