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Question: HTSeq-Count: Maximum alignment buffer size exceeded while pairing SAM alignments
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gravatar for marp.p
11 months ago by
marp.p • 20
marp.p • 20 wrote:

Hi

I'm working on Cloudman doing RNASeq analysis. I am trying to use htseq-count tool for gene quantification, but I have this error:

Fatal error: Unknown error occured 100000 GFF lines processed. 200000 GFF lines processed. [.....] 105500000 SAM alignment record pairs processed. Error occured when processing SAM input (record #214145509 in file /mnt/galaxy/files/000/dataset_227.dat): Maximum alignment buffer size exceeded while pairing SAM alignments. [Exception type: ValueError, raised in __init__.py:671]

The input are a BAM file obtained by using HTSAT2 and the GFT file from https://www.gencodegenes.org/releases/current.html.

Did I miss something? Thanks
rna-seq sort galaxy bam htseq_count • 752 views
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by marp.p • 20
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gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

On the htseq_count tool form set the option "Force sorting of SAM/BAM file by NAME" to "Yes".

Sorting can help avoid errors across tools and is good to know about. Not all tool forms include the option to sort, so if you need to sort before using other tools in the future, how-to is explained here:

Thanks! Jen, Galaxy team
ADD COMMENT • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k
1

Thank you so much, solved!

ADD REPLY • link written 11 months ago by marp.p • 20
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