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Question: What does this HTseq-count error mean?
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gravatar for zhihuahuang
2.6 years ago by
zhihuahuang • 0
zhihuahuang • 0 wrote:

I am running HTseq-count on galaxy cloud on some BAM files generated from galaxy Tophat. But I got some error in several files (9-10G BAM), 2-5G BAM seems OK. Does HTseq need a lot of space to run?

I am not sure what I should do next, your advice are appreciated.

Fatal error: Unknown error occured 100000 GFF lines processed. 200000 GFF lines processed. .. ..

37100000 SAM alignment record pairs processed. Error occured when processing SAM input (record #77273454 in file /mnt/galaxy/files/000/dataset_420.dat): Maximum alignment buffer size exceeded while pairing SAM alignments. [Exception type: ValueError, raised in __init__.py:671]

Thanks
galaxy cloudman htseq • 1.6k views
ADD COMMENT • link •
modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by zhihuahuang • 0
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gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The job is running out of resource to execute.

Try this first, wherever you are working: Re-run the job(s) to make sure this is a persistent failure and not related to the server or cluster condition at the time of the original execution.

Section 2.8 of the Galaxy support wiki explains alternatives for working with data/jobs that exceed the compute resources at http://usegalaxy.org. Much of the same advice will apply to other servers. https://wiki.galaxyproject.org/Support

Thanks for using Galaxy, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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