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Question: Error: htseq-count exceeds memory buffer, Solution: Set sort option on tool form to Yes
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gravatar for chaudhry
11 months ago by
chaudhry • 0
chaudhry • 0 wrote:

Hello, I am dealing with RNA-seq data and I was successfully able to align my raw FASTQ data to the built-in input hg19 genome using HISAT2. I am now having problems with measuring my reads using htseq-counts. I am using the hg19 GTF file for the genome and I keep getting either an error saying:

An error occurred with this dataset: Fatal error: Unknown error occured 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 500000 GFF lines processed. 600000 GFF lines processed. 700000 GFF lines processed. 800000 GFF lines processed.

Can anyone point me in the right direction? Thank you!
rna-seq sort paired htseq_count htseq • 461 views
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by chaudhry • 0
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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,

The full error ends with:

Maximum alignment buffer size exceeded while pairing SAM alignments.
[Exception type: ValueError, raised in __init__.py:671]

Try setting the option Force sorting of SAM/BAM file by NAME to Yes.

Help from the tool form: This option can be used for for paired-end data that has many unmapped mates. Use this if you get the warning about paired end data missing or not being properly sorted.

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