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<div>Hi all,</div>
<div><br>
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<div>I am running miso (0.5.2). I downloaded annotation file from <a href="http://genes.mit.edu/burgelab/miso/annotations/miso_annotations_hg19_v1.zip">http://genes.mit.edu/burgelab/miso/annotations/miso_annotations_hg19_v1.zip</a>, and unzipped the files,
Then I run</div>
<div><br>
</div>
<div>
<div>unzip miso_annotations_hg19_v1.zip</div>
<div><br>
</div>
<div>for gff in A3SS A5SS SE ALE MXE RI TandemUTR</div>
<div>do</div>
<div> index_gff --index $gff.hg19.gff3 indexed_${gff}_events/</div>
<div>done</div>
<div><br>
</div>
<div>for gff in SE A3SS A5SS ALE MXE RI TandemUTR</div>
<div>do</div>
<div> miso --run /home/jo83w/miso/hg19/indexed_${gff}_events/ ${bams[$i]} --output-dir ${tag[$i]}.${gff}/ --read-len 100 -p 16 --paired-end 165 50 --event-type ${gff}</div>
<div> summarize_miso --summarize-samples ${tag[$i]}.${gff}/ ${tag[$i]}.${gff}.summaries/</div>
<div>done</div>
<div><br>
</div>
<div>for gff in SE A3SS A5SS ALE MXE RI TandemUTR</div>
<div>do</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>compare_miso --compare-samples NS.${gff}/ ${tag[$i]}.${gff}/ ${tag[$i]}.${gff}.comparison/</div>
<div>done</div>
</div>
<div><br>
</div>
<div>Until compare_miso, everything goes smoothly. However, I got error when run compare_miso,</div>
<div><br>
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<div>
<div>$ compare_miso --compare-samples FOX.MXE/ NS.MXE/ FOX.MXE.comparison/</div>
<div>Given output dir: /project/miso/FOX.MXE.comparison</div>
<div>Retrieving MISO files in sample directories...</div>
<div>Computing sample comparison between /project/miso/FOX.MXE and /project/miso/NS.MXE...</div>
<div> - No. of events in /project/miso/FOX.MXE: 2322</div>
<div> - No. of events in /project/miso/NS.MXE: 2241</div>
<div>Creating comparisons parent directory: /project/miso/FOX.MXE.comparison/FOX.MXE_vs_NS.MXE</div>
<div>WARNING: Could not parse event chr18:30661555:30661638:+@chr18:30663362:30663451:+@chr18:30672056:30672133:+@chr18:30682258:30682345:+ samples</div>
<div>WARNING: Could not parse event chr19:42517388:42517999:+@chr19:42527352:42527516:+@chr19:42527676:42527763:+@chr19:42529932:42530058:+ samples</div>
<div>Traceback (most recent call last):</div>
<div> File "/share/pkg/python/2.7.5/bin/compare_miso", line 9, in <module></div>
<div> load_entry_point('misopy==0.5.2', 'console_scripts', 'compare_miso')()</div>
<div> File "/share/pkg/python/2.7.5/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/compare_miso.py", line 94, in main</div>
<div> use_compressed=use_compressed)</div>
<div> File "/share/pkg/python/2.7.5/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/hypothesis_test.py", line 274, in output_samples_comparison</div>
<div> sample2_label=sample2_label)</div>
<div> File "/share/pkg/python/2.7.5/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/hypothesis_test.py", line 148, in compute_delta_densities</div>
<div> posterior_samples2[:, iso_num]</div>
<div>IndexError: too many indices</div>
</div>
<div><br>
</div>
<div>
<div>$ compare_miso --compare-samples NS.MXE/ FOX.MXE/ FOX.MXE.comparison/</div>
<div>Given output dir: /project/miso/FOX.MXE.comparison</div>
<div>Retrieving MISO files in sample directories...</div>
<div>Computing sample comparison between /project/miso/NS.MXE and /project/umw_pgfe_michael_green/iCLIP/18APR14_PE100_C4AK4AC-B/miso/FOX.MXE...</div>
<div> - No. of events in /project/miso/NS.MXE: 2241</div>
<div> - No. of events in /project/miso/FOX.MXE: 2322</div>
<div>Creating comparisons parent directory: /project/FOX.MXE.comparison/NS.MXE_vs_FOX.MXE</div>
<div>WARNING: Could not parse event chr18:30661555:30661638:+@chr18:30663362:30663451:+@chr18:30672056:30672133:+@chr18:30682258:30682345:+ samples</div>
<div>Traceback (most recent call last):</div>
<div> File "/share/pkg/python/2.7.5/bin/compare_miso", line 9, in <module></div>
<div> load_entry_point('misopy==0.5.2', 'console_scripts', 'compare_miso')()</div>
<div> File "/share/pkg/python/2.7.5/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/compare_miso.py", line 94, in main</div>
<div> use_compressed=use_compressed)</div>
<div> File "/share/pkg/python/2.7.5/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/hypothesis_test.py", line 255, in output_samples_comparison</div>
<div> samples1 = sample1_results[0]</div>
<div>TypeError: 'NoneType' object has no attribute '__getitem__'</div>
</div>
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</div>
<div>Could anybody help me to figure out this error? Thank you very much.</div>
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</div>
<div>
<div>Yours Sincerely,</div>
<div><br>
</div>
<div>Jianhong Ou</div>
<div><br>
</div>
<div>LRB 670A</div>
<div>Program in Gene Function and Expression</div>
<div>364 Plantation Street Worcester,</div>
<div>MA 01605</div>
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