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

[Mar Gonzàlez-Porta]

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
>>
>>
>
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