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Old 11-29-2011, 07:37 AM   #1
tomiczeek
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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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Old 12-13-2011, 01:53 PM   #2
tirohia
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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.
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Old 12-29-2011, 09:49 AM   #3
koadman
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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.
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Old 02-14-2012, 10:58 AM   #4
koadman
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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.
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Old 02-15-2012, 11:53 AM   #5
rskr
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Quote:
Originally Posted by tirohia View Post
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.
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Old 02-15-2012, 02:53 PM   #6
koadman
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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.
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Old 02-15-2012, 07:43 PM   #7
rskr
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Quote:
Originally Posted by koadman View Post
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.
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Old 02-16-2012, 09:09 AM   #8
koadman
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You are awesome rskr, I love you.
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Old 02-16-2012, 10:21 AM   #9
SES
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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.
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Old 02-16-2012, 11:42 AM   #10
flxlex
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@koadman thanks for the wonderful Mauve program, I use it a lot! Also thanks for taking time to answer user questions on SeqAnswers!
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Old 02-16-2012, 11:44 AM   #11
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Quote:
Originally Posted by flxlex View Post
@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!
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Old 02-16-2012, 11:54 AM   #12
lebetimonas
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I use the GUI Mauve all the time and absolutely love it.
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Old 03-17-2012, 06:37 PM   #13
SeqMonster
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Default 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?
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Old 03-30-2012, 11:14 AM   #14
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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.
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Old 06-01-2013, 09:07 PM   #15
Shlomo Blum
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Default 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
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Old 06-01-2013, 09:09 PM   #16
Shlomo Blum
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Quote:
Originally Posted by koadman View Post
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.
Koadman: so to get a single pseudo-genome from the mauve output one would only need to add N's between the ordered contigs and separate the unaligned contigs?
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Old 08-11-2015, 09:23 PM   #17
shashankgupta
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Quote:
Originally Posted by koadman View Post
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.
Hi,
i am trying to align 5 bacterial genome using Progressive MAUVE, i got the output, now i would like to create a phylogenetic tree for the alignement, so which software should i use for phylogenetic tree, and which output file of MAUVE should use ?

Best !
SG
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Old 10-09-2015, 01:20 AM   #18
Jepang-Beriman
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Unhappy Failed to generate identity percentage matrix using progressiveMauve

Greetings,

We were trying to make a genome comparison analysis using progressiveMauve of S. aureus contig in multiFASTA format from several strains (approx. 2.9 mbps each) produced from SPAdes assembly. We tried to generate identity percentage matrix using progressiveMauve by typing in --input-id-matrix command as it was documented from the manual, however the program acted as if it doesn't recognize such command (instead of error message, the screen showed as if --version was typed).

Was it there something wrong with the data type or the progressiveMauve itself? Please assist. Thank you beforehands.
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Old 04-15-2016, 11:10 AM   #19
Reinator
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Greetings,

First of all, I would like to congratulate Koadman and all the team for have developed such an amazing tool as Mauve.

But there are some errors that I am facing and still can't find out a solution. I'm trying to order contigs using the command line suggested in the Mauve webpage:

java -Xmx500m -cp Mauve.jar org.gel.mauve.contigs.ContigOrderer -output results_dir -ref reference.gbk -draft draft.fasta

When I run the command, I get the following output:

ref file: org.gel.mauve.contigs.ContigMauveAlignFrame[frame0,0,0,343x383,invalid,hidden,title=Align and Reorder Contigs,normal]
shown
OS name is: Linux arch: amd64
trying path ./progressiveMauve
Executing:
progressiveMauve --output=/home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/alignment1 --skip-refinement --weight=200 --output-guide-tree=/home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/alignment1.guide_tree --backbone-output=/home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/alignment1.backbone /home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/Cupriavidus_metallidurans_CH34.fasta /home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/ContigsDeNovoNaoMapeados.fasta
Storing raw sequence at /tmp/rawseq19925.000
Sequence loaded successfully.
/home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/Cupriavidus_metallidurans_CH34.fasta 3928089 base pairs.
Storing raw sequence at /tmp/rawseq19925.001
Sequence loaded successfully.
/home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/ContigsDeNovoNaoMapeados.fasta 1170599 base pairs.
Using weight 15 mers for initial seeds
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 0 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: 200
using default bp estimate min score: 446916
Starting with 11198 multi-matches
Computing genome content distance matrix...


Genome conservation distance matrix:
0 0.895972
0.895972 0

Writing guide tree to /home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/alignment1.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 8168 initial LCBs
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Caught signal 11
Cleaning up and exiting!
Temporary files deleted.


Is there some solution?

Thanks in advance.
Reinator is offline   Reply With Quote
Old 09-20-2017, 01:09 PM   #20
Coline Jaworski
Junior Member
 
Location: Tucson AZ

Join Date: Sep 2017
Posts: 1
Default Caught signal 11

Hello, I am new to Mauve,

I am trying to use progressiveMause on command line to align 2 assemblies to a D. melanogaster gff file, using:

progressiveMauve --output=Dmel.xmfa --seed-weight=15 Dmel_7_gff.gff assembly1.fasta assembly2.fasta

I got this error message, but no other output or piece of information which could guide me to how to fix the bug:
Caught signal 11
Cleaning up and exiting!
Temporary files deleted.

I thought it might be due to memory issues, so I used a lighter annotated reference file (611M only) and increased memory available (running it on a cluster), but I still got the issue. However, when I use a simple .fasta instead of a .gff I don't have the issue and it looks like it's running. Any idea how to fix my problem ?

I am using Mauve version downloaded from mauve_linux_snapshot_2015-02-13.tar.gz

Thank you very much !

Last edited by Coline Jaworski; 09-20-2017 at 01:14 PM.
Coline Jaworski is offline   Reply With Quote
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