Here is my code for generating counts from the BAM file.
bsub -J "htseq-count" htseq-count \ -e /scratch/workspace/rnaseq/counts/err.txt \ -o /scratch/workspace/rnaseq/counts/log.out \ -f bam \ -r name \ -s no \ -a 10 \ -t exon \ -i gene_id \ -m intersection-nonempty \ /scratch/workspace/rnaseq/bam/Aligned.sortedByCoord.out.bam \ /scratch/workspace/rnaseq/refs/gencode.v22.annotation.gtf > /scratch/workspace/rnaseq/counts/SRR3088529_counts.txt
But it only generates a txt file which have only one line of information telling the job number and time that I had submitted. Here is the error file.
Traceback (most recent call last): File "/scratch/shilpeelab/.local/bin/htseq-count", line 4, in <module> __import__('pkg_resources').run_script('HTSeq==0.11.1', 'htseq-count') File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 3007, in <module> working_set.require(__requires__) File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 728, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 626, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: pysam>=0.9.0
Based on this can you please help me as I am a newbie in this and could not figure out the problem. Thank you.