HTSeq issue with stdout/stdin

[norafar]

Hello All,

I like to apply HTSeq-count on a .bam file, but if I directly pipe the output of samtools to htseq it gives me an error. However, if I first write the sorted file in a temporary file and then apply samtools-view and htseq-count on this temp file, there is no error!
Do you know what might be causing this problem?

Case (1): [generates error]

$ samtools sort -on -m 300000000 accepted_hits.bam | samtools view -h - | htseq-count -m union - hg19.gtf > output.count

Error occured when reading first line of sam file.
[Exception type: StopIteration, raised in count.py:83]

Case (2): [no error!]
$ samtools sort -n -m 300000000 accepted_hits.bam temp-sorted.bam
$ samtools view -h temp-sorted.bam | htseq-count -m union - hg19.gtf > output.count

Thank You,
NF

[Simon Anders]

'samtools sort' does not write to stdout, so you cannot use piping.

[arm55]

norafar, include the - file marker as output on the sort and it should work.

samtools sort -on -m 300000000 accepted_hits.bam - | samtools view -h - | htseq-count -m union - hg19.gtf > output.count