Question: bowtie2: ImportError: No module named argparse
0
gravatar for BioBaby
7 days ago by
BioBaby0
BioBaby0 wrote:

hi all, I am beginner for NGS analysis.I installed bowtie2 and when I run bowtie2 for indexing the genome it gave this following error: ImportError: No module named argparse I tried to install this module by yum install python-argparse then it gave same error: File "/usr/local/bin/bowtie2-build", line 27, in <module> import argparse ImportError: No module named argparse. OS :centOS

ADD COMMENTlink modified 7 days ago by WouterDeCoster35k • written 7 days ago by BioBaby0

How did you install bowtie? Which is your python version?

ADD REPLYlink written 7 days ago by WouterDeCoster35k

sir, I simply download from https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.3/bowtie2-2.3.4.3-linux-x86_64.zip and unzip it.Python 2.6.6

ADD REPLYlink written 7 days ago by BioBaby0

That's a really old python version. I agree with colindaven, just use bioconda for all your bioinformatics software.

ADD REPLYlink written 7 days ago by WouterDeCoster35k

i updated python version still I got same error.

ADD REPLYlink written 7 days ago by BioBaby0

How did you update python? Which version do you have now? Look, just use bioconda okay?

ADD REPLYlink written 7 days ago by WouterDeCoster35k

solved...I copy argparse.py script and paste into bowtie2 folder. Thanks WouterDeCoster and colindaven

ADD REPLYlink written 7 days ago by BioBaby0
1

You temporarily patched the problem, but all of this is suggestive of far more problems you will encounter later. Anyway, good luck.

ADD REPLYlink written 7 days ago by WouterDeCoster35k

I'd go for bioconda and follow their tutorial. It'll save you a world of pain ....

ADD REPLYlink written 7 days ago by colindaven840
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