[miso-users] Errors when summarizing gene expression

[Yarden Katz]

Hi,

Are you running in multi-isoform mode or two isoform?  Could you please send me a link to the directory "/mnt/disk3/NGSData/chip_seq/Ian_Maze_H3.3_Stimu/rnaseq/in_vitro_kcl/miso/SE/kcl"?  Then I can try to reproduce the error and see what has happened.  

I suspect it might be due to incomplete run of MISO, which would cause truncated output files.  I will add better error handling to deal with this case.  Looking at your output would help narrow what happened.

Best, --Yarden


On Jan 14, 2013, at 10:10 AM, Li Shen wrote:

> 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)
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