Hi Brianna, It looks like you're using version 2.3.1 of Mauve to align some 2Gbp+ mouse genomes. There was an unfortunate bug in that release which prevented the alignment of such large genomes. The snapshot releases available here should have that fixed: http://gel.ahabs.wisc.edu/mauve/snapshots
Also be aware that the alignment is likely to require a computer with a lot of memory, probably 50-100GB of RAM to align mammalian genomes. Best, -Aaron On Thu, 2013-09-12 at 15:17 -0400, Brianna Flynn wrote: > Hi there, > I am new to Mauve, but it has come highly recommended to me instead of > the aligner I was using previously. All I want to start with is > aligning 2 genomes and I used the progressiveMauve GUI according to > the directions on the source page. I got the following error from the > computer: > > > OS name is: Linux arch: amd64 > trying path /opt/mauve_2.3.1/progressiveMauve > Executing: > /opt/mauve_2.3.1/linux-x64/progressiveMauve > --output=/data2/indices/peromyscus/peroDraftVmm10_progMauve_def > --output-guide-tree=/data2/indices/peromyscus/peroDraftVmm10_progMauve_def.guide_tree > > --backbone-output=/data2/indices/peromyscus/peroDraftVmm10_progMauve_def.backbone > /data2/indices/peromyscus/deermouse.20121127.agp.fa > /data2/indices/mm10/mm10.fasta > Storing raw sequence at /tmp/rawseq44553.000 > Sequence loaded successfully. > /data2/indices/peromyscus/deermouse.20121127.agp.fa 2820775490 base > pairs. > Storing raw sequence at /tmp/rawseq44553.001 > Sequence loaded successfully. > /data2/indices/mm10/mm10.fasta 2730871774 base pairs. > Using weight 21 mers for initial seeds > Creating sorted mer list > Create time was: 1664 seconds. > Creating sorted mer list > Create time was: 1384 seconds. > 0%..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%..100%.. > done. > using default bp penalty: 219592 > using default bp estimate min score: 658776 > Starting with 27926135 multi-matches > Computing genome content distance matrix... > > > > > Genome conservation distance matrix: > 0 0.769011 > 0.769011 0 > > > Writing guide tree > to /data2/indices/peromyscus/peroDraftVmm10_progMauve_def.guide_tree > reading tree... > initializing alignment tree... > matches[matchI - 1]->Length(0) = 2820775490 > matches[matchI - 1]->LeftEnd(0) = 1 > oh skeethockey mushrooms > matches[0]->Length(0) = 2820775490 > matches[0]->LeftEnd(0) = 1 > oh skeethockey mushrooms too > matches[matchI - 1]->Length(0) = 2730871774 > matches[matchI - 1]->LeftEnd(0) = 1 > oh skeethockey mushrooms > matches[0]->Length(0) = 2730871774 > matches[0]->LeftEnd(0) = 1 > oh skeethockey mushrooms too > Constructing seed occurrence lists for repeat detection > terminate called after throwing an instance of > 'std::ios_base::failure' > what(): failed mapping file: Invalid argument > Exited with error code: 134 > > > > > I would sincerely appreciate any advice that anyone can offer about > what the code means or if there is something about my input sequences > that could be mucking things up. They are both FastA files so I > thought they would be fine. > -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ How ServiceNow helps IT people transform IT departments: 1. Consolidate legacy IT systems to a single system of record for IT 2. Standardize and globalize service processes across IT 3. Implement zero-touch automation to replace manual, redundant tasks http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
