[miso-users] Tread failed error

[Yarden Katz]

Hi Delong,

The details of the error message will be in the logs/scripts_output directories in the MISO output dir.  

However, looking at your output below, are you sure that your BAM file has a right bracket in it, ']'?  It appears that you're running MISO on:

 /home/delong/s4_50_ accepted_hits].bam

If that's not the right filename, that will cause the failure error.  

  --Yarden

On Sep 9, 2013, at 11:06 AM, Delong, Zhou wrote:

> Hello,
> I have successfully used miso on one of my dataset without paired-end option, when I try to use the paired end option, it fails with the warings "thread batch-0 might have failed" etc. Then I retry this dataset without paired-end option, fails with the same massege. But it goes well with other datasets.
> Complete log can be found below, I deleted the loading gene parts so that the message does not exeed size limite.
> Could someone please explain the problem?
> Thanks,
> Delong
> 
> 
> 
> 
> Probabilistic analysis of RNA-Seq data to detect differential isoforms
> Use --help argument to view options.
> 
> Loading settings from: /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt
> Computing Psi values...
>   - GFF index: /home/delong/hg19/indexed_SE_events
>   - BAM: /home/delong/s4_50_ accepted_hits].bam
>   - Read length: 50
>   - Output directory: /home/delong/s4-50-paired-end
> Checking your GFF annotation and BAM for mismatches...
> Checking if BAM has mixed read lengths...
> Found reads of length 50 in BAM.
> Mapping genes to their indexed GFF representation, using /home/delong/hg19/indexed_SE_events
> Loading indexed gene filenames from: /home/delong/hg19/indexed_SE_events/chrUn_gl000223
>   - Loading 3 genes
> ...
>   - Loading 278 genes
> Preparing to run 4 batches of jobs...
> Running batch of 10621 genes..
>   - Executing: python /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_miso.py --compute-genes-from-file "/home/delong/s4-50-paired-end/batch-genes/batch-0_genes.txt" /home/delong/s4_50_ accepted_hits].bam /home/delong/s4-50-paired-end --read-len 50  --paired-end 50.0 50.0 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt
>   - Submitted thread batch-0
> Running batch of 10621 genes..
>   - Executing: python /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_miso.py --compute-genes-from-file "/home/delong/s4-50-paired-end/batch-genes/batch-1_genes.txt" /home/delong/s4_50_ accepted_hits].bam /home/delong/s4-50-paired-end --read-len 50  --paired-end 50.0 50.0 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt
>   - Submitted thread batch-1
> Running batch of 10621 genes..
>   - Executing: python /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_miso.py --compute-genes-from-file "/home/delong/s4-50-paired-end/batch-genes/batch-2_genes.txt" /home/delong/s4_50_ accepted_hits].bam /home/delong/s4-50-paired-end --read-len 50  --paired-end 50.0 50.0 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt
>   - Submitted thread batch-2
> Running batch of 10622 genes..
>   - Executing: python /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_miso.py --compute-genes-from-file "/home/delong/s4-50-paired-end/batch-genes/batch-3_genes.txt" /home/delong/s4_50_ accepted_hits].bam /home/delong/s4-50-paired-end --read-len 50  --paired-end 50.0 50.0 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt
>   - Submitted thread batch-3
> Waiting on 4 threads...
> WARNING: Thread batch-0 might have failed...
> WARNING: Thread batch-1 might have failed...
> WARNING: Thread batch-2 might have failed...
> WARNING: Thread batch-3 might have failed...
>   - Threads completed in 0.00 hours.
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