[miso-users] IndexError: string index out of range

[Yarden Katz]

Hi,

It sounds like the input directory might have been malformed.  Could you please send me a couple of the files in event_analysis/se/Hip (or the entire directory) and I'll take a look?

You can upload it to Dropbox and share the link with me if you'd like, offline from the mailing list.

Best, --Yarden

On Mar 19, 2013, at 10:56 AM, Ao Zhou wrote:

> Hi, there,
> 
> I'm recently encountering an error when implementing MISO summary.
> I ran MISO on several samples, and some output summary successfully, while some returned this error.
> Would you help me to find out the cause please?
> This is the command and the message I've got.
> 
> ################### Error Message ###################
> $ run_miso.py --summarize-samples event_analysis/se/Hip summary/se/Hip
> 
> Loading settings from: /N/soft/rhel6/miso/0.4.6/lib/
> python2.7/site-packages/misopy/settings/miso_settings.txt
> Settings: 
>    filter_results True
>    min_event_reads 20
>    cluster_command qsub
>    long_queue_name long
>    short_queue_name quick
>    burn_in 500
>    lag 10
>    num_iters 5000
>    num_chains 6
> Loading events from: /N/dcwan/projects/ngs/users/aozhou/Project_Rat_Brain/4.miso_merged/event_analysis/se/Hip
> Writing summary to: /N/dcwan/projects/ngs/users/aozhou/Project_Rat_Brain/4.miso_merged/summary/se/Hip/summary/Hip.miso_summary
> Traceback (most recent call last):
>   File "/N/soft/rhel6/miso/0.4.6/bin/run_miso.py", line 615, in <module>
>     main()
>   File "/N/soft/rhel6/miso/0.4.6/bin/run_miso.py", line 586, in main
>     use_compressed=use_compressed)
>   File "/N/soft/rhel6/miso/0.4.6/lib/python2.7/site-packages/misopy/samples_utils.py", line 185, in summarize_sampler_results
>     params = parse_sampler_params(samples_filename)
>   File "/N/soft/rhel6/miso/0.4.6/lib/python2.7/site-packages/misopy/samples_utils.py", line 58, in parse_sampler_params
>     if header[0] == '#':
> IndexError: string index out of range
> 
> 
> -- 
> Ao Zhou
> Ph.D. Student, 
> Bioinformatics Program,
> School of Informatics, IUPUI
> Tel: 317-372-7004 _______________________________________________
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