Trackster Error: Needlargemem: Trying To Allocate 0 Bytes (Limit: 100000000000)

Question: Trackster Error: Needlargemem: Trying To Allocate 0 Bytes (Limit: 100000000000)

5.1 years ago by

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

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modified 5.1 years ago by Jeremy Goecks • 2.2k • written 5.1 years ago by Guest, Simon • 20

5.1 years ago by

Jeremy Goecks • 2.2k

Jeremy Goecks • 2.2k 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 COMMENT • link written 5.1 years ago by Jeremy Goecks • 2.2k

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

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5.1 years ago by

Björn Grüning • 350

Björn Grüning • 350 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 COMMENT • link written 5.1 years ago by Björn Grüning • 350

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