HTSeq counts problem

[erickson]

Hello, I am attempting to analyzing some bacterial RNA-seq data.
My pipeline is:
Bowtie2 to generate .sam files -> samtools to sort by position (generates file.sorted.bam from the .sam) -> HTSeq for counts -> DESeq

But I can't seem to satisfy HTSeq. I'm running a script that looks something like this:

/opt/samtools/0.1.18/samtools view file.sorted.bam | /opt/python-2.7.3/bin/python -m HTSeq.scripts.count -r pos -t gene -i ID - file.gff 1> counts.txt 2> counts.stderr

My .stderr says:

18111 GFF lines processed.
Error occured when reading beginning of SAM/BAM file.

[Exception type: StopIteration, raised in count.py:88]

I'm using a .gff3 from Ensembl bacteria, though I got the reference genome fasta from NCBI RefSeq. Not sure if that makes a difference.

Any help is appreciated!

[jsage8]

I am having the same error, did you ever find a resolution for this? I'm starting to suspect that it has something to do with the headers in the fastq files (which must affect the headers produced by bowtie2 in the bam file. I am using Tophat rather than using Bowtie2 directly, but Tophat uses Bowtie2 (I am running Bowtie version 2.2.5.0).