htseq-count Error '_StepVector_Iterator_obj' object has no attribute 'next'

Question

[Sara]

I am trying to run htseq-count (v. 0.13.5) on a sorted and indexed bam file. The command I entered looks like this:

htseq-count -f bam -r pos -s yes -t CDS -i gene_id -m union filename_sorted.bam filename.gtf

I get the following error from htseq-count:

'_StepVector_Iterator_obj' object has no attribute 'next'
  [Exception type: AttributeError, raised in StepVector.py:409]

Does anyone know the cause of this error? I have played around with other alignment file input formats (unsorted bam, sam, etc.), but I keep getting the same error.

Answer 1

[lieven.sterck]

are you using the correct python version?

[Sara]

I am using Python 3.7 (htseq-count specifies Python >=3.6)

[lieven.sterck]

I see, should be OK then I assume.

I remember that we needed to use the version that was installed in the python libs of a specific python version and we thus could not use it with eg 3.6 if it was installed in the 3.4 python version.

anyway, if you're stuck: FeatureCount is a more than decent alternative (faster, better, ...)

[mlist2014]

In my case conda had for some reason downgraded python to 3.6 w/o me noticing it. And htseq started producing those errors. Upgrading python again (to 3.9) fixed the error. Thanks for the pointer!