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

[Yarden Katz]

Hi,

Sounds great, good to hear!  misopy made the Python-only version obsolete by now, so it's a good idea to upgrade.

Just note that if you're going from a pre-misopy release to a misopy release, you'll have to reindex your annotations (i.e. run "index_gff.py") with the misopy release.  Reindexing will not be needed if you're upgrading from one misopy release to another, just if you're going from a pre-standard package version to a standard package version.

Best, --Yarden




On Jan 31, 2012, at 5:48 AM, Mar Gonzàlez-Porta wrote:

> Hi again,
> 
> Just to let you know that installing misopy solved the issue.
> 
> Thanks!
> 
> Mar Gonzàlez-Porta
> PhD student - Functional Genomics Group
> EMBL - European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge
> CB10 1SD
> UK
> 
> 
> 2011/12/13 Mar Gonzàlez-Porta <mar.gonzalezporta at ebi.ac.uk>
> 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
> 
> 
>