Settings: Output files: "Montipora_capitata_HIv3.*.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/M_capitata/genomes/Montipora_capitata_HIv3.assembly.fasta 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: 00:00:04 Time to read SNPs and splice sites: 00:00:02 Generation 0 (780541870 -> 780541870 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 1 Generation 1 (780716764 -> 780716764 nodes, 0 ranks) COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 0 Generation 2 (781066561 -> 781066561 nodes, 0 ranks) COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 1 Generation 3 (781766571 -> 781766571 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: 8 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 1 1 32231702 2 31328288 1 21534859 6 24347530 2 19867053 6 23574809 2 21859645 6 26533487 2 35117857 37 18166336 2 20962000 6 24529211 3 20882938 7 18142603 7 25717175 2 26927205 37 16907836 2 18262869 6 22191080 3 22034227 6 16497635 7 25597221 2 18626521 1 15229048 37 17777513 2 19125639 1 15014676 5 15441583 2 17264814 1 13896029 5 15440418 2 21605618 1 15620476 5 17762816 1 16871337 1 18127142 1 32153689 0 0 38 1 108 1 FINISHED RECURSIVE SORTS: 5 SORT NODES: 7 MERGE, UPDATE RANK: 13 Generation 4 (783170887 -> 782584814 nodes, 364645477 ranks) ALLOCATE FROM_TABLE: 7 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 10 21041264 10 21029240 10 21062328 10 21027170 10 21042702 10 21029783 10 21032644 10 21044622 10 21023299 10 21042668 10 21049948 10 21028430 9 18951650 10 21027962 9 18953432 9 18940683 9 18938986 9 18922059 9 18931554 9 18944118 9 18912803 9 18928904 9 18918306 9 18923365 9 18938592 9 18931394 9 18927129 9 18926009 9 18932828 9 18919559 9 18933108 9 18918301 9 18949070 9 18923139 9 18926833 9 18891806 9 18895548 9 18898159 9 18899839 9 17025580 FINISHED RECURSIVE SORTS: 3 BUILD TABLE: 4 BUILD INDEX: 2 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 3 MERGEUPDATERANK: 14 TOTAL TIME: 35 Generation 5 (783317295 -> 782766543 nodes, 538619513 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 10 21044415 10 21033972 10 21063150 10 21032596 10 21045505 10 21035131 10 21038338 10 21046825 10 21027726 10 21044904 10 21053843 10 21032559 9 18952644 10 21032567 9 18954442 9 18943303 9 18941924 9 18927272 9 18933591 9 18945978 9 18917766 9 18933418 9 18924723 9 18927773 9 18940641 9 18934888 9 18931902 9 18929102 9 18935941 9 18925477 9 18936172 9 18925745 9 18951948 9 18927573 9 18932788 9 18899597 9 18905855 9 18908462 9 18911274 9 17034813 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 4 BUILD INDEX: 3 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 9 TOTAL TIME: 22 Generation 6 (783223644 -> 783099902 nodes, 633835572 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 10 21051062 10 21042058 10 21069795 10 21041092 10 21052912 10 21044182 10 21048230 10 21053138 10 21035885 10 21051537 10 21061515 10 21039743 9 18958455 10 21040138 9 18960322 9 18950214 9 18949140 9 18935869 9 18939558 9 18953152 9 18925718 9 18940521 9 18934102 9 18935781 9 18946131 9 18942707 9 18939579 9 18934993 9 18942990 9 18934410 9 18942495 9 18935219 9 18959719 9 18935059 9 18942035 9 18909345 9 18919045 9 18922808 9 18929008 9 17050240 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 4 BUILD INDEX: 2 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 7 TOTAL TIME: 19 Generation 7 (783619260 -> 783468221 nodes, 699612380 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 10 21057735 10 21050125 10 21077388 10 21049273 10 21060151 10 21055030 10 21058595 10 21059420 10 21046041 10 21058771 10 21069966 10 21047320 9 18965096 10 21048421 9 18967129 9 18959053 9 18957227 9 18944494 9 18946112 9 18961951 9 18933199 9 18947711 9 18943856 9 18944612 9 18951800 9 18952616 9 18947545 9 18941994 9 18950664 9 18943726 9 18949067 9 18943291 9 18968600 9 18943158 9 18952129 9 18918248 9 18933221 9 18938648 9 18952857 9 17071981 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 4 BUILD INDEX: 2 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 3 RESIZED NODES: 0 MADE NEW NODES: 2 MERGEUPDATERANK: 5 TOTAL TIME: 17 Generation 8 (784014585 -> 783853708 nodes, 738331862 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 10 21064678 10 21058976 10 21085098 10 21056872 10 21067618 10 21066073 10 21070354 10 21065137 10 21055811 10 21067337 10 21078208 10 21055809 9 18972829 10 21059140 9 18975304 9 18968732 9 18966249 9 18954077 9 18951114 9 18972505 9 18940220 9 18954525 9 18953454 9 18953467 9 18957310 9 18963088 9 18955618 9 18947714 9 18959216 9 18951264 9 18956353 9 18951255 9 18979278 9 18949172 9 18960863 9 18925430 9 18945975 9 18955723 9 18981438 9 17100424 FINISHED RECURSIVE SORTS: 3 BUILD TABLE: 4 BUILD INDEX: 2 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 3 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 4 TOTAL TIME: 15 Generation 9 (784396861 -> 784223731 nodes, 759623093 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 1 10 21071989 10 21067647 10 21093200 10 21063414 10 21074959 10 21077825 10 21080571 10 21070251 10 21065535 10 21077581 10 21086545 10 21063787 9 18981029 10 21070828 9 18983047 9 18978262 9 18975768 9 18962797 9 18955258 9 18981520 9 18947353 9 18959354 9 18960414 9 18963423 9 18963993 9 18970667 9 18962204 9 18953988 9 18967173 9 18957516 9 18963400 9 18959420 9 18990263 9 18952646 9 18967697 9 18930098 9 18952947 9 18970875 9 19013684 9 17134803 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 4 BUILD INDEX: 3 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 4 TOTAL TIME: 16 Generation 10 (784723803 -> 784516803 nodes, 772022652 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 10 21077657 10 21074789 10 21102394 10 21066215 10 21080342 10 21088322 10 21088661 10 21072295 10 21075094 10 21083874 10 21093194 10 21067531 9 18989217 10 21082665 9 18989036 9 18988043 9 18983860 9 18969537 9 18960635 9 18987142 9 18954741 9 18963315 9 18963998 9 18973671 9 18968701 9 18975099 9 18967685 9 18958699 9 18972193 9 18962378 9 18969022 9 18964815 9 18999195 9 18955436 9 18971074 9 18932114 9 18957518 9 18983227 9 19039327 9 17164092 FINISHED RECURSIVE SORTS: 3 BUILD TABLE: 4 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 3 TOTAL TIME: 14 Generation 11 (784926490 -> 784725221 nodes, 779182267 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 1 10 21082603 10 21078621 10 21110202 10 21066557 10 21083346 10 21094442 10 21093051 10 21072551 10 21080863 10 21086967 10 21096614 10 21071898 9 18998850 10 21095420 9 18993767 9 18999302 9 18994362 9 18973814 9 18963232 9 18988913 9 18957248 9 18966386 9 18965355 9 18979041 9 18973730 9 18976755 9 18971425 9 18962121 9 18973638 9 18966594 9 18976019 9 18968874 9 19005184 9 18958290 9 18972186 9 18934883 9 18962307 9 18994302 9 19054726 9 17180782 FINISHED RECURSIVE SORTS: 3 BUILD TABLE: 5 BUILD INDEX: 2 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 4 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 3 TOTAL TIME: 15 Generation 12 (784998421 -> 784828289 nodes, 782881785 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 2 10 21082751 10 21076965 10 21121991 10 21065370 10 21083466 10 21099550 10 21094120 10 21073748 10 21081953 10 21090928 10 21101541 10 21079680 9 19004445 10 21105229 9 18991151 9 19003773 9 19008690 9 18973530 9 18961022 9 18989091 9 18956561 9 18965092 9 18964084 9 18981213 9 18982342 9 18981393 9 18974870 9 18962037 9 18972540 9 18969363 9 18982364 9 18971980 9 19003600 9 18957166 9 18970476 9 18938459 9 18963598 9 18995446 9 19065885 9 17180826 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 4 BUILD INDEX: 2 COUNTED NEW NODES: 1 COUNTED TEMP NODES: 0 RESIZED NODES: 3 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 3 TOTAL TIME: 14 Generation 13 (784941642 -> 784833087 nodes, 784289680 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 1 10 21083762 10 21072696 10 21127398 10 21065296 10 21082757 10 21099678 10 21093879 10 21072165 10 21080332 10 21091156 10 21108329 10 21078540 9 19007390 10 21099914 9 18994785 9 19004775 9 19009527 9 18972110 9 18960314 9 18984970 9 18952537 9 18962701 9 18964084 9 18982300 9 18985366 9 18978547 9 18975750 9 18964295 9 18972192 9 18967626 9 18988780 9 18972867 9 19001965 9 18957166 9 18970476 9 18938969 9 18963213 9 18993325 9 19075119 9 17176036 FINISHED RECURSIVE SORTS: 3 BUILD TABLE: 5 BUILD INDEX: 3 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 3 TOTAL TIME: 12 Generation 14 (784846995 -> 784830531 nodes, 784771836 ranks) ALLOCATE FROM_TABLE: 0 COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 1 10 21083762 10 21072368 10 21124959 10 21065296 10 21082757 10 21099678 10 21093879 10 21070166 10 21080332 10 21091156 10 21108329 10 21076516 9 19007813 10 21099486 9 18994785 9 19004775 9 19009283 9 18972110 9 18960314 9 18984970 9 18952417 9 18962701 9 18964084 9 18982300 9 18984850 9 18978547 9 18975750 9 18963856 9 18971936 9 18967016 9 18987427 9 18972867 9 19001346 9 18956588 9 18970476 9 18938969 9 18963213 9 18993325 9 19081099 9 17179030 FINISHED RECURSIVE SORTS: 2 BUILD TABLE: 4 BUILD INDEX: 3 COUNTED NEW NODES: 0 COUNTED TEMP NODES: 0 RESIZED NODES: 0 RESIZED NODES: 0 MADE NEW NODES: 1 MERGEUPDATERANK: 2 TOTAL TIME: 10 Generation 15 (784830531 -> 784829449 nodes, 784829449 ranks) COUNT NUMBER IN EACH BIN: 1 FINISHED FIRST ROUND: 1 10 21083762 10 21072368 10 21124959 10 21065296 10 21082757 10 21099678 10 21093879 10 21070166 10 21080332 10 21091156 10 21108329 10 21076516 9 19007813 10 21099486 9 18994785 9 19004775 9 19009254 9 18972110 9 18960314 9 18984970 9 18952417 9 18962701 9 18964084 9 18982300 9 18984850 9 18978517 9 18975750 9 18963856 9 18971936 9 18967016 9 18987427 9 18972867 9 19001346 9 18956588 9 18970476 9 18938969 9 18963213 9 18993325 9 19080076 9 17179030 FINISHED RECURSIVE SORTS: 3 Generating edges... NODE.TO -> GENOME POS: 3 BUILD FROM_INDEX 2 COUNTED NEW EDGES: 1 MADE NEW EDGES: 4 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 8 6228181 8 6279716 8 6396035 8 6197214 7 5927742 8 6059534 9 6365343 8 5960991 9 6525229 8 5997203 8 6265659 9 6402331 8 5936763 9 6109053 10 6250084 10 6095053 10 5996992 11 6362447 10 5940764 10 5792243 10 5885628 10 6227127 10 6254250 10 6184714 10 6180590 9 5556188 10 5995237 10 6003497 10 5992499 10 5937557 9 5602772 10 5555724 11 5548526 10 5369690 10 5398332 10 5325332 10 5566792 11 5299829 10 5373902 9 4591266 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 9 4002368 9 4067133 9 4160432 9 4031586 10 4307137 9 4293731 8 3932899 8 3961144 8 3946450 8 3925054 9 4162954 9 4182983 8 3909053 10 4155673 9 4047531 9 3872235 9 4043289 10 4148716 10 4115713 9 3923543 9 3810176 12 3999355 11 3892343 11 3976714 12 3998105 12 3869213 11 3952710 11 3817226 10 3775737 11 3851085 9 3724998 8 3792910 9 3802689 8 3557740 8 3562153 9 3489812 9 3612718 8 3367048 9 3531283 9 3128616 FINISHED RECURSIVE SORTS: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 9 4020671 10 4221417 10 4309999 11 4127241 10 4064374 10 4151414 9 4068825 9 4083273 10 3982575 10 4133805 11 4146069 10 4138065 9 3798704 10 4182923 9 4058345 9 4119809 9 4096281 9 4103156 9 3980718 9 3960054 9 3904396 9 3831909 9 3966167 9 3962189 9 3990636 9 3778961 9 3800164 9 3607294 9 3760580 9 3835558 9 3595648 10 3849470 10 3793604 9 3630471 9 3621695 9 3417050 10 3575896 9 3430419 9 3397851 9 3220051 FINISHED RECURSIVE SORTS: 0 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 0 14 5994525 15 6325226 13 6102187 12 5933828 14 6142971 15 6242361 12 6001070 12 5977891 11 6306098 10 6170751 10 6222038 10 6267926 10 6383389 10 6240949 10 6372316 9 5931170 9 6243212 9 6073587 8 5793844 9 6013359 9 6396956 8 5725615 8 6085700 8 5632016 8 6070909 8 5643742 8 5662419 8 5996855 8 6052808 8 5948033 8 6094669 8 5716488 8 5599971 7 5336979 7 5490264 7 5789303 7 5692979 7 5496449 7 5479749 6 3997961 FINISHED RECURSIVE SORTS: 1 SORTED NEW EDGES: 6 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 10 20971520 10 20971520 10 20971520 10 20971520 10 20971520 10 20971520 10 20971520 10 20971520 10 20971520 10 20971520 10 20971520 10 20971520 10 20971520 10 20971520 10 20971520 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 18874368 9 17271817 FINISHED RECURSIVE SORTS: 3 RE-SORTED NODES: 8 PROCESS EDGES: 3 REMOVE Y: 1 COUNT NUMBER IN EACH BIN: 0 FINISHED FIRST ROUND: 1 10 20972176 10 20972708 10 20973462 10 20972213 10 20975476 10 20980500 10 20984966 10 20993456 10 20976176 10 20973061 10 20972833 10 20973707 10 20980062 10 20977880 10 20980111 9 18888660 9 18877489 9 18885522 9 18890470 9 18879089 9 18877430 9 18878469 9 18876734 9 18879776 9 18881289 9 18876911 9 18877702 9 18875665 9 18876317 9 18875213 9 18875617 9 18874985 9 18875121 9 18875127 9 18875143 9 18875311 9 18875482 9 18875838 9 18875565 9 17272863 FINISHED RECURSIVE SORTS: 1 SORT, Make index: 7 TOTAL: 35 Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 236938029 fchr[G]: 392640284 fchr[T]: 548358011 fchr[$]: 785006574 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 487386530 bytes to primary GFM file: Montipora_capitata_HIv3.1.ht2 Wrote 196207368 bytes to secondary GFM file: Montipora_capitata_HIv3.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Warning: a local graph exploded (offset: 125108518, length: 57344) Warning: a local graph exploded (offset: 125108518, length: 57344) Warning: a local graph exploded (offset: 143464038, length: 57244) Warning: a local graph exploded (offset: 202692854, length: 57344) Warning: a local graph exploded (offset: 208211214, length: 57344) Warning: a local graph exploded (offset: 220712054, length: 57344) Warning: a local graph exploded (offset: 253202994, length: 57244) Warning: a local graph exploded (offset: 278269695, length: 57344) Warning: a local graph exploded (offset: 303107774, length: 57244) Warning: a local graph exploded (offset: 314424294, length: 57344) Warning: a local graph exploded (offset: 333942300, length: 57244) Warning: a local graph exploded (offset: 495424544, length: 57244) Warning: a local graph exploded (offset: 495424544, length: 57244) Warning: a local graph exploded (offset: 525549844, length: 57344) Warning: a local graph exploded (offset: 607747438, length: 57344) Warning: a local graph exploded (offset: 718200534, length: 57344) Warning: a local graph exploded (offset: 748781898, length: 57344) Returning from initFromVector Wrote 547749433 bytes to primary GFM file: Montipora_capitata_HIv3.5.ht2 Wrote 198811154 bytes to secondary GFM file: Montipora_capitata_HIv3.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HGFM constructor Headers: len: 780366976 gbwtLen: 785006575 nodes: 784829448 sz: 390183488 gbwtSz: 392503288 lineRate: 7 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 49051841 offsSz: 196207364 lineSz: 128 sideSz: 128 sideGbwtSz: 104 sideGbwtLen: 208 numSides: 3774071 numLines: 3774071 gbwtTotLen: 483081088 gbwtTotSz: 483081088 reverse: 0 linearFM: No Total time for call to driver() for forward index: 00:13:47