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Old 11-29-2011, 07:37 AM   #1
tomiczeek
Junior Member
 
Location: London

Join Date: Nov 2011
Posts: 2
Unhappy mauveAligner & progressiveMauve

Dear users
I am trying to make a genome alignment with:
-rwxr-xr-x 1 bartek bartek 3858328 Nov 11 2009 progressiveMauve
-rwxr-xr-x 1 bartek bartek 2901448 Nov 11 2009 mauveAligner
from the command line using version for linux. Since the visual interface is working fine for me the command line is constantly exiting with the error:

attempt 1:

-rw-r--r-- 1 bartek bartek 372948 Nov 11 2009 mauve_user_guide.pdf
-rwxr-xr-x 1 bartek bartek 3858328 Nov 11 2009 progressiveMauve
-rwxr-xr-x 1 bartek bartek 2901448 Nov 11 2009 mauveAligner
-rwxr-xr-x 1 bartek bartek 855 Nov 11 2009 Mauve
-rw-r--r-- 1 bartek bartek 3563 Nov 11 2009 README
-rw-r--r-- 1 bartek bartek 18332 Nov 11 2009 COPYING
-rw-r--r-- 1 bartek bartek 422194 Nov 12 2009 Mauve.jar
-rw-r--r-- 1 bartek bartek 31510 Nov 12 2009 ChangeLog.html
drwxrwxr-x 2 bartek bartek 1024 Nov 29 13:22 linux-x64
drwxrwxr-x 2 bartek bartek 1024 Nov 29 13:22 ext
-rw-r--r-- 1 bartek bartek 19760 Nov 29 14:19 Sp.may2011.extras_mito.fasta
-rw-r--r-- 1 bartek bartek 84856 Nov 29 14:20 Sp.may2011.extras_mito.fasta.sslist
-rw-r--r-- 1 bartek bartek 12531568 Nov 29 14:21 jb50contigs.fa
-rw-r--r-- 1 bartek bartek 52296828 Nov 29 14:21 jb50contigs.fa.sslist
[[email protected] mauve_2.3.1]$ mauveAligner --output=jb50vsSpmito.mauve --output-alignment=jb50vsSpmito.alignment jb50contigs.fa Sp.may2011.extras_mito.fasta
-bash: mauveAligner: command not found
[[email protected] mauve_2.3.1]$ ./mauveAligner --output=jb50vsSpmito.mauve --output-alignment=jb50vsSpmito.alignment jb50contigs.fa Sp.may2011.extras_mito.fasta
Sequence loaded successfully.
jb50contigs.fa 12304601 base pairs.
Using weight 17 mers for initial seeds
Creating sorted mer list
Create time was: 8 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%..Starting with 0 MUMs
Eliminating overlaps yields 0 MUMs

*** ERROR *** Clust::SetLeafCount(0)

attempt 2:

[[email protected] mauve_2.3.1]$ ./mauveAligner --output=jb50vsSpmito.mauve --output-alignment=jb50vsSpmito.alignment jb50contigs.fa jb50contigs.fa.sslist Sp.may2011.extras_mito.fasta Sp.may2011.extras_mito.fasta.sslist
Sequence loaded successfully.
jb50contigs.fa 12304601 base pairs.
Sequence loaded successfully.
Sp.may2011.extras_mito.fasta 6835866 base pairs.
Using weight 17 mers for initial seeds
Sorted mer list loaded successfully
Sorted mer list loaded successfully
Segmentation fault

attempt 3:

[[email protected] mauve_2.3.1]$ ./progressiveMauve --output=jb50vsSpmito.mauve jb50contigs.fa Sp.may2011.extras_mito.fasta
Storing raw sequence at /tmp/rawseq21551.000
Sequence loaded successfully.
jb50contigs.fa 12304601 base pairs.
Storing raw sequence at /tmp/rawseq21551.001
Sequence loaded successfully.
Sp.may2011.extras_mito.fasta 6835866 base pairs.
Using weight 17 mers for initial seeds
Sorted mer list loaded successfully
Sorted mer list loaded successfully
Caught signal 11
Cleaning up and exiting!
Temporary files deleted.

In all of the above examples the output file is produced but is empty. Do I need any additional software or am I running it in a wrong way ?
Please help me with this problem or give the contact to a person that can help.

Last edited by tomiczeek; 11-30-2011 at 04:10 AM.
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