<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>I found it odd because perl.exe is a windows extension not used in Linux, but it confirmed my suspicions. You can't use maker with cygwin. There are several things that will break because it's not really Linux. You can use Virtual Box instead to install a virtual Linux machine --> <a href="https://www.virtualbox.org/">https://www.virtualbox.org/</a>. Alternatively you can try and dual boot your system with a Linux partition.</div><div><br></div><div>Virtual Box will allow you to run maker on small datasets, depending on the size of the genome you want to run maker with it may be fine. But I would not recommend running anything over 10 megabases (it won't fail, it will just take a very long time).</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> Monday, 1 April, 2013 4:21 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [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 style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"><span><br></span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;">1. owh its odd?im using windows8 but for maker im using cygwin</div><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;">2. when i type which perl i get this /usr/bin/perl</div><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;">3. when i type ./Build repeatmasker i got this </div><div><span class="Apple-tab-span" style="font-size: 12pt; white-space: pre; font-family: arial, helvetica, sans-serif; "> </span><span style="background-color: rgb(208, 208, 208);">cygwin warning:
MS-DOS style path detected: \Users\Dora Preferred POSIX equivalent is: /cygdrive/c/Users/Dora CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
<a href="http://cygwin.com/cygwin-ug-net/using.html#using-pathnames">http://cygwin.com/cygwin-ug-net/using.html#using-pathnames</a>
WARNING: RepeatMasker was already found on this system.
Do you still want MAKER to install RepeatMasker for you?</span></div><div style="color: rgb(0, 0, 0); font-size: 12pt; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"> is there any prob with this, or can i just proceed with the installation?<span style="background-color: transparent; font-size: 12pt;"> </span></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br> <b><span style="font-weight: bold;">To:</span></b> Hud Hud <<a href="mailto:hudarul@yahoo.com">hudarul@yahoo.com</a>> <br><b><span style="font-weight: bold;">Cc:</span></b> "<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> <b><span style="font-weight: bold;">Sent:</span></b> Tuesday,
April 2, 2013 3:59 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [maker-devel] Help on error-Repeat masker<br> </font> </div> <br><div id="yiv782745707"><div><div style="font-family: Calibri, sans-serif;">What kind of system (OS) are you running on? '<span class="yiv782745707Apple-style-span" style="font-size: 16px; font-family: 'times new roman', 'new york', times, serif; ">perl.exe</span>' seems odd.</div><div style="font-family: Calibri, sans-serif;"><br></div><div style="font-family: Calibri, sans-serif;">It appears that the perl is different for maker and RepeatMasker. What do you get when you type 'which perl' on the command line?</div><div style="font-family: Calibri, sans-serif;"><br></div><div style="font-family: Calibri, sans-serif;">I think you need to reinstall RepeatMasker at a minimum. <span class="yiv782745707Apple-style-span" style="font-family: Calibri;">To do that --></span></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px;"><div>cd <span class="yiv782745707Apple-style-span" style="font-size:16px;"> /home/maker-2.27-beta/maker/src</span></div><div><span class="yiv782745707Apple-style-span" style="font-size:16px;">./Build repeatmasker</span></div></blockquote><div><span class="yiv782745707Apple-style-span" style="font-size:16px;"><br></span></div><div><span class="yiv782745707Apple-style-span" style="font-size:16px;">--Carson</span></div><div style="font-family: Calibri, sans-serif;"><span class="yiv782745707Apple-style-span" style="font-size: 16px; font-family: 'times new roman', 'new york', times, serif; "><br></span></div><div style="font-family: Calibri, sans-serif;"><br></div><span id="yiv782745707OLK_SRC_BODY_SECTION" style="font-family: Calibri, sans-serif; "><div style="font-family: Calibri; font-size: 11pt; text-align: left; color: black; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223);"><span style="font-weight:bold;">From: </span> Hud
Hud <<a rel="nofollow" ymailto="mailto:hudarul@yahoo.com" target="_blank" href="mailto:hudarul@yahoo.com">hudarul@yahoo.com</a>><br><span style="font-weight:bold;">Reply-To: </span> Hud Hud <<a rel="nofollow" ymailto="mailto:hudarul@yahoo.com" target="_blank" href="mailto:hudarul@yahoo.com">hudarul@yahoo.com</a>><br><span style="font-weight:bold;">Date: </span> Monday, 1 April, 2013 3:53 PM<br><span style="font-weight:bold;">To: </span> Carson Holt <<a rel="nofollow" ymailto="mailto:carsonhh@gmail.com" target="_blank" href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold;">Subject: </span> Re: [maker-devel] Help on error-Repeat masker<br></div><div><br></div><div><div><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><div><span><span style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; ">Thanks for the reply</span></span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal;"><span><span style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; ">1. Yes i set up the maker myself as own user but i dont know how to check for the mounting things</span></span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal;"><span><span style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; ">2. Im calling maker directly and i've tried this
cat /home/maker-2.27-beta/maker/bin/maker | grep "#\!" and it gaves me this </span><font face="times new roman,new york,times,serif">#!/usr/bin/perl.exe<br></font></span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"><span><span style="font-size:12pt;"><br></span></span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Carson Holt <<a rel="nofollow" ymailto="mailto:carsonhh@gmail.com" target="_blank" href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br> <b><span style="font-weight:bold;">To:</span></b> Hud Hud <<a rel="nofollow" ymailto="mailto:hudarul@yahoo.com" target="_blank" href="mailto:hudarul@yahoo.com">hudarul@yahoo.com</a>>; "<a rel="nofollow" ymailto="mailto:maker-devel@yandell-lab.org" target="_blank" href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a rel="nofollow" ymailto="mailto:maker-devel@yandell-lab.org" target="_blank" href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>> <br> <b><span style="font-weight:bold;">Sent:</span></b> Monday, April 1, 2013
10:50 PM<br> <b><span style="font-weight:bold;">Subject:</span></b> Re: [maker-devel] Help on error-Repeat masker<br> </font> </div> <br><div id="yiv782745707"><div><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-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; background-color: rgb(249, 249, 249); display: inline; 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; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 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-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; background-color: rgb(249, 249, 249); display: inline; 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="yiv782745707OLK_SRC_BODY_SECTION"><div style="font-family: Calibri; font-size: 11pt; text-align: left; color: black; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223);"><span style="font-weight:bold;">From: </span> Hud Hud <<a rel="nofollow" ymailto="mailto:hudarul@yahoo.com" target="_blank" href="mailto:hudarul@yahoo.com">hudarul@yahoo.com</a>><br><span style="font-weight:bold;">Reply-To: </span> Hud Hud <<a rel="nofollow" ymailto="mailto:hudarul@yahoo.com" target="_blank" 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 rel="nofollow" ymailto="mailto:maker-devel@yandell-lab.org" target="_blank" href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a rel="nofollow" ymailto="mailto:maker-devel@yandell-lab.org" target="_blank" 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: rgb(0, 0, 0); background-color: rgb(255, 255, 255); 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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