<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>This appears to be a permissions issue either for the /u1/local/bin/ directory or RepeatMasker setup. Did you set maker up yourself as your own user or did someone else do it for you, perhaps as root? Is /u1/local/bin/ on an NFS mount.</div><div><br></div><div>If it's a mounting issue I found this via google the exact same issue--></div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div><span style="color: rgb(0, 0, 0); font-size: 11px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(249, 249, 249); display: inline !important; float: none; font-family: verdana, arial, sans-serif; ">I needed to add the 'exec' option to the /etc/fstab file when mounting that partition.</span><br style="color: rgb(0, 0, 0); font-family: verdana, arial, sans-serif; font-size: 11px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"><span style="color: rgb(0, 0, 0); font-size: 11px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(249, 249, 249); display: inline !important; float: none; font-family: verdana, arial, sans-serif; ">If it says 'defaults' on the line in /etc/fstab, then it also means you don't have exec rights on it. </span></div></blockquote></blockquote><div><br></div><div>Are you using the same perl to run maker as you are using for RepeatMasker? For example, are you calling perl directly and giving the path to maker or are you calling maker directly and letting it use the version of perl it was installed with. Try this to see which perl maker was installed with --></div><div>cat /home/maker-2.27-beta/maker/bin/maker | grep "#\!"</div><div><br></div><div>You may have to have to reinstall RepeatMasker and possibly maker.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Hud Hud <<a href="mailto:hudarul@yahoo.com">hudarul@yahoo.com</a>><br><span style="font-weight:bold">Reply-To: </span> Hud Hud <<a href="mailto:hudarul@yahoo.com">hudarul@yahoo.com</a>><br><span style="font-weight:bold">Date: </span> Sunday, 31 March, 2013 4:02 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Help on error-Repeat masker<br></div><div><br></div><div><div><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><div><span style="font-family: arial, helvetica, sans-serif; ">Hello, i have some problem when runnning maker, i've got this kind of error, what could possibly go wrong here? Thnks so much</span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);"><br></font></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);"><br></font></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">setting up GFF3 output and fasta chunks</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">doing repeat masking</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">running repeat masker.</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">#--------- command -------------#</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">Widget::RepeatMasker:</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">cd /tmp/maker_WOVHsi; /home/maker-2.27-beta/maker/exe/RepeatMasker/RepeatMasker /home/maker-2.27-beta/maker/data/contig.maker.output/contig_datastore/61/0D/contig172//theVoid
.contig172/contig172.0.simple.rb -dir /home/maker-2.27-beta/maker/data/contig.maker.output/contig_datastore/61/0D/contig172//theVoid.contig172 -pa 1 - lib /tmp/maker_WOVHsi/b1piBcWHlH</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">#-------------------------------#</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">sh: /home/maker-2.27-beta/maker/exe/RepeatMasker/RepeatMasker: /u1/local/bin/perl: bad interpreter: Permission denied</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">ERROR: RepeatMasker failed</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">--> rank=NA, hostname=Homis</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">ERROR:
Failed while doing repeat masking</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">ERROR: Chunk failed at level:0, tier_type:1</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">FAILED CONTIG:contig172</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);"><br></font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">ERROR: Chunk failed at level:2, tier_type:0</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">FAILED CONTIG:172</font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);"><br></font></div><div><font face="arial,helvetica,sans-serif" style="background-color: rgb(255, 255, 0);">examining contents of the fasta file and run log</font></div><div><font face="arial,helvetica,sans-serif"><br></font></div><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div></div></div></div></div>_______________________________________________
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