Re: [galaxy-user] Trackster Error: needLargeMem: trying to allocate 0 bytes (limit: 100000000000)
At Wed, 30 Oct 2013 21:51:05 -0400, Jeremy Goecks 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 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 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Trackster Error: needLargeMem: trying to allocate 0 bytes (limit: 100000000000)
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. On Oct 30, 2013, at 5:44 PM, "Guest, Simon" 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: 1000) 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 > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Trackster Error: needLargeMem: trying to allocate 0 bytes (limit: 100000000000)
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 > 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: 1000) 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 > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
