Question: Htseq-Count Error: Command Not Found
1
gravatar for venkateshr89
5.5 years ago by
venkateshr89690
United States
venkateshr89690 wrote:

I was trying to use

htseq-count --mode /home/user/test.sam home/homo_sapiens.GRCh37.70.gtf

I get

htseq-count: Command not found

error.

I have installed the HTSeq package and I am running this command from command line and not in python shell. Can somebody help me with this issue.

Thanks in advance.

htseq rnaseq sam rna-seq • 3.4k views
ADD COMMENTlink modified 3.1 years ago by Biostar ♦♦ 20 • written 5.5 years ago by venkateshr89690
3
gravatar for Istvan Albert
5.5 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:

htseq-count is probably a script that was installed into a location that is has not been added to your path.

find that script and run it directly or via python:

python htseq-count
ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Istvan Albert ♦♦ 77k
1

Thanks Albert. I still get an error that says "Python: Can't open file 'htseq-count' : [Errno 2] No such file or direcotory " ..

ADD REPLYlink written 5.5 years ago by venkateshr89690
2

you need to actually find the script and run it from where it is located not just invoke it any place - you also need to learn what it means to run scripts in a command line environment

it will look like:

python /some/place/on/my/computer/htseq-count

and we don't know where it was installed, it should have informed you of it while you installed it

ADD REPLYlink written 5.5 years ago by Istvan Albert ♦♦ 77k

Thanks. Sorry about that and that works.

ADD REPLYlink written 5.5 years ago by venkateshr89690

also note fomr the htseq-count website, you will need to use at least python 2.5.

Check your python version by typing

python -V
ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Zack0
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