miso_main - WARNING - Thread batch-0 might have failed...

Question

[JoeDoasi]

Hi everyone,

I started using miso and got results for my data-set, 2 conditions(3 samples each) so the first run was successful.

after that I downloaded another data-set for 2 more conditions and 3 samples each..

I used the same commands but indeed put the new samples names..

Unfortunately the second run failed..I don't know why !!

the successful command :

miso --run miso/miso_index/indexed_A3SS_events Tophat/SRR_963_964_965.bam --output-dir miso/A3SS_SRR_963_964_965 --read-len 100

the failed command :

miso --run ./ ~/Desktop/iRP2/Tophat/SRR1178009_thout/accepted_hits.bam --output-dir SE_SRR_8009 --read-len 100

here is the log:

miso --run ./ ~/Desktop/iRP2/Tophat/SRR1178009_thout/accepted_hits.bam --output-dir SE_SRR_8009 --read-len 100
MISO (Mixture of Isoforms model)
Probabilistic analysis of RNA-Seq data for detecting differential isoforms
Use --help argument to view options.

Using MISO settings file: /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
Computing Psi values...
- GFF index: /home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events
- BAM: /home/ya73/Desktop/iRP2/Tophat/SRR1178009_thout/accepted_hits.bam
- Read length: 100
- Output directory: /home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events/SE_SRR_8009
Checking your GFF annotation and BAM for mismatches...
Checking if BAM has mixed read lengths...
09/19/2016 11:00:02 PM - miso_main - WARNING - Found mixed length reads in your BAM file: /home/ya73/Desktop/iRP2/Tophat/SRR1178009_thout/accepted_hits.bam
 MISO does not support mixed read lengths. Please trim your reads to a uniform length and re-run or run MISO separately on each read length. Proceeding anyway, though this may result in errors or        
 inability to match reads to your annotation.
 Read lengths were:
36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101

Mapping genes to their indexed GFF representation, using /home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events
Searching for /home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events/genes_to_filenames.shelve..
- Found shelved file.
Preparing to run 4 batches of jobs...
Running batch of 94 genes..
- Executing: python /usr/local/lib/python2.7/dist-packages/misopy/run_miso.py --compute-genes-from-file "/home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events/SE_SRR_8009/batch -             
genes/batch-0_genes.txt" /home/ya73/Desktop/iRP2/Tophat/SRR1178009_thout/accepted_hits.bam /home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events/SE_SRR_8009 --read-len 100  --      
overhang-len 1 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
- Submitted thread batch-0
Running batch of 95 genes..
- Executing: python /usr/local/lib/python2.7/dist-packages/misopy/run_miso.py --compute-genes-from-file "/home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events/SE_SRR_8009/batch- 
genes/batch-1_genes.txt" /home/ya73/Desktop/iRP2/Tophat/SRR1178009_thout/accepted_hits.bam /home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events/SE_SRR_8009 --read-len 100  --
overhang-len 1 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
- Submitted thread batch-1
Running batch of 95 genes..
- Executing: python /usr/local/lib/python2.7/dist-packages/misopy/run_miso.py --compute-genes-from-file "/home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events/SE_SRR_8009/batch-   
genes/batch-2_genes.txt" /home/ya73/Desktop/iRP2/Tophat/SRR1178009_thout/accepted_hits.bam /home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events/SE_SRR_8009 --read-len 100  --
overhang-len 1 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
- Submitted thread batch-2
Running batch of 95 genes..
- Executing: python /usr/local/lib/python2.7/dist-packages/misopy/run_miso.py --compute-genes-from-file "/home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events/SE_SRR_8009/batch-   
 genes/batch-3_genes.txt" /home/ya73/Desktop/iRP2/Tophat/SRR1178009_thout/accepted_hits.bam /home/ya73/Desktop/iRP2/miso/miso_index/indexed_A3SS_events/SE_SRR_8009 --read-len 100  -- 
 overhang-len 1 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
 - Submitted thread batch-3
 Waiting on 4 threads...
 09/19/2016 11:00:11 PM - miso_main - WARNING - Thread batch-0 might have failed...
 09/19/2016 11:00:11 PM - miso_main - WARNING - Thread batch-1 might have failed...
 09/19/2016 11:00:11 PM - miso_main - WARNING - Thread batch-2 might have failed...
 09/19/2016 11:00:11 PM - miso_main - WARNING - Thread batch-3 might have failed...

Looking forward to your advice..

Thanks