Hello ! Am a new user for Mauve and I tried aligning two mammalian bat genomes (rna.gbk files) but the error code 134 was returned and I am not able to find out a solution for the same. I used the Progressive Mauve and retained the default values for parameters and scoring. Do suggest a solution. The console log is as follows.
OS name is: Linux arch: i386 trying path /home/mku/Downloads/mauve_2.3.1/progressiveMauve Executing: /home/mku/Downloads/mauve_2.3.1/progressiveMauve --output=/home/mku/Pictures/mauve --output-guide-tree=/home/mku/Pictures/mauve.guide_tree --backbone-output=/home/mku/Pictures/mauve.backbone /media/SWETHA/My Project!/Sequences/M.brandtii/M.brandtii rna.gbk /media/SWETHA/My Project!/Sequences/P.alecto/P.alecto rna.gbk Storing raw sequence at /tmp/rawseq7653.000 Sequence loaded successfully. /media/SWETHA/My Project!/Sequences/M.brandtii/M.brandtii rna.gbk 81248420 base pairs. Storing raw sequence at /tmp/rawseq7653.001 Sequence loaded successfully. /media/SWETHA/My Project!/Sequences/P.alecto/P.alecto rna.gbk 57233395 base pairs. Using weight 19 mers for initial seeds Creating sorted mer list Create time was: 77 seconds. Creating sorted mer list Create time was: 55 seconds. 0%..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%..82%..83%..84%..85%..86%..87%..88%..89%..90%.. 91%..92%..93%..94%..95%..96%..97%..98%..99%..done. using default bp penalty: 182316 using default bp estimate min score: 546948 Starting with 189877 multi-matches Computing genome content distance matrix... Genome conservation distance matrix: 0 0.786507 0.786507 0 Writing guide tree to /home/mku/Pictures/mauve.guide_tree reading tree... initializing alignment tree... Constructing seed occurrence lists for repeat detection Calculating pairwise breakpoint distances Pair 0, 1 has 57809 initial LCBs Using scaled bp penalty: 4000 Pair (0,1) has 7854 well-supported breakpoints genome content distance matrix: 0 0.786507 0.786507 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 172041 tracking matches There are 344082 / 516123 components used init tracking match LCB tracking pairwise score tracking matches get pairwise LCBs there are 57731 pairwise LCBs scaling bp penalty by conservation weight: 0.786507 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%..done Arrived at 8076 intervals Adding unaligned intervals addUnalignedIntervals yields 24211 intervals Merging unaligned intervals Marbling gaps Propagating descendant breakpoints descendant 0(1) has 1 intervals descendant 1(2) has 1 intervals propagateDescendantBreakpoints yields 8076 intervals Creating ancestral ordering Previous anchoring score: -1.79769e+308, new anchor score: 8.83463e+08 Backing up alignment tree... propagating ancestral breakpoints recursive anchor search Creating dmSML for seqI 0 Wrote raw sequence for seqI 0 Loaded sequence 023837698b.p. MemTotal: 3966888 kB Crap. It's broke, return value 1 terminate called after throwing an instance of 'genome::gnException' Exited with error code: 134 ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
