[miso-users] Tread failed error

[Delong, Zhou]

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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