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

[Yarden Katz]

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
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