[miso-users] Errors when summarizing gene expression

[Yarden Katz]

Hi,

Could you please upload it to a webserver as a folder and send me a link?  Or alternatively, use dropbox. I sent you a private invite to a folder where you could upload the files.  

Thanks, --Yarden




On Jan 14, 2013, at 10:34 AM, Li Shen wrote:

> 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)