Question: HTSeq-count, maximum buffer size exceeded
gravatar for sherryanddear
20 months ago by
sherryanddear0 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]

I don't know what's happened. How to solve this problem? Your advice are appreciated.

rna-seq galaxy htseq-count • 951 views
ADD COMMENTlink modified 20 months ago by Devon Ryan1.9k • written 20 months ago by sherryanddear0
gravatar for Devon Ryan
20 months ago by
Devon Ryan1.9k
Devon Ryan1.9k 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 COMMENTlink written 20 months ago by Devon Ryan1.9k
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