[miso-users] miso file format

[Yarden Katz]

It sounds like your cluster system does not support the queue name "long".  You can change that in your MISO settings file, under the "[cluster]" section, to be a valid queue name.  The queue names are system specific so you'll have to find out what yours are.

  --Yarden




On Dec 19, 2012, at 11:33 PM, mykhwab wrote:

> 
> 
> Dear MISO
> 
> I am trying to make sashimi plot using Arabidopsis genome.
> but i am acing problem in making .miso files. 
> i can run the test data for making plot but even not able to make .miso for test data.
> what could be the possible reason.? 
> 
> when i run this command 
> 
> python run_events_analysis.py --compute-genes-psi indexed_SE_events/ my_sample1.bam --output-dir my_output1/ --read-len 36 --use-cluster
> 
> 
> 
> the errors.....
> 
> 
> Running batch 39 (batch size = 199)
> Submitting job: gene_psi_batch_39
> Loading settings from: /usr/local/lib/python2.7/dist-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
> cls.global_settings:  {'cluster_command': 'qsub', 'filter_results': True, 'num_iters': 5000, 'lag': 10, 'long_queue_name': 'long', 'burn_in': 500, 'num_chains': 6, 'short_queue_name': 'quick', 'min_event_reads': 20}
>   - queue: long, using queue name long
> Unable to run job: Colon (':') not allowed in objectname
> Job was rejected because job requests unknown queue "long".
> Exiting.
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