mauveAligner & progressiveMauve

[tomiczeek]

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
[bartek@jb-analysis1 mauve_2.3.1]$ mauveAligner --output=jb50vsSpmito.mauve --output-alignment=jb50vsSpmito.alignment jb50contigs.fa Sp.may2011.extras_mito.fasta
-bash: mauveAligner: command not found
[bartek@jb-analysis1 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:

[bartek@jb-analysis1 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:

[bartek@jb-analysis1 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.

[tirohia]

I've got this as well. A couple of differences, the first being that I don't get any output files produced at all. the second, more worrying difference is that it then completely destroys one of my input files. i.e. reduces it to size 0.
And there is no other indication of anything being wrong and google's not being very helpful.

mauveAligner NC_004578.fna Nz1334-contigs.fa
Sequence loaded successfully.
NC_004578.fna 6397126 base pairs.
Using weight 17 mers for initial seeds
Sorted mer list loaded successfully
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)

Any thoughts on possible solutions would be welcome.

[koadman]

The problems you're experiencing are happening because you've used the wrong command-line syntax for mauveAligner. The command-line syntax is documented in the manual, please read it carefully. mauveAligner requires one to specify a sequence file followed by a name for a genome-specific index file (.sslist or .sml) for that sequence that the software will create. By neglecting to include a path for the .sslist file and instead giving the next sequence name immediately, the software took that file to be the desired path for the .sslist and tried to write the index there.

tirohia, you should be running mauveAligner as:
mauveAligner --output=something NC_004578.fna NC_004578.fna.sslist Nz1334-contigs.fa Nz1334-contigs.fa.sslist

tomiczeek, your command should be:
./mauveAligner --output=jb50vsSpmito.mauve --output-alignment=jb50vsSpmito.alignment jb50contigs.fa jb50contigs.fa.sslist Sp.may2011.extras_mito.fasta Sp.may2011.extras_mito.fasta.sslist

Both of you will need to check that your sequence files are intact as they may have been overwritten by incorrect use of mauveAligner.

2nd, unless you have a compelling reason I would strongly suggest using progressiveMauve instead of mauveAligner. mauveAligner requires manual tuning of its parameters and is generally nowhere near as accurate as progressiveMauve. See this paper for details: http://www.plosone.org/article/info%...l.pone.0011147

Finally, there's a chance that the .sslist created by some versions of mauveAligner may be unreadable by progressiveMauve and it may cause a mysterious crash. If that seems to be happening and your .sslist were created by mauveAligner just delete them and progressiveMauve will recreate them. It only takes a few seconds.

[koadman]

yes, just to confirm: progressiveMauve command line syntax doesn't use an .sslist argument, it makes those files based on the sequence file names which appear on the command line. this is different to mauveAligner's syntax, which does require those to be specified.

[rskr]

Any thoughts on possible solutions would be welcome.

Mauve isn't a very mature tool, it seems like much of the tool was implemented on the cheap in java, and the command line is a bit flaky, and difficult to compile on alternate platforms. Though the paper seems like a good proof of principle, the UCSC liftover tool is more functional, IMHO.

[koadman]

Thanks for the kind words rskr and good day to you too. I am the author of mauveAligner and progressiveMauve in case you weren't aware.

liftOver is a really useful tool for porting annotations and is what I usually recommend to other people for that purpose. progressiveMauve itself just does alignment, and was never intended to solve the issue of porting annotation across assemblies by itself (though tools based on genome alignment are an effective way to do that).

If you have specific and constructive comments or questions about the Mauve GUI (implemented in Java) or the command-line tools (written in C++) please do share and I will try to respond, but silly flames are not appreciated.

[rskr]

If you have specific and constructive comments or questions about the Mauve GUI (implemented in Java) or the command-line tools (written in C++) please do share and I will try to respond, but silly flames are not appreciated.

You want me to be more specific. Seriously? Given peoples problems with the program, I thought it was pretty clear the way we felt about how your program behaves on the command line.

[koadman]

You are awesome rskr, I love you.

[SES]

I have personally only used progressiveMauve, but in any case, you need to make sure you are using the correct executable for your system architecture (32-bit vs. 64-bit). The GUI application will make this decision for you and that may explain why the command line tool throws errors.

[flxlex]

@koadman thanks for the wonderful Mauve program, I use it a lot! Also thanks for taking time to answer user questions on SeqAnswers!

[nickloman]

@koadman thanks for the wonderful Mauve program, I use it a lot! Also thanks for taking time to answer user questions on SeqAnswers!

Yes, I echo that! Mauve is one of my most used programmes - even if it is written in Java!

[lebetimonas]

I use the GUI Mauve all the time and absolutely love it.

[SeqMonster]

Move Contigs function in Mauve

I love the visualization in Mauve and I just discovered the "Move Contigs" function. I have a question about the output file. The file with .tab extension gives you the order of the contigs. However, when you look at the coordinate of the left and right_end, the number is one after another, which doesn't really make sense. Any idea how these numbers are generated and whether modifications were done on the fasta file in the alignment folder?

Another question, is there a way to export the scaffold as one single fasta file, i.e. gaps are filled with Ns?

[koadman]

Hi SeqMonster, the fasta file of contigs produced by mauve contig mover contains the contigs ordered and oriented according to the reference genome. These aren't gap-filled with N, mainly because there are many situations where one might use the contig mover when estimates of the inter-contig distance based on a reference genome would be extremely unreliable. I can't comment on the .tab file, but you might ask Anna Rissman (author of the contig mover module) about this.

[Shlomo Blum]

Exited with error code: -1073741819

Could anyone help me on this error?

Searching with seed pattern 11110011010101011001111
Sorted mer list loaded successfully
Sorted mer list loaded successfully
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%..
Exited with error code: -1073741819