[miso-users] miso file format

[mykhwab]

Thank you Yarden,

here is the next problem :)  Can you please tell me what is the possible
solution...

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
Computing Psi for 1 genes...
  - AT2G43010
  - GFF filename:
/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_events/chrChr2/AT2G43010.pickle
  - BAM: /BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.bam
  - Outputting to: /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_out1
Loading genes from indexed GFF...
  - Loading took: 0.00 seconds
Loading BAM filename from:
/BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.bam
Loading took 0.02 seconds
Traceback (most recent call last):
  File "/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/run_miso.py", line 615, in
<module>
    main()
  File "/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/run_miso.py", line 564, in
main
    event_type=options.event_type)
  File "/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/run_miso.py", line 310, in
compute_gene_psi
    gene_obj)
  File "/usr/local/lib/python2.7/dist-packages/misopy/sam_utils.py", line
211, in fetch_bam_reads_in_gene
    chrom = chrom.split("chr")[1]
IndexError: list index out of range
  - Executing: python /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/run_miso.py
--compute-gene-psi "AT1G49040"
"/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_events/chrChr1/AT1G49040.pickle"
/BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.bam
/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_out1 --read-len 36
--overhang-len 1 --settings-filename
/usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt



Regards



On Thu, Dec 20, 2012 at 1:36 PM, Yarden Katz <yarden at mit.edu> wrote:

> 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.
> > _______________________________________________
> > miso-users mailing list
> > miso-users at mit.edu
> > http://mailman.mit.edu/mailman/listinfo/miso-users
>
>
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