[miso-users] executing MISO: ERROR - MH ratio is ~0

[Mar Gonzàlez-Porta]

Hi Yarden,

Thank you for your quick response. I'm using the Pyhton version which I
just downloaded last week (ie I have the sashimi-plot functionality). I'll
try to install fastmiso instead and I'll come back to you if the error
persists.

Mar Gonzàlez-Porta
PhD student - Functional Genomics Group
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
UK


2011/12/13 Yarden Katz <yarden at mit.edu>

> Hi,
>
> Could you please let me know what version of MISO you are running?  Based
> on the output it looks like an older version.  Do you mind re-running this
> with the latest version from the "dev" branch if you're using Python-only
> MISO, or the latest version from the "fastmiso" branch if you're using the
> C version?  You can also download these from our website.
>
> If the error persists, please send me the BAM file containing the reads
> for the event and a GFF containing the event and I'll take a closer look.
>
> Thanks.
>
> Best, --Yarden
>
>
>
>
> On Dec 13, 2011, at 6:48 AM, Mar Gonzàlez-Porta wrote:
>
> > Hi!
> >
> > While running MISO I came across the error/warning below, and I was
> wondering what is causing it and if there's any way to avoid it.
> >
> > Thanks in advance!
> >
> > ----
> >
> > 2011-12-12 17:00:49,326 - miso_logger - WARNING - MH ratio is ~0! Gene:
> ENSG00000104408
> > 2011-12-12 17:00:49,326 - miso_logger - ERROR - MH ratio is ~0!
> > curr_joint_score: -167802.64
> > proposed_joint_score: -168929.67
> > Gene: ENSG00000104408
> > Loading settings from: /homes/mar/system/MISO/settings/miso_settings.txt
> > Settings:
> >    filter_results True
> >    min_event_reads 20
> >    cluster_command bsub
> >    long_queue_name research
> >    short_queue_name research
> >    burn_in 500
> >    lag 10
> >    num_iters 5000
> > Computing Psi for 1 genes...
> >   - ENSG00000104408
> >   - GFF filename:
> /homes/mar/svn_microarray/annotation/Homo_sapiens.GRCh37.63/indexed_miso/chr8/ENSG00000104408.pickle
> >   - BAM:
> /homes/mar/svn_microarray/illumina_body_map/data/2.miso/2x50bp.FCB.s_5_1_sequence.fastq.filtB.fixed.tophat/accepted_hits.bam
> >   - Outputting to: /net/isilon5/ma/home/mar/illumina_body_map/8.miso/test
> >   - Paired-end mode:  (220.0, 70.0)
> > Loading BAM filename from:
> /homes/mar/svn_microarray/illumina_body_map/data/2.miso/2x50bp.FCB.s_5_1_sequence.fastq.filtB.fixed.tophat/accepted_hits.bam
> > Loading took 0.03 seconds
> > Aligning reads to gene...
> > Filtered out 138 read pairs that were on same strand.
> > Filtered out 6 reads that had no paired mate.
> > Filtered out 1599 reads that were not consistent with any isoform
> > Alignment to gene took 40.15 seconds (10945 reads).
> > Filtered out 0 reads that posited improbable fragment lengths with with
> all isoforms.
> > MH ratio is ~0!
> > Traceback (most recent call last):
> >   File "/homes/mar/system/MISO/run_miso.py", line 658, in <module>
> >     main()
> >   File "/homes/mar/system/MISO/run_miso.py", line 612, in main
> >     event_type=options.event_type)
> >   File "/homes/mar/system/MISO/run_miso.py", line 438, in
> compute_gene_psi
> >     lag=lag)
> >   File "/net/nas17b/vol_homes/homes/mar/system/MISO/miso_sampler.py",
> line 1050, in run_sampler
> >     raise Exception, "MH ratio is ~0!"
> > Exception: MH ratio is ~0!
> >
> > ----
> >
> > Mar Gonzàlez-Porta
> > PhD student - Functional Genomics Group
> > EMBL - European Bioinformatics Institute
> > Wellcome Trust Genome Campus
> > Hinxton, Cambridge
> > CB10 1SD
> > UK
> > _______________________________________________
> > miso-users mailing list
> > miso-users at mit.edu
> > http://mailman.mit.edu/mailman/listinfo/miso-users
>
>
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