Question: custom build processing takes > 2 days
1
gravatar for friederike.grosse-holz
2.6 years ago by
United Kingdom
friederike.grosse-holz10 wrote:

Hey guys,

I just wondered whether it is normal for a custom build to take longer than two days? I had a fasta genome file in my history already and added that as a custom build. The genome is ca 3 Gb. I can view it under User > custom builds, but it always just says "processing" there...

thanks for your help!

Friederike

software error galaxy • 583 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by friederike.grosse-holz10
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Where are you using Galaxy? Perhaps a local? If so, there could be insufficient resources for the job.

Please let us know. This would not be expected on the public Main Galaxy instance at http://usegalaxy.org.

Thanks, Jen, Galaxy team

 

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson23k
0
gravatar for friederike.grosse-holz
2.6 years ago by
United Kingdom
friederike.grosse-holz10 wrote:

Hey,

thanks for your reply! Indeed I am using http://usegalaxy.org. So I thought it was weird... I started it a second time yesterday and now they are both "processing" still. What could I/you do to fix this?

ADD COMMENTlink written 2.6 years ago by friederike.grosse-holz10

Hi - I'd like to take a look at your history in detail. in particular the custom ref genomes. If these are highly fragmented (worst case - all or mostly comprised of unassembled NGS reads) that could certainly be a trigger for this issue. I found your usegalaxy.org account and will provide generalized feedback here and specific feedback directly to your email address as appropriate/needed. Best, Jen, Galaxy team

ADD REPLYlink written 2.6 years ago by Jennifer Hillman Jackson23k

Hello,

I am able to locate the source for the first genome (which indexed successfully). The other two I cannot - in the active or other histories. I would start by double checking format. Please see: Custom Builds (and the fasta dataset trouble-shooing help in section 8 of the same wiki)

Please note that the "len" style inputs differ from "fasta" format, of course. See here for help on that type of Custom Build input.

If format is truly ok, the number of contigs could be a problem. It very many shorter fragments (the base is already highly fragmented). If so, the data being too large for the memory dedicated to this tool is the second most likely issue. 

Please let us know what you discover and if this some part of this resolves the issue. If not, we can move forward. Jen, Galaxy team

ADD REPLYlink written 2.6 years ago by Jennifer Hillman Jackson23k

Dear Jen,

I have now checked the format, line length, identifier and so on - all looks fine. The file I'm trying to use is called Niben.genome.v1.0.1.contigs.fasta. I tried again to add it as a custom build and again, it takes really long.

Would be strange if this is too big, seeing that I successfully used the Niben.genome.v1.0.1.scf.nrctgs file as a custom build, which has the same genome sequence - just the organization is different, the identifiers in the Niben.genome.v1.0.1.scf.nrctgs file only give scaffolds, while the ones in Niben.genome.v1.0.1.contigs.fasta gives scaffolds and contigs. Therefore, the sequences in Niben.genome.v1.0.1.contigs.fasta are shorter and there are more of them, but the overall content is the same. Could this fragmentation be the problem? If so, could I get the information about the contigs into my visualization of the Niben.genome.v1.0.1.scf.nrctgs file?

My problem is that I recieved mapped reads from my sequencing provider, which were mapped against the Niben.genome.v1.0.1.contigs.fasta file. So after running cufflinks, I now need to examine my result, which is why I want that contig information in there.

Best wishes, Friederike

ADD REPLYlink written 2.6 years ago by friederike.grosse-holz10

Dear Jen,

just to let you know, I worked around that issue by using a different genome build that is less fragmented.

btw, thanks for the Galaxy Server!!!

Best, Friederike

ADD REPLYlink written 2.5 years ago by friederike.grosse-holz10

Dear Jen,

my disk usage is stuck at 100% and does not come back down although I permanently deleted most of my stuff already. As far as I get it from the forums, this seems to be resolvable by calculating the quota manually, so could you please do that for my account at your earliest convenience?

Thanks a lot! Friederike

ADD REPLYlink written 2.4 years ago by friederike.grosse-holz10

Taken care of, you should be fine now.

ADD REPLYlink written 2.4 years ago by Dannon Baker3.6k
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