Progressive Mauve error

[Ramprasad]

Hi all,

I'm trying to run progressive mauve on three Drosophila genomes with the following command,

/data/programs/mauve_2.4.0/linux-x64/progressiveMauve --output=alignment.xmfa dmel-short.fasta dsim-short.fasta dyak-short.fasta

Mauve runs for a while, prints the below messages on the screen and then quits with a caught signal 11 error message.

Storing raw sequence at /tmp/rawseq62738.000
Sequence loaded successfully.
dmel-short.fasta 168736537 base pairs.
Storing raw sequence at /tmp/rawseq62738.001
Sequence loaded successfully.
dsim-short.fasta 137828247 base pairs.
Storing raw sequence at /tmp/rawseq62738.002
Sequence loaded successfully.
dyak-short.fasta 165693946 base pairs.
Using weight 19 mers for initial seeds
Creating sorted mer list
Create time was: 28 seconds.
Creating sorted mer list
Create time was: 22 seconds.
Creating sorted mer list
Create time was: 28 seconds.
0%..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: 190610
using default bp estimate min score: 571831
Starting with 5185471 multi-matches
Computing genome content distance matrix...


Genome conservation distance matrix:
0 0.490367 0.677225
0.490367 0 0.647685
0.677225 0.647685 0

Writing guide tree to /tmp/guide_tree62738.000
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 494135 initial LCBs
Caught signal 11
Cleaning up and exiting!
Temporary files deleted.

Input files seem to be in the right format so, I have no idea what is going wrong here. Any thoughts are welcome.

[GenoMax]

Have you checked memory consumption to see if you are running out of memory?

[Ramprasad]

Thank you very much for your reply GenoMax.

I did check. But I don't think memory was really a problem here, because I am running this on a server with a terabyte of RAM. And moreover mauve was the only program I was running at that time.

Cheers,
Ram

[GenoMax]

Couple of general suggestions. Are you using the latest mauve snapshot from here: http://darlinglab.org/mauve/download.html? You may also want to post this to the mauve-users list that Aaron Darling seems to monitor regularly (not sure if he checks this forum).

[Ramprasad]

Thank you very much GenoMax.

Using the latest one did it for me. The program is now running past that stage. Hopefully, it will run to the end.

Cheers,
Ram