[miso-users] miso file format
mykhwab
mykhwab at gmail.com
Thu Dec 20 21:55:03 EST 2012
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
> >
> >
>
>
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