[Shlomo Blum]

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?

[shashankgupta]

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

[Jepang-Beriman]

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.

[Reinator]

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.

[Coline Jaworski]

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 !

[koadman]

Hi Coline, Mauve is unable to take gff files as input, it can take .fasta and Genbank flat files, with the .gbk suffix.

[Ali May]

List of SNPs and the alignment image via command line?

Hello,

Is it possible to generate the SNP list and the graphical image (e.g. jpeg) of the alignment via the command line using ./linux-x64/progressiveMauve?