Question: Error: htseq-count exceeds memory buffer, Solution: Set sort option on tool form to Yes
gravatar for chaudhry
3 months ago by
chaudhry0 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!

ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson24k • written 3 months ago by chaudhry0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson24k wrote:


The full error ends with:

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

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 COMMENTlink written 3 months ago by Jennifer Hillman Jackson24k
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