[miso-users] miso file format

Thu Dec 20 22:00:04 EST 2012

I still need to see parts of the original GFF and parts of the BAM (i.e. "samtools view yourfile.bam | head -n 20") to see what is going on.  It still looks like a headers mismatch. 

  --Yarden

On Dec 20, 2012, at 9:55 PM, mykhwab wrote:

> yes Yarden you are right, I changed the Chr to chr. but got another issue. :(
> 
> I am also attaching a file...
> .......................................................
> 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...
>   - AT3G15020
>   - GFF filename: /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/indexed_SE_events/chr3/AT3G15020.pickle
>   - BAM: /BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.sorted.bam
>   - Outputting to: /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_output1
> Loading genes from indexed GFF...
>   - Loading took: 0.00 seconds
> Loading BAM filename from: /BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.sorted.bam
> Loading took 0.07 seconds
> Cannot fetch reads in region: 3:5056068-5058248
> Only 0 reads in gene, skipping (needed >= 20 reads)
>   - Executing: python /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/run_miso.py --compute-gene-psi "AT5G01650" "/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/indexed_SE_events/chr5/AT5G01650.pickle" /BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.sorted.bam /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_output1 --read-len 36  --overhang-len 1 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
> 
> 
> Regards
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Fri, Dec 21, 2012 at 11:38 AM, Yarden Katz <yarden at mit.edu> wrote:
> 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
> >
> >
> 
> 
> <files.doc>