[miso-users] Errors when summarizing gene expression

[Li Shen]

Hi Yarden,

I'm simply following the example given in your online manual:

run_events_analysis.py --compute-genes-psi

then

run_miso.py --summarize-samples

I'm doing this for all events types. I finished running on MXE and
TandemUTR but had problems with other events.

I now noticed that in run_miso.py, there are options for two-isoforms
and multipl-isoforms. But how shall I choose under certain
circumstances? In your online manual, they are not explained very
well.

How can I send you a link to the directory? The directory itself is
nearly 500MB. I don't think I can send it through email.

Thanks,

- L



On Mon, Jan 14, 2013 at 10:16 AM, Yarden Katz <yarden at mit.edu> wrote:
> 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)
>> _______________________________________________
>> miso-users mailing list
>> miso-users at mit.edu
>> http://mailman.mit.edu/mailman/listinfo/miso-users
>



-- 
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)