[Mauve-users] Crap. It's broke.
Brought to you by:
koadman
From: ZACHARY C. <zc...@wi...> - 2016-10-03 03:12:34
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trying path ./linux-x64/progressiveMauve Running alignment. Executing ./linux-x64/progressiveMauve --output=/home/molecularecology/Desktop/mauveSPadesREf --output-guide-tree=/home/molecularecology/Desktop/mauveSPadesREf.guide_tree --backbone-output=/home/molecularecology/Desktop/mauveSPadesREf.backbone /home/molecularecology/Desktop/zcpb/refo/Ldec.genome.10062013.fa /home/molecularecology/Desktop/zcpb/spades_outputs/scaffolds.fasta Storing raw sequence at /tmp/rawseq21575.000 Sequence loaded successfully. /home/molecularecology/Desktop/zcpb/refo/Ldec.genome.10062013.fa 1170241964 base pairs. Storing raw sequence at /tmp/rawseq21575.001 Sequence loaded successfully. /home/molecularecology/Desktop/zcpb/spades_outputs/scaffolds.fasta 597642283 base pairs. Using weight 21 mers for initial seeds Creating sorted mer list Create time was: 154 seconds. Creating sorted mer list Create time was: 82 seconds. 0%..27%.. 28%..29%..30%.. 31%..32%..33%..34%..35%..36%..37%..38%..39%..40%.. 41%..42%..43%..44%..45%..46%..47%..48%..49%..50%.. 51%..52%..53%..54%..55%..56%..57%..58%..59%..60%.. 61%..62%..63%..64%..65%..66%..67%..68%..69%..70%.. 71%..72%..73%..74%..75%..76%..77%..78%..79%..80%.. 81%..82%..83%..84%..85%..86%..87%..88%..89%..90%.. 91%..92%..93%..94%..95%..96%..97%..98%..99%..100%.. done. using default bp penalty: 208036 using default bp estimate min score: 624107 Starting with 6987946 multi-matches Computing genome content distance matrix... Genome conservation distance matrix: 0 0.7505 0.7505 0 Writing guide tree to /home/molecularecology/Desktop/mauveSPadesREf.guide_tree reading tree... initializing alignment tree... Constructing seed occurrence lists for repeat detection Calculating pairwise breakpoint distances Pair 0, 1 has 4841563 initial LCBs Using scaled bp penalty: 4000 Pair (0,1) has 189698 well-supported breakpoints genome content distance matrix: 0 0.7505 0.7505 0 bp distance matrix: 0.9 0.9 0.9 0.9 Aligning... Aligning node 1 to 2 via 0! get ancestral matches Performing Sum-of-pairs Greedy Breakpoint Elimination construct LCB tracking matches There are 6381046 tracking matches There are 12762092 / 19143138 components used init tracking match LCB tracking pairwise score tracking matches get pairwise LCBs there are 4842018 pairwise LCBs scaling bp penalty by conservation weight: 0.7505 scaling bp penalty by bp weight: 0.9 Greedy BPE Scoring with scaled breakpoint penalty: 4000 1%..2%..3%..4%..5%..6%..7%..8%..9%.. 10%..11%..12%..13%..14%..15%..16%..17%..18%..19%.. 20%..21%..22%..23%..24%..25%..26%..27%..28%..29%.. 30%..31%..32%..33%..34%..35%..36%..37%..38%..39%.. 40%..41%..42%..43%..44%..45%..46%..47%..48%..49%.. 50%..51%..52%..53%..54%..55%..56%..57%..58%..59%.. 60%..61%..62%..63%..64%..65%..66%..67%..68%..69%.. 70%..71%..72%..73%..74%..75%..76%..77%..78%..79%.. 80%..81%..done Arrived at 188889 intervals Adding unaligned intervals addUnalignedIntervals yields 566486 intervals Merging unaligned intervals Marbling gaps Propagating descendant breakpoints descendant 0(1) has 1 intervals descendant 1(2) has 1 intervals propagateDescendantBreakpoints yields 188889 intervals Creating ancestral ordering Previous anchoring score: -1.79769e+308, new anchor score: 6.48718e+09 Backing up alignment tree... propagating ancestral breakpoints recursive anchor search Creating dmSML for seqI 0 Wrote raw sequence for seqI 0 Loaded sequence 0363140026b.p. MemTotal: 32840720 kB Crap. It's broke, return value 1 terminate called after throwing an instance of 'genome::gnException' Exited with error code: 134 |