[mira_talk] Re: Lots of contigs, then segmentation fault
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 23 Apr 2011 18:22:54 +0200
On Apr 19, 2011, at 18:14 , Egon Ozer wrote:
> I'll email you the first part of the log file directly.
Got it. From the log file itself, it looks like you have a happy little
prokaryote with not too many repeats ... and the sequencing quality also looks
pretty good as the clipping algorithms did not find excessive amounts of things
to clip.
> I also wondered if it was a problem with how I extracted my sff files, but I
> know I used the right linker sequences (I checked with our sequencing
> provider) and other assemblers can give me pretty nice assemblies with the
> same data. Also, last night I tried running Mira on the 454 reads alone and
> it looks like it constructed just one pretty good-sized contig containing
> 61583 reads, but then segmentation faulted right after "Marking tricky 454
> runs in 387063 cases."
Good, one step further. If the 454 alone get assembled into larger contigs by
MIRA and other assemblers also do that, it's a start.
> Could my 454 and Illumina reads be discrepant? Possible, since I did do the
> sequencing at different places at different times. I don't think so,
> however, because just using Blast, there is nice overlap between my separate
> 454 and Illumina assembly contigs.
That would be something to be looked at now.
> I'd be happy to provide my data to you for testing. Do you want the sff
> files or my extracted fasta, qual, and xml files for the 454 data?
Can you please contact me off-list to discuss details?
> Thanks so much for the help.
Well, every bug reported to me and subsequently squashed is a bug less other
people will trip over :-)
B.
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