pysam.libchtslib.HTSFile has the wrong size

[MeHelmy]

I have installed pysam 0.15.1

when I run pysamstats:

import pysamstats.opt as opt
  File "libchtslib.pxd", line 2590, in init pysamstats.opt
ValueError: pysam.libchtslib.HTSFile has the wrong size, try recompiling. Expected 88, got 80

Knowing that pysam works normally, Is that error related to which version of pysam I have?

Thanks,
Medhat

[alimanfoo]

Yes maybe. Possibly this means that the version of pysam that is currently installed is different from the version that pysamstats was compiled against. Did you install pysamstats from pypi or bioconda? If installing from pypi via pip, the current release version of pysamstats needs to be built against pysam 0.11. The version of pysamstats in GitHub master can be built against pysam 0.14.

…

On Thu, 4 Oct 2018, 18:15 Medhat, ***@***.***> wrote: I have installed pysam 0.15.1 when I run pysamstats: import pysamstats.opt as opt File "libchtslib.pxd", line 2590, in init pysamstats.opt ValueError: pysam.libchtslib.HTSFile has the wrong size, try recompiling. Expected 88, got 80 Knowing that pysam works normally, Is that error related to which version of pysam I have? Thanks, Medhat — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#94>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAq8QnDu_adnYD3LScro4nEhuz9xIEfFks5uhkIWgaJpZM4XIi9J> .

[MeHelmy]

Actually I used conda to install it (but I installed also pysam via conda before installing pysamstats)

[alimanfoo]

I'd suggest to uninstall both pysam and pysamstats, running the uninstall command several times for each to make sure definitely gone (sometimes there can be multiple installations present, don't understand why). Then reinstall, pinning pysam at version 0.11.2.2 and pysamstats at version 1.0.1.

…

On Thu, 11 Oct 2018 at 16:59, Medhat ***@***.***> wrote: Actually I used conda to install it (but I installed also pysam via conda before installing pysamstats) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#94 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAq8QnQAA8R-DbRP8IMbvg4QgQvGWoyCks5uj2rkgaJpZM4XIi9J> .

-- Please feel free to resend your email and/or contact me by other means if you need an urgent reply. Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health Big Data Institute Li Ka Shing Centre for Health Information and Discovery Old Road Campus Headington Oxford OX3 7LF United Kingdom Phone: +44 (0)1865 743596 or +44 (0)7866 541624 Email: alimanfoo@googlemail.com Web: http://a <http://purl.org/net/aliman>limanfoo.github.io/ Twitter: @alimanfoo <https://twitter.com/alimanfoo>

[fkokocinski]

I had the same issue and can confirm that the following combination worked on an Ubuntu system:

conda install -y pysam=0.14
sudo apt-get install zlib1g-dev
git clone git://github.com/alimanfoo/pysamstats.git
cd pysamstats
python setup.py install

For reference: The system was missing zlib before, producing the following error:

...
/home/ubuntu/anaconda/envs/ngspipe/lib/python2.7/site-packages/pysam/include/htslib/htslib/bgzf.h:35:18:  fatal error: zlib.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1

[alimanfoo]

Thanks @fkokocinski.

[lparsons]

I believe this should be resolved in the latest bioconda build: bioconda/bioconda-recipes#15827