<html><head><style type='text/css'>p { margin: 0; }</style></head><body><div style='font-family: arial,helvetica,sans-serif; font-size: 12pt; color: #000000'><font face="arial, helvetica, sans-serif" size="3">Hi all,</font><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br>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.</div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;">Thanks in advance,</div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;">J</div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;">Output of test_miso.py:</div><div><div><font face="arial, helvetica, sans-serif">[jgbaum@compute-0-6 site-packages]$ /share/apps/bin/python2.7 misopy/test_miso.py </font></div><div><font face="arial, helvetica, sans-serif">Testing fr-unstranded...</font></div><div><font face="arial, helvetica, sans-serif">Checking read f_read against +</font></div><div><font face="arial, helvetica, sans-serif">Checking read f_read against -</font></div><div><font face="arial, helvetica, sans-serif">Checking read r_read against +</font></div><div><font face="arial, helvetica, sans-serif">Checking read r_read against -</font></div><div><font face="arial, helvetica, sans-serif">Testing fr-firststrand...</font></div><div><font face="arial, helvetica, sans-serif">Testing fr-secondstrand...</font></div><div><font face="arial, helvetica, sans-serif">.Testing conversion of SAM to BAM...</font></div><div><font face="arial, helvetica, sans-serif">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</font></div><div><font face="arial, helvetica, sans-serif">Converting SAM to BAM...</font></div><div><font face="arial, helvetica, sans-serif"> - 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</font></div><div><font face="arial, helvetica, sans-serif">[samopen] SAM header is present: 35 sequences.</font></div><div><font face="arial, helvetica, sans-serif">Sorting BAM file...</font></div><div><font face="arial, helvetica, sans-serif"> - 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</font></div><div><font face="arial, helvetica, sans-serif">Indexing BAM...</font></div><div><font face="arial, helvetica, sans-serif"> - Executing: samtools index /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam</font></div><div><font face="arial, helvetica, sans-serif">Conversion took 0.00 minutes.</font></div><div><font face="arial, helvetica, sans-serif">.Testing gene-level Psi...</font></div><div><font face="arial, helvetica, sans-serif">Testing GFF indexing of: /share/apps/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff</font></div><div><font face="arial, helvetica, sans-serif">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</font></div><div><font face="arial, helvetica, sans-serif"> File "/share/apps/lib/python2.7/site-packages/misopy/index_gff.py", line 151</font></div><div><font face="arial, helvetica, sans-serif"> with open(gff_filename) as gff_in:</font></div><div><font face="arial, helvetica, sans-serif"> ^</font></div><div><font face="arial, helvetica, sans-serif">SyntaxError: invalid syntax</font></div><div><font face="arial, helvetica, sans-serif">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 </font></div><div><font face="arial, helvetica, sans-serif"> File "/share/apps/lib/python2.7/site-packages/misopy/run_events_analysis.py", line 123</font></div><div><font face="arial, helvetica, sans-serif"> with open(batch_fname, "w") as batch_out:</font></div><div><font face="arial, helvetica, sans-serif"> ^</font></div><div><font face="arial, helvetica, sans-serif">SyntaxError: invalid syntax</font></div><div><font face="arial, helvetica, sans-serif">.</font></div><div><font face="arial, helvetica, sans-serif">----------------------------------------------------------------------</font></div><div><font face="arial, helvetica, sans-serif">Ran 3 tests in 0.177s</font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">OK</font></div></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;">Output of module_availability.py:</div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><div>[jgbaum@compute-0-6 site-packages]$ /share/apps/bin/python2.7 misopy/module_availability.py</div><div>Looking for required Python modules..</div><div>Checking for availability of: numpy</div><div>Checking for availability of: scipy</div><div>Checking for availability of: json</div><div>Checking for availability of: matplotlib</div><div>Checking for availability of: pysam</div><div>All modules are available!</div><div>Looking for required executables..</div><div>Checking if samtools is available</div><div> - samtools is available</div><div>Checking if bedtools is available</div><div> - bedtools is available</div></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br>Module/program versions:</div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><span style="font-size: 12pt;">pysam 0.7.4</span></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;">numpy 1.6.1</div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;">scipy 0.9.0</div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;">matplotlib: 1.1.0</div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;">samtools: 0.1.18</div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;">bedtools: v2.16.2-zip-466a9f0<br><div style="font-size: 12pt;">Python: 2.7</div><div><br></div><div><span name="x"></span><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; "><div><span style="font-family: arial, helvetica, sans-serif; font-size: 12pt; "><br></span></div><div><span style="font-family: arial, helvetica, sans-serif; font-size: 12pt; ">--</span></div></div><font class="Apple-style-span" face="garamond, 'new york', times, serif" style="font-family: arial, helvetica, sans-serif; color: rgb(0, 0, 0); "><b>Jason Greenbaum, Ph.D.<br></b>Manager, Bioinformatics Core | <a href="mailto:jgbaum@liai.org">jgbaum@liai.org</a><br>La Jolla Institute for Allergy and Immunology</font><div><font class="Apple-style-span" face="garamond, 'new york', times, serif" style="font-family: arial, helvetica, sans-serif; color: rgb(0, 0, 0); "><br></font></div><div><font class="Apple-style-span" face="garamond, 'new york', times, serif" style="font-family: arial, helvetica, sans-serif; color: rgb(0, 0, 0); "><br></font></div><span name="x"></span><br></div></div></div></body></html>