[miso-users] miso file format

[Yarden Katz]

Could you please show the first 10-20 lines of your GFF and the first 10-20 lines of your BAM file?  That will help tell what is happening.

It sounds like a mismatch between the GFF chromosome naming conventions and the BAM file.  
When you index GFFs, miso adds a "chr" prefix to directories if they don't have it already.

Since it created "fahim_events/chrChr2", it means that your chromosome in the GFF is named "Chr2" (note capital C).  Your BAMs were most likely not aligned to a genome where the chromosomes are named this way.  If "Chr2" is really "chr2" or "2" in your BAM, then that could generate the error.

The current version in GitHub has more elaborate error checking so it catches this and produces a more reasonable error, but the latest stable version of MISO does not.

  --Yarden

On Dec 20, 2012, at 11:09 AM, mykhwab wrote:

> 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
> 
>