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Old 04-15-2016, 11:17 AM   #1
Reinator
Junior Member
 
Location: Belém, Brazil

Join Date: Nov 2015
Posts: 4
Default Mauve exited with error code 11

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 (althoug I've already got this error while simply aligning sequences) 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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Exited with error code: 11
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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 04-18-2016, 05:37 AM   #2
Reinator
Junior Member
 
Location: Belém, Brazil

Join Date: Nov 2015
Posts: 4
Default

I'm startig to think that this error is associated with the order of the fasta files that are used as input.

For example, if I try to align a fasta file A to a fasta file B (respectively in that order), I get that error 11. But, if I try to align in the inverted order, the aligment occur without error.

The problem is that when you are trying to order contigs against a reference genome, the order really matters, as I have to input first the reference file, and then the draft file.

I hope this observation helps in solving this problem.
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Old 04-18-2016, 05:50 AM   #3
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,794
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@Reinator: Not answering your question but have you posted this error to Mauve list? Dr. Darling monitors that regularly and you should get an answer there.
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Old 04-18-2016, 06:33 AM   #4
Reinator
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Location: Belém, Brazil

Join Date: Nov 2015
Posts: 4
Default

I searched for that list and couldn't find it.
Thanks!
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Old 04-18-2016, 06:44 AM   #5
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,794
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Quote:
Originally Posted by Reinator View Post
I searched for that list and couldn't find it.
Thanks!
You will need to subscribe to mauve-users list before you can post your question (https://lists.sourceforge.net/lists/...fo/mauve-users) there.
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