cython error

[Sangwoo Kim]

Hi,
I just installed JointSNVMix, but I got an error like below when I
run.

================================================
rachmani@rachmani-****-D3:~/Downloads/JointSNVMix-0.7.5$ jsm.py
Traceback (most recent call last):
File "/usr/local/bin/jsm.py", line 9, in <module>
from joint_snv_mix.runners.train import snv_mix_one_train,
snv_mix_two_train, joint_snv_mix_one_train, \
File "/usr/local/lib/python2.7/dist-packages/joint_snv_mix/runners/
train.py", line 8, in <module>
from joint_snv_mix.counters.joint_binary_counter import
JointBinaryBaseCounter
File "joint_binary_counter.pyx", line 1, in init
joint_snv_mix.counters.joint_binary_counter (joint_snv_mix/counters/
joint_binary_counter.c:3141)
File "csamtools.pxd", line 388, in init
joint_snv_mix.counters.ref_iterator (joint_snv_mix/counters/
ref_iterator.c:3116)
ValueError: csamtools.Samfile has the wrong size, try recompiling
==================================================

Here's the information of my platform
OS: Ubuntu 11.10
Python: 2.7.2
Cython: 0.15.1

What is this error?

Thanks

Sangwoo

[aroth]

Are you using pysam-0.6? There is currently a bug causing
incompatibility with this version, if you uninstall and use pysam-0.5
that will fix the error.
This error will be resolved in the future version of JointSNVMix.

If that doesn't fix it let me know.

Cheers,
Andy

[Sangwoo Kim]

Andy

Yes I was using pysam-0.6
The error is resolved after installing pysam-0.5 and removing 0.6

I think you should change the corresponding part in the "Installation
instruction" page (http://code.google.com/p/joint-snv-mix/wiki/
installation) from "Pysam >= 0.5.0" to "Pysam 0.5.0"
People are likely to install the newest version when it is not
mentioned otherwise.

Thank you

Sangwoo

[aroth]

Thanks Sanwoo, I have updated the wiki.

I hope to have a new version out next week which will remove the
dependence on pysam, so this bug will disappear.

Cheers,
Andy