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.
Hope to here back soon.
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