Settings: Output files: "Cladocopium_goreaui_genome.*.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: /gscratch/srlab/sam/data/C_goreaui/genomes/Cladocopium_goreaui_genome_fa Reading reference sizes Time reading reference sizes: 00:00:09 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:06 Time to read SNPs and splice sites: 00:00:54 Generation 0 (1171486326 -> 1171486326 nodes, 0 ranks) COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 2 Generation 1 (1172160873 -> 1172160873 nodes, 0 ranks) COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 5 RESIZED NODES: 0 MADE NEW NODES: 1 Generation 2 (1173509969 -> 1173509969 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 1 Generation 3 (1176208436 -> 1176208436 nodes, 0 ranks) BUILT FROM_INDEX: 3 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 1 RESIZE NODES: 16 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 1 34088321 2 40702266 6 47079368 3 41584107 6 35455151 2 31623567 6 46847659 2 50814000 37 27136090 2 38377785 1 27299032 6 40948030 7 34866371 3 27034270 6 26813316 2 40206223 38 35930165 2 35819330 6 34897799 2 25319179 6 33436297 2 32259333 6 26339541 2 38703390 38 27494593 2 37844250 5 23657961 1 18581637 2 29465696 5 23662886 1 20039301 1 25514595 1 23566776 5 14368513 1 22653644 1 27129305 1 34066921 18 1 28 1 100 1 FINISHED RECURSIVE SORTS: 7 SORT NODES: 9 MERGE, UPDATE RANK: 33 Generation 4 (1181626671 -> 1179196845 nodes, 591272768 ranks) ALLOCATE FROM_TABLE: 12 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 2 7 29552673 7 29573812 7 29569456 7 29593036 7 29593729 7 29552846 7 29564023 7 29570850 7 29577539 7 29554769 7 29567132 7 29566626 7 29581253 7 29563151 7 29592322 7 29549494 7 29586600 7 29571784 7 29558686 7 29570428 7 29576927 7 29584548 7 29569658 7 29565260 7 29556336 7 29566687 7 29577996 7 29566850 7 29599666 7 29557333 7 29577544 7 29573677 7 29583141 7 29585447 7 29547647 7 29559655 7 29562652 7 29565850 7 29576153 7 25933609 FINISHED RECURSIVE SORTS: 4 BUILD TABLE: 7 BUILD INDEX: 3 COUNTED NEW NODES: 2 COUNTED TEMP NODES: 0 RESIZED NODES: 11 RESIZED NODES: 0 MADE NEW NODES: 4 MERGEUPDATERANK: 22 TOTAL TIME: 61 Generation 5 (1182018963 -> 1179188485 nodes, 867620915 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 2 FINISHED FIRST ROUND: 2 7 29554759 7 29573855 7 29567697 7 29592122 7 29593114 7 29555020 7 29563926 7 29569934 7 29574709 7 29555789 7 29563816 7 29565259 7 29578614 7 29565641 7 29592276 7 29548504 7 29587606 7 29574186 7 29556867 7 29574541 7 29575781 7 29580376 7 29570199 7 29566431 7 29556626 7 29564945 7 29576514 7 29566758 7 29596865 7 29556666 7 29575838 7 29572250 7 29582207 7 29585250 7 29549053 7 29563247 7 29564419 7 29566947 7 29575186 7 25934692 FINISHED RECURSIVE SORTS: 4 BUILD TABLE: 8 BUILD INDEX: 4 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 3 MERGEUPDATERANK: 13 TOTAL TIME: 29 Generation 6 (1180413361 -> 1180220728 nodes, 968334897 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 7 29582519 7 29601155 7 29591437 7 29620616 7 29621941 7 29583477 7 29587510 7 29595789 7 29597453 7 29582654 7 29584160 7 29589274 7 29601665 7 29594994 7 29622330 7 29569052 7 29617606 7 29603648 7 29577469 7 29606882 7 29601176 7 29602425 7 29596464 7 29592996 7 29580904 7 29588760 7 29602883 7 29592445 7 29623210 7 29581156 7 29599846 7 29595358 7 29609859 7 29611716 7 29574431 7 29592822 7 29592233 7 29594240 7 29600116 7 25956057 FINISHED RECURSIVE SORTS: 4 BUILD TABLE: 6 BUILD INDEX: 4 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 11 RESIZED NODES: 0 MADE NEW NODES: 3 MERGEUPDATERANK: 10 TOTAL TIME: 35 Generation 7 (1182034710 -> 1181703363 nodes, 1043740323 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 2 7 29623926 7 29639105 7 29625344 7 29661949 7 29664859 7 29626157 7 29619321 7 29635332 7 29631311 7 29623131 7 29613132 7 29623039 7 29636516 7 29637302 7 29665097 7 29598608 7 29662240 7 29644098 7 29606661 7 29653005 7 29637774 7 29634598 7 29634077 7 29629501 7 29616537 7 29622517 7 29641259 7 29629566 7 29661135 7 29615513 7 29632724 7 29629112 7 29649618 7 29647338 7 29610007 7 29634539 7 29632899 7 29633621 7 29633538 7 25987357 FINISHED RECURSIVE SORTS: 4 BUILD TABLE: 7 BUILD INDEX: 4 COUNTED NEW NODES: 3 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 7 TOTAL TIME: 29 Generation 8 (1184200849 -> 1183639299 nodes, 1101040691 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 2 7 29679076 7 29684249 7 29670345 7 29717392 7 29721753 7 29682270 7 29658229 7 29690643 7 29676821 7 29677864 7 29652151 7 29667606 7 29684357 7 29694625 7 29721093 7 29635064 7 29720866 7 29696435 7 29644764 7 29712081 7 29684426 7 29675170 7 29683466 7 29677345 7 29665079 7 29668405 7 29690566 7 29679706 7 29706833 7 29661616 7 29673620 7 29673924 7 29702111 7 29689464 7 29656837 7 29686755 7 29687059 7 29684981 7 29674834 7 26029418 FINISHED RECURSIVE SORTS: 3 BUILD TABLE: 6 BUILD INDEX: 4 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 9 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 7 TOTAL TIME: 27 Generation 9 (1186957249 -> 1185873675 nodes, 1141524808 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 7 29743896 7 29740119 7 29722128 7 29782423 7 29790269 7 29744608 7 29698943 7 29757874 7 29729264 7 29741738 7 29696639 7 29723534 7 29742166 7 29765480 7 29785426 7 29673082 7 29791179 7 29759569 7 29689720 7 29779496 7 29735333 7 29721922 7 29741333 7 29730982 7 29722143 7 29723219 7 29751688 7 29740706 7 29752306 7 29712661 7 29715741 7 29721774 7 29760138 7 29736743 7 29710592 7 29744887 7 29750692 7 29745562 7 29720591 7 26077109 FINISHED RECURSIVE SORTS: 4 BUILD TABLE: 6 BUILD INDEX: 4 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 6 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 7 TOTAL TIME: 25 Generation 10 (1189685237 -> 1187828095 nodes, 1166727811 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 7 29807673 7 29788699 7 29765979 7 29837704 7 29859607 7 29800827 7 29727150 7 29820247 7 29778856 7 29802948 7 29733750 7 29773199 7 29793078 7 29826477 7 29846377 7 29704771 7 29855554 7 29811901 7 29729912 7 29839326 7 29779904 7 29770645 7 29790249 7 29775315 7 29777036 7 29769013 7 29802025 7 29792373 7 29783118 7 29758848 7 29749938 7 29760972 7 29812077 7 29782214 7 29755655 7 29790258 7 29804062 7 29794201 7 29757926 7 26118231 FINISHED RECURSIVE SORTS: 4 BUILD TABLE: 6 BUILD INDEX: 3 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 8 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 6 TOTAL TIME: 25 Generation 11 (1191267570 -> 1188866299 nodes, 1180388473 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 2 7 29829551 7 29812058 7 29785800 7 29863357 7 29916695 7 29825367 7 29740620 7 29844048 7 29809115 7 29828842 7 29747933 7 29800557 7 29819852 7 29861161 7 29888454 7 29719541 7 29902980 7 29835757 7 29755815 7 29877997 7 29790926 7 29795771 7 29818817 7 29794813 7 29809414 7 29785107 7 29828020 7 29809212 7 29791523 7 29788813 7 29764803 7 29786670 7 29842525 7 29813241 7 29780524 7 29821706 7 29843061 7 29809940 7 29778249 7 26147664 FINISHED RECURSIVE SORTS: 4 BUILD TABLE: 7 BUILD INDEX: 5 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 5 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 6 TOTAL TIME: 25 Generation 12 (1191087256 -> 1189030984 nodes, 1186577404 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 7 29828203 7 29802594 7 29778319 7 29855826 7 29942149 7 29838955 7 29736436 7 29841366 7 29811776 7 29819522 7 29748801 7 29818851 7 29821428 7 29875338 7 29897700 7 29730283 7 29909183 7 29834766 7 29765447 7 29902178 7 29784555 7 29811267 7 29821525 7 29789847 7 29830381 7 29778132 7 29828813 7 29803305 7 29786114 7 29791551 7 29757572 7 29779313 7 29868042 7 29826859 7 29783665 7 29825178 7 29848759 7 29802642 7 29786797 7 26167546 FINISHED RECURSIVE SORTS: 4 BUILD TABLE: 6 BUILD INDEX: 5 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 6 TOTAL TIME: 18 Generation 13 (1189911339 -> 1188914116 nodes, 1188532394 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 2 7 29824723 7 29787443 7 29763973 7 29831855 7 29951838 7 29833874 7 29731839 7 29833522 7 29799621 7 29814124 7 29753278 7 29830316 7 29821594 7 29860507 7 29894354 7 29729217 7 29894357 7 29824002 7 29761746 7 29909101 7 29777954 7 29809279 7 29825469 7 29781363 7 29844586 7 29777631 7 29830910 7 29799829 7 29780917 7 29788354 7 29753247 7 29775445 7 29879803 7 29828303 7 29792373 7 29829361 7 29845558 7 29784020 7 29772709 7 26185721 FINISHED RECURSIVE SORTS: 3 BUILD TABLE: 6 BUILD INDEX: 5 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 5 TOTAL TIME: 17 Generation 14 (1189036715 -> 1188843872 nodes, 1188822670 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 7 29825497 7 29787415 7 29761708 7 29830608 7 29957554 7 29831693 7 29730679 7 29833132 7 29802735 7 29810454 7 29750008 7 29830486 7 29823575 7 29848816 7 29892986 7 29730107 7 29892205 7 29817811 7 29759491 7 29904458 7 29777954 7 29806066 7 29821887 7 29780811 7 29838503 7 29773289 7 29824282 7 29791690 7 29780917 7 29788040 7 29752810 7 29770672 7 29880456 7 29825906 7 29793178 7 29829361 7 29845321 7 29782554 7 29773036 7 26185721 FINISHED RECURSIVE SORTS: 4 BUILD TABLE: 6 BUILD INDEX: 5 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 5 TOTAL TIME: 17 Generation 15 (1188843985 -> 1188841416 nodes, 1188841416 ranks) COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 7 29825497 7 29787415 7 29761708 7 29830608 7 29957554 7 29831693 7 29730679 7 29833132 7 29802735 7 29810454 7 29750008 7 29830486 7 29823575 7 29848816 7 29892986 7 29730107 7 29892205 7 29817811 7 29759491 7 29904458 7 29777954 7 29806066 7 29821887 7 29780811 7 29838503 7 29773289 7 29824282 7 29791690 7 29780917 7 29786815 7 29752810 7 29770672 7 29880456 7 29824675 7 29793178 7 29829361 7 29845321 7 29782554 7 29773036 7 26185721 FINISHED RECURSIVE SORTS: 4 Generating edges... NODE.TO -> GENOME POS: 4 BUILD FROM_INDEX 3 COUNTED NEW EDGES: 1 MADE NEW EDGES: 9 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 0 6 8812465 6 9219249 7 9354480 6 9063702 7 9066729 7 9043550 7 8848464 7 8964849 9 8939990 8 8569059 8 8479328 8 8230482 9 9293207 8 8909548 8 8810598 8 8375984 8 8395731 9 8458272 8 8162788 7 7823392 7 8260208 7 7772276 7 7820046 8 8202808 8 8170976 8 7951927 8 8433902 6 8244363 5 7776433 4 7933784 6 8197809 6 7437656 6 7513353 6 7530599 7 7605017 6 8084147 6 7465459 8 7911338 7 6884086 7 6383469 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 6 6938525 6 7043231 6 7435504 7 7450883 6 7111362 6 7183638 6 7185671 5 6844588 6 7225026 7 6787142 5 6703996 6 7282505 6 7274301 6 7156237 6 6834591 6 6718617 6 7076371 7 6874994 7 6852413 7 7068695 7 6700186 6 6213286 7 6313058 10 6443679 11 6210683 10 6441978 10 6096783 12 6610267 11 6698565 8 6387545 8 6239786 7 5971611 7 6085746 7 6042075 6 6179589 7 6067369 8 6398584 6 6028101 7 5908537 6 4360419 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 7 6884589 8 7750229 7 6734649 8 6668506 8 6995094 8 7182913 7 6599024 9 6974732 7 6831124 7 6716483 7 6846998 8 7351641 7 6486670 8 7092137 7 6744418 7 6804915 7 7129741 7 6915090 6 6380673 6 6432433 6 6351456 6 6558085 7 7195154 6 6492101 7 7002860 7 6839374 6 6199224 6 6334828 6 6483419 7 6506810 8 6592506 8 6492271 8 6157145 8 6357814 8 6528219 7 5871373 8 6390599 7 5973038 6 5680171 6 4885828 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 15 8609119 12 8681587 10 8645166 11 8405171 10 9180541 6 8735604 10 9279264 9 8825186 8 8584349 8 8471623 8 9224482 7 8337792 7 8283707 7 8196859 7 8373917 7 8474699 6 8318617 6 8050408 6 8586443 6 8523790 6 8179455 6 9472374 5 8195437 5 8008223 5 8342357 6 8492308 6 9218373 8 8048435 9 8266315 6 7958535 6 7792137 6 8004667 6 7439355 6 7480828 7 8031145 5 7316968 5 7338769 5 6996933 5 7148541 5 6751908 FINISHED RECURSIVE SORTS: 0 SORTED NEW EDGES: 12 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 8 33554432 8 33554432 8 33554432 8 33554432 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 29360128 7 27019208 FINISHED RECURSIVE SORTS: 4 RE-SORTED NODES: 12 PROCESS EDGES: 5 REMOVE Y: 2 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 8 33555147 8 33559074 8 33557222 8 33567282 7 29382900 7 29365620 7 29474170 7 29361128 7 29362190 7 29360845 7 29362702 7 29373922 7 29399459 7 29368907 7 29377426 7 29436327 7 29390499 7 29371997 7 29384276 7 29373394 7 29379750 7 29380229 7 29386686 7 29411995 7 29385155 7 29379407 7 29388121 7 29392957 7 29375261 7 29361139 7 29360478 7 29367323 7 29386220 7 29364342 7 29364745 7 29361224 7 29360728 7 29362409 7 29361040 7 27019686 FINISHED RECURSIVE SORTS: 2 SORT, Make index: 13 TOTAL: 61 Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 330401523 fchr[G]: 594847660 fchr[T]: 859261994 fchr[$]: 1189533381 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 736518244 bytes to primary GFM file: Cladocopium_goreaui_genome.1.ht2 Wrote 297210360 bytes to secondary GFM file: Cladocopium_goreaui_genome.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Warning: a local graph exploded (offset: 9503294, length: 57144) Warning: a local graph exploded (offset: 9503294, length: 57144) Warning: a local graph exploded (offset: 9503294, length: 57144) Warning: a local graph exploded (offset: 101390208, length: 57344) Warning: a local graph exploded (offset: 137696952, length: 57344) Warning: a local graph exploded (offset: 208469330, length: 57344) Warning: a local graph exploded (offset: 208469330, length: 57344) Warning: a local graph exploded (offset: 363972703, length: 57344) Warning: a local graph exploded (offset: 474141473, length: 57344) Warning: a local graph exploded (offset: 516805082, length: 57344) Warning: a local graph exploded (offset: 601586925, length: 57344) Warning: a local graph exploded (offset: 709831934, length: 57344) Warning: a local graph exploded (offset: 717319675, length: 57344) Warning: a local graph exploded (offset: 780568558, length: 57344) Warning: a local graph exploded (offset: 780568558, length: 57344) Warning: a local graph exploded (offset: 999396126, length: 57344) Warning: a local graph exploded (offset: 1114246784, length: 57344) Warning: a local graph exploded (offset: 1115750854, length: 57344) Warning: a local graph exploded (offset: 1154559769, length: 57344) Returning from initFromVector Wrote 837809197 bytes to primary GFM file: Cladocopium_goreaui_genome.5.ht2 Wrote 298123864 bytes to secondary GFM file: Cladocopium_goreaui_genome.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HGFM constructor Headers: len: 1170811778 gbwtLen: 1189533382 nodes: 1188841415 sz: 585405889 gbwtSz: 594766692 lineRate: 7 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 74302589 offsSz: 297210356 lineSz: 128 sideSz: 128 sideGbwtSz: 104 sideGbwtLen: 208 numSides: 5718911 numLines: 5718911 gbwtTotLen: 732020608 gbwtTotSz: 732020608 reverse: 0 linearFM: No Total time for call to driver() for forward index: 00:31:06