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Question: HTSeq-count, maximum buffer size exceeded
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gravatar for sherryanddear
20 months ago by
sherryanddear • 0
sherryanddear • 0 wrote:

Hi all,

I am new of RNA-seq analysis. I am running HTSeq-count on galaxy with defaut parameters. I use GenePattern Tophat to align my data. The accepted_hit.bam is about 2.55 GiB. And it turns out a fatal error as following:

5700000 SAM alignment record pairs processed. Error occured when processing SAM input (record #14420795 in file /galaxy-repl/main/files/019/167/dataset_19167797.dat): Maximum alignment buffer size exceeded while pairing SAM alignments. [Exception type: ValueError, raised in __init__.py:671]

I don't know what's happened. How to solve this problem? Your advice are appreciated.
rna-seq galaxy htseq-count • 951 views
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modified 20 months ago by Devon Ryan • 1.9k • written 20 months ago by sherryanddear • 0
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gravatar for Devon Ryan
20 months ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

There's nothing you can do to prevent this from happening. If the instance of Galaxy you're using has featureCounts installed, then use it instead.
ADD COMMENT • link written 20 months ago by Devon Ryan • 1.9k
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