These are chat archives for cboursnell/transfuse

22nd
Oct 2015
Will
@willblev
Oct 22 2015 14:55
I've been running into an error at the vsearch step: running vsearch...*** glibc detected *** /soft/bio/sequence/vsearch-1.4.4/bin/vsearch: realloc(): invalid next size: 0x0000000001c2f2e0 ***
This may be due to an issue between our Scientific Linux machines and the Fedora repos- will report back once our admin installs vsearch in the right place
Chris Boursnell
@cboursnell
Oct 22 2015 15:02
I haven't tested transfuse with the latest versions of vsearch
Will
@willblev
Oct 22 2015 15:14
which version do you use/recommend? It was working on my laptop w/ Ubutu and vsearch version 1.4.4, just not on Fedora/Scientific linux
Chris Boursnell
@cboursnell
Oct 22 2015 15:16
It was tested with 1.1.3, but it doesn't look like there are any changes to the command line options in the latest version so it should work fine with the latest, which is 1.8.0 now
Will
@willblev
Oct 22 2015 15:16
Even though everything seems to be working on my laptop, I'd rather not leave it running for two weeks (as you said vsearch took ~48h w/ 24cores...)
Chris Boursnell
@cboursnell
Oct 22 2015 15:19
I'm not sure the size of your assemblies compared with what I was using. I don't know the time complexity/scaling of vsearch with regards to number of contigs.
Will
@willblev
Oct 22 2015 15:22
True- yeast genomes are miniscule compared to humans :smile: I'll try to merge 2 assemblies (~7500 contigs total) this weekend and let you know how long it takes
Chris Boursnell
@cboursnell
Oct 22 2015 15:25
Yeah I think that would take less time. Some of my assemblies had >130,000 contigs
Will
@willblev
Oct 22 2015 15:28
I love yeast more and more each day...
Chris Boursnell
@cboursnell
Oct 22 2015 15:30
I'm glad I work with rice and not wheat