Problems to run pysamstats

[joette18]

Hello,
I wanted to install and run pysamstats under my Ubuntu-System.
To install I used pip with following commands

sudo -H pip install pysam==0.11.2.2
sudo -H pip install pysamstats

I got no error or warning messages during the installation, but everytime I use the command
pysamstats --help

I get following error message;

Traceback (most recent call last):
  File "/usr/local/bin/pysamstats", line 10, in <module>
    import pysamstats
  File "/usr/local/lib/python2.7/dist-packages/pysamstats/__init__.py", line 8, in <module>
    from .pileup import *
  File "/usr/local/lib/python2.7/dist-packages/pysamstats/pileup.py", line 6, in <module>
    import pysamstats.opt as opt
  File "libcfaidx.pxd", line 51, in init pysamstats.opt (pysamstats/opt.c:34893)
AttributeError: 'module' object has no attribute 'PersistentFastqProxy'


I tried to uninstall pysamstats and pysam via pip uninstall and then reinstall both packages again. But this doesn't help either.

Can somebody help me?
 

[Alistair Miles]

Hi there, 

I've seen this error where a version of pysam > 0.11 is installed. I see you did try to pin pysam to 0.11.2.2 in your install which is the right thing to do, however if you are installing system-wide I think you can sometimes run into cryptic situations where more than one version of pysam is installed, or where pysamstats is linking against a different version of the pysam from what you expect. My suggestion would be to run sudo pip uninstall pysam several times, then install pysam==0.11.2.2 and pysamstats into either a virtual environment or a conda environment, and see if that works.

Hth,

Alistair

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Alistair Miles
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[joette18]

Hi Alistair,

thank you so much!! It wasn't even necessary to use virtual or conda environment. I just uninstalled pysamstats multiple times. And so I discovered that I had much more versions of pysamstats, as you supposed. Now it works. :) Thank you!

[Alistair Miles]

No problem, glad you got it sorted, that's happened to me before and can be very confusing.

On Wed, Nov 22, 2017 at 11:52 AM, joette18 <pel...@web.de> wrote:

Hi Alistair,

thank you so much!! It wasn't even necessary to use virtual or conda environment. I just uninstalled pysamstats multiple times. And so I discovered that I had much more versions of pysamstats, as you supposed. Now it works. :) Thank you!

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To unsubscribe from this group and stop receiving emails from it, send an email to pysam-user-group+unsubscribe@googlegroups.com.
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