[miso-users] MISO tests appear to be failing

[J. Greenbaum]

Hi all, 

I've recently installed MISO (and all prerequisites) on our cluster and have run into an issue when I run the test_miso.py script (output below). I was hoping someone might have had a similar experience but haven't had any luck searching the archives for these error messages. I've posted the output of test_miso.py and module_availability.py as well as the versions of each of the prerequisite modules below. Any insight would be appreciated. If more information is required, please let me know. 


Thanks in advance, 


J 




Output of test_miso.py: 

[jgbaum at compute-0-6 site-packages]$ /share/apps/bin/python2.7 misopy/test_miso.py 
Testing fr-unstranded... 
Checking read f_read against + 
Checking read f_read against - 
Checking read r_read against + 
Checking read r_read against - 
Testing fr-firststrand... 
Testing fr-secondstrand... 
.Testing conversion of SAM to BAM... 
Executing: python /share/apps/lib/python2.7/site-packages/misopy/sam_to_bam.py --convert /share/apps/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output 
Converting SAM to BAM... 
- Executing: samtools view -Sbh /share/apps/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam > /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam 
[samopen] SAM header is present: 35 sequences. 
Sorting BAM file... 
- Executing: samtools sort /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted 
Indexing BAM... 
- Executing: samtools index /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam 
Conversion took 0.00 minutes. 
.Testing gene-level Psi... 
Testing GFF indexing of: /share/apps/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff 
Executing: python /share/apps/lib/python2.7/site-packages/misopy/index_gff.py --index /share/apps/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /share/apps/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed 
File "/share/apps/lib/python2.7/site-packages/misopy/index_gff.py", line 151 
with open(gff_filename) as gff_in: 
^ 
SyntaxError: invalid syntax 
Executing: python /share/apps/lib/python2.7/site-packages/misopy/run_events_analysis.py --compute-genes-psi /share/apps/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /share/apps/lib/python2.7/site-packages/misopy/test-output/gene-psi-output --read-len 35 
File "/share/apps/lib/python2.7/site-packages/misopy/run_events_analysis.py", line 123 
with open(batch_fname, "w") as batch_out: 
^ 
SyntaxError: invalid syntax 
. 
---------------------------------------------------------------------- 
Ran 3 tests in 0.177s 


OK 




Output of module_availability.py: 

[jgbaum at compute-0-6 site-packages]$ /share/apps/bin/python2.7 misopy/module_availability.py 
Looking for required Python modules.. 
Checking for availability of: numpy 
Checking for availability of: scipy 
Checking for availability of: json 
Checking for availability of: matplotlib 
Checking for availability of: pysam 
All modules are available! 
Looking for required executables.. 
Checking if samtools is available 
- samtools is available 
Checking if bedtools is available 
- bedtools is available 



Module/program versions: 
pysam 0.7.4 
numpy 1.6.1 
scipy 0.9.0 
matplotlib: 1.1.0 
samtools: 0.1.18 
bedtools: v2.16.2-zip-466a9f0 

Python: 2.7 






-- Jason Greenbaum, Ph.D. 
Manager, Bioinformatics Core | jgbaum at liai.org 
La Jolla Institute for Allergy and Immunology 




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