<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" id="owaParaStyle"></style>
</head>
<body fpstyle="1" ocsi="0">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Yarden and MISO-users,
<div>I encountered an error in MISO (version 0.5.3) that was also described recently by Ankit Arora.</div>
<div>I couldn't figure out how to reply to the old thread, but I think I have found the source of the error and thought I should share so it can be fixed for next release.</div>
<div><br>
</div>
<div>The error message looks like the following:</div>
<div><br>
</div>
<div>
<p class="p1">Traceback (most recent call last):</p>
<p class="p1"> File "/usr/local/bin/miso", line 9, in <module></p>
<p class="p1"> load_entry_point('misopy==0.5.3', 'console_scripts', 'miso')()</p>
<p class="p1"> File "/usr/local/lib/python2.7/dist-packages/misopy/miso.py", line 591, in main</p>
<p class="p1"> wait_on_jobs=wait_on_jobs)</p>
<p class="p1"> File "/usr/local/lib/python2.7/dist-packages/misopy/miso.py", line 372, in compute_all_genes_psi</p>
<p class="p1"> given_read_len=read_len)</p>
<p class="p1"> File "/usr/local/lib/python2.7/dist-packages/misopy/run_events_analysis.py", line 171, in check_gff_and_bam</p>
<p class="p1"> miso_<span class="s1">logger</span>.warning("It looks like your GFF annotation file and your BAM " \</p>
<p class="p1">NameError: global name 'miso_<span class="s1">logger</span>' is not defined</p>
<p class="p1"><br>
</p>
<p class="p1">I know that this occurs because the chromosomes in the beginning of my bam-files does not have the "chr" prefix, while those in the beginning of the gff file do. However, this should not crash the script, only print a warning and continue. Looking
closer into the source code of run_events_analysis.py I can see that a logger object is input into the function and given the variable name <span style="font-size: 13.3333330154419px;">"main_logger". In the section where mismatches between the files are handled,
"miso_logger" is used instead which is not defined anywhere in the script. I changed "miso_logger" to "main_logger" in the code, and now MISO runs perfectly.</span></p>
<p class="p1"><span style="font-size: 13.3333330154419px;"><br>
</span></p>
<p class="p1"><span style="font-size: 13.3333330154419px;">Best regards,</span></p>
<p class="p1"><span style="font-size: 13.3333330154419px;">Helena Storvall</span></p>
<p class="p1"><br>
</p>
<p class="p1"><br>
</p>
</div>
</div>
</body>
</html>