[miso-users] no events found by miso

[longxiyao]

Hi all, I'm running MISO but constantly getting no events found, that means in miso_output/ I have a list of subfolders:batch-genes  batch-logs  cluster_scripts  scripts_outputwith a list of batch-X_genes.txt files in batch-genes.
But in miso_comopare the file .miso_bf have no values besides the column head.  Could sb advise me about possible causes? Thank you.
Regards,Long


Following is part of the output of my sh:
The end which indicates no event found: 
Retrieving MISO files in sample directories...Computing sample comparison between /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20N and /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20T...  - No. of events in /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20N: 0  - No. of events in /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20T: 0Creating comparisons parent directory: /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_compare/SE/CH20/CH20N_vs_CH20TCompared a total of 0 events.

The beginning :Computing Psi values...  - GFF index: /ifshk1/ST/COMG/PMO/long/annotationFile/hg19/indexedSEhg19  - BAM: /ifshk1/ST/COMG/PMO/long/splicingSamples/RNA/CH20N.rna.bam  - Read length: 90  - Output directory: /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20NChecking your GFF annotation and BAM for mismatches...Checking if BAM has mixed read lengths...Found reads of length 90 in BAM.WARNING: No genes.gff file found in /ifshk1/ST/COMG/PMO/long/annotationFile/hg19/indexedSEhg19. Did you index your GFF with an older version of MISO?Mapping genes to their indexed GFF representation, using /ifshk1/ST/COMG/PMO/long/annotationFile/hg19/indexedSEhg19Searching for /ifshk1/ST/COMG/PMO/long/annotationFile/hg19/indexedSEhg19/genes_to_filenames.shelve..  - Found shelved file.Preparing to run 212 batches of jobs...Running batch of 200 genes..  - Executing: python /ifshk1/ST/COMG/PMO/long/software/python2/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/run_miso.py --compute-genes-from-file "/ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20N/batch-genes/batch-0_genes.txt" /ifshk1/ST/COMG/PMO/long/splicingSamples/RNA/CH20N.rna.bam /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20N --read-len 90  --paired-end 250.0 15.0 --settings-filename /ifshk1/ST/COMG/PMO/long/software/python2/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt 		 	   		  
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