Question: Trackster Error: Needlargemem: Trying To Allocate 0 Bytes (Limit: 100000000000)
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gravatar for Guest, Simon
4.1 years ago by
Guest, Simon20
Guest, Simon20 wrote:
I'm having problems getting Trackster working on my own Galaxy instance, so I thought I would check on the usegalaxy public server. However, I'm getting the same Trackster Error: needLargeMem: trying to allocate 0 bytes (limit: 100000000000) that was reported on this list in July, but there was no followup: http://user.list.galaxyproject.org/Trackster-Error-td4655737.html My history is at https://usegalaxy.org/u/simon-guest/h/trackster-error This is just an artificial test I made using a fragment of a reference genome, but I thought it should work OK. Any clues? cheers, Simon
trackster • 2.7k views
ADD COMMENTlink modified 4.1 years ago by Jeremy Goecks2.2k • written 4.1 years ago by Guest, Simon20
1
gravatar for Jeremy Goecks
4.1 years ago by
Jeremy Goecks2.2k
Jeremy Goecks2.2k wrote:
It turns out that your artificial test is a bit too artificial. In order to display a coverage plot, Trackster converts reads in a BAM to BigWig using a two step process: (1) BAM to bedgraph; (2) bedgraph to bigwig Your super simple example generates an empty file in step 1 because your single read does not map to Araly1, and the tool used in step 2 (bedGraphToBigWig) fails with the error that you're seeing. This is a corner-case bug, and I've create a card for this so you can track its resolution: https://trello.com/c/kMFUNawL Best, J.
ADD COMMENTlink written 4.1 years ago by Jeremy Goecks2.2k
At Wed, 30 Oct 2013 21:51:05 -0400, Hi Jeremy, Bjoern, Thanks for your help. Yes, my data file wasn't very good. I tried again with a more realistic sample, and it worked fine. Sorry for the noise. cheers, Simon
ADD REPLYlink written 4.1 years ago by Guest, Simon20
1
gravatar for Björn Grüning
4.1 years ago by
Björn Grüning350 wrote:
Hi Simon, I had that error before, not with trackster ... somewhere else. I think it's an error of one of these UCSC tools and it occurs if you supply empty files. Can you check that none of your file is empty? Or your file will be automatically converted during trackster visualisation and that is resulting in an empty file. Just a guess ... Cheers, Bjoern
ADD COMMENTlink written 4.1 years ago by Björn Grüning350
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