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

[Mar Gonzàlez-Porta]

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!

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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!

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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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