[miso-users] Errors when summarizing gene expression

[Li Shen]

I don't know if anyone has ever encountered the following errors. It
seems the Psi values were calculated without problems. However, when I
ran "run_miso.py --summarize-samples", I got the following errors:

Loading events from:
/mnt/disk3/NGSData/chip_seq/Ian_Maze_H3.3_Stimu/rnaseq/in_vitro_kcl/miso/SE/kcl
Writing summary to:
/mnt/disk3/NGSData/chip_seq/Ian_Maze_H3.3_Stimu/rnaseq/in_vitro_kcl/miso/SE/kcl/summary/kcl.miso_summary
Traceback (most recent call last):
  File "/usr/local/bin/run_miso.py", line 5, in <module>
    pkg_resources.run_script('misopy==0.4.6', 'run_miso.py')
  File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py",
line 499, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py",
line 1239, in run_script
    execfile(script_filename, namespace, namespace)
  File "/usr/local/lib/python2.7/dist-packages/misopy-0.4.6-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_miso.py",
line 615, in <module>
    main()
  File "/usr/local/lib/python2.7/dist-packages/misopy-0.4.6-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_miso.py",
line 586, in main
    use_compressed=use_compressed)
  File "/usr/local/lib/python2.7/dist-packages/misopy-0.4.6-py2.7-linux-x86_64.egg/misopy/samples_utils.py",
line 207, in summarize_sampler_results
    samples_results = load_samples(samples_filename)
  File "/usr/local/lib/python2.7/dist-packages/misopy-0.4.6-py2.7-linux-x86_64.egg/misopy/samples_utils.py",
line 31, in load_samples
    data, h = csv2array(samples_file, skiprows=1, raw_header=True)
  File "/usr/local/lib/python2.7/dist-packages/misopy-0.4.6-py2.7-linux-x86_64.egg/misopy/parse_csv.py",
line 74, in csv2array
    deletechars='', skiprows=skiprows)
  File "/usr/lib/python2.7/dist-packages/numpy/lib/npyio.py", line
1560, in genfromtxt
    raise ValueError(errmsg)
ValueError: Some errors were detected !
    Line #2703 (got 1 columns instead of 2)


What might be the reasons that caused this? I'd appreciate any help! Thx!


--
Li Shen, Ph.D. Computer Science
Assistant Professor
Department of Neuroscience
Mount Sinai School of Medicine
One Gustave L. Levy Place, Box 1065
New York, NY 10029
Phone: 212-659-8622 (office)