search

Roth-Lab / JointSNVMix

Automatically exported from code.google.com/p/joint-snv-mix
1 stars 1 forks source link

can not run #7

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?

1. after installation, when running jsm.py,error as follow:

Traceback (most recent call last):

  File "/lustre/users/lsssh/wenming//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 "/lustre/users/lsssh/wenming/lib/python2.7/site-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:3157)

  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

What is the expected output? What do you see instead?

What version of the product are you using? On what operating system?
version of the product  JointSNVMix-0.7.4 python 2.7
operating system:
Linux wuserver 2.6.24-24-server #1 SMP Tue Jul 7 19:39:36 UTC 2009 x86_64 
GNU/Linux

Please provide any additional information below.

Original issue reported on code.google.com by youyo...@gmail.com on 11 Dec 2011 at 9:59

GoogleCodeExporter commented 9 years ago 
I believe the issue has to do with using the latest version of pysam (0.6).  I 
got around this issue by using an older version (0.5).

Original comment by fongchun...@gmail.com on 4 Jan 2012 at 6:10

GoogleCodeExporter commented 9 years ago 
Integration with newest version of pysam will be a target for the next release.

Original comment by AndrewJL...@gmail.com on 11 Jan 2012 at 1:15

GoogleCodeExporter commented 9 years ago 
The new version 0.8 removes the Pysam dependency, fixing this bug.

Original comment by AndrewJL...@gmail.com on 21 Mar 2012 at 3:24

GoogleCodeExporter commented 9 years ago 
I am still having the same error.  I am using Python 2.7.2 with Pysam version 
0.7 installed.

Thanks,
Derek

$ python jsm.py classify MODEL -h

Traceback (most recent call last):
  File "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 "/home/chiande1/.local/lib/python2.7/site-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

Original comment by derekchi...@gmail.com on 4 Jan 2013 at 9:13