Dear Jeremy,<div>Thank You very much, I will try your suggestion. Could you please guide me to the link/webpage that talks about checking the job manually using  <span style="background-color:rgb(255,255,255);font-family:arial,sans-serif;font-size:13px">top/qstat/similar.</span></div>
<div>Happy New Year,</div><div>Bassam Tork. </div><div><br><div class="gmail_quote">On Thu, Dec 29, 2011 at 9:18 AM, Jeremy Goecks <span dir="ltr">&lt;<a href="mailto:jeremy.goecks@emory.edu">jeremy.goecks@emory.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><div class="im"><blockquote type="cite"><div style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<div>My idea was to pass all above including main.bash as parameters to the<br>python wrapper (called run.py, attached), as follows:<br><font color="#000099" face="arial, sans-serif"></font><br>
where the last parameter sys.argv[7] is the output file, specified by xml file.<br></div></div></blockquote><div><br></div></div>This is the correct approach.</div><div class="im"><div><br><blockquote type="cite"><div style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<div>But galaxy was running for more than 3 hours, although it should take<br>only 7-10 minutes on our server with no results.<br><br>Vispa should write its output to dataset_192_I_2_20_CNTGS_DIST0_EM20.txt<br>
, where  dataset_192 .txt is the reads file.But dataset_192_I_2_20_CNTGS_DIST0_EM20.txt did not appear in <font face="arial, sans-serif">galaxy-dist/database/files/000.</font></div><div>run.py: simply coppies data from  dataset_192_I_2_20_CNTGS_DIST0_EM20.txt to galaxy output file, but nothing is coppied since dataset_192_I_2_20_CNTGS_DIST0_EM20.txt was not created.</div>

<div><br>How could the results appear?Could somebody help me ?<br><br></div></div></blockquote></div><div><br></div></div><div>The first thing to check is if run.py functions correctly outside of Galaxy. If so, try checking the job manually using top/qstat/similar system utilities to figure out where the job is stuck.</div>
<div><br></div><div>Good luck,</div><div>J.</div></div></blockquote></div><br></div>