<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); "><div style="font-family: Calibri, sans-serif; font-size: 14px; ">The best evidence is from mRNAseq or ESTs of the same species. ESTs and mRNAseq from related species can be used, but if protein annotations are available use those instead. This is because cross species nucleotide alinements must be translated in all 6 reading frames (3 for the query and 3 for the subject), which would basically make run times increase by 6 fold. You can try giving the cross species alignments to maker as if they were from the same species instead (est= option), fewer will align, but run times will not be overwhelming. Then provide the protein annotations from the related species combined with uniprot (maker can take comma separated lists for the input files). You can use either the program CEGMA from Ian Korf's lab or alternatively maker's protein2genome option to build an initial annotation set to use for training. Then train SNAP, Augustus, and GeneMark (Genemark self trains). For the last run let all 3 predictors run together with protein2genome now turned off. Given that the genome is only 50Mb and you have a lack of alignment evidence, you can probably safely set keep_preds=1 on the second run as the false positive rate is usually quite low for gene dense organisms and you won't get many annotations from maker otherwise without more evidence alignments. Perform your first and second runs in the same location, so maker can automatically reuse the same alignments (the second run is always very fast this way as maker won't have to rerun blast and exonerate).</div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="font-family: Calibri, sans-serif; font-size: 14px; ">If your organism is a fungi (I'm just guessing because of the small genome size) you can also use this <span class="Apple-style-span" style="font-family: Calibri; font-size: medium; "> </span><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; ">gene prediction parameter</span><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; "> </span>resource from Jason Stajich</div><div style="font-family: Calibri, sans-serif; font-size: 14px; ">--> <span class="Apple-style-span" style="font-family: Calibri; font-size: medium; "><a href="https://github.com/hyphaltip/fungi-gene-prediction-params">https://github.com/hyphaltip/fungi-gene-prediction-params</a></span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="font-family: Calibri, sans-serif; font-size: 14px; ">Thanks,</div><div style="font-family: Calibri, sans-serif; font-size: 14px; ">Carson</div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION" style="font-size: 14px; font-family: Calibri, sans-serif; "><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 9:16 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>Thanks, i now have better insight regard to the cpu cores.. i have other questions...i dont have other info or evidences of my own genome, i only have assembled contigs....recently JGI sequenced a species that closely related to my genome (at genus level), and i have access to the data (protein, est, rna-seq reads,transcript, gene models,gff)</div><div><br></div><div>1.I have run maker (MWAS) using diff set of evidences, such as protein and est(JGI) and est(JGI) and uniprot database ..but both run produced diferent no of predicted genes....so my question, what is the best evidences to be used to support my annotation..is it more preferred to use larger dataset such as uniprot rather than using the data from JGI (even it closely related)</div><div><br></div><div>2. can i use rna-seq data (from JGI) to be used in maker...ive denovo
assembled the rnaseq using clc genomics.<span style="font-size: 12pt;"> </span></div><div style="color: rgb(0, 0, 0); font-size: 12pt; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"><span style="font-size: 12pt;">Thanks</span></div><div><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 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;">Sent:</span></b> Tuesday, April 2, 2013 5:01 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="yiv836316177"><div><div>That's not too bad It's best to choose a few large contigs (1-2Mb total) to run with at first and then use those results to help configure the rest of the run. For the final run you may want to consider splitting onto multiple machines if your machine has limited cpu power. It will take you ~150 hours on 1 cpu core depending on the size of alignment datasets - ESTs and proteins. More cpu cores will allow it to run faster (see graph below from the MAKER2 paper). I imagine that your machine probably has at least 4 cpu cores.</div><div><br></div><div>Most bioinformatics labs have multi cpu Linux boxes (I.e. 24-32 cpu cores), some have clusters available to them (100's to 1000's of cpu cores), and a few just launch maker on multiple lab desktop machines all writing to the same network mounted output
directory.</div><div><br></div><div><div>Thanks,</div><div>Carson</div></div><div><br></div><div><img src="cid:1.2904077979@web164901.mail.bf1.yahoo.com"></div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="yiv836316177OLK_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> Monday, 1 April, 2013 4:48 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>Its about 50mb</span></div><div><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>> <br> <b><span style="font-weight:bold;">Sent:</span></b> Tuesday, April 2, 2013 4:44 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="yiv836316177"><div><div>How big is the genome?</div><div><br></div><div>--Carson</div><div><br></div><span id="yiv836316177OLK_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> Monday, 1 April, 2013 4:37 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>owh thanks so much,now i know whats going wrong, its the cygwin... i'll try dual boot then as my genome over 10 mb..thanks for your time</span></div><div><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>> <br><b><span style="font-weight:bold;">Cc:</span></b> "<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> Tuesday, April 2, 2013 4:29 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="yiv836316177"><div><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 rel="nofollow" target="_blank" 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="yiv836316177OLK_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> Monday, 1 April, 2013 4:21 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 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="yiv836316177Apple-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 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>> <br><b><span style="font-weight:bold;">Cc:</span></b> "<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> 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="yiv836316177"><div><div style="font-family: Calibri, sans-serif;">What kind of system (OS) are you running on? '<span class="yiv836316177Apple-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="yiv836316177Apple-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="yiv836316177Apple-style-span" style="font-size:16px;"> /home/maker-2.27-beta/maker/src</span></div><div><span class="yiv836316177Apple-style-span" style="font-size:16px;">./Build repeatmasker</span></div></blockquote><div><span class="yiv836316177Apple-style-span" style="font-size:16px;"><br></span></div><div><span class="yiv836316177Apple-style-span" style="font-size:16px;">--Carson</span></div><div style="font-family: Calibri, sans-serif;"><span class="yiv836316177Apple-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="yiv836316177OLK_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="yiv836316177"><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="yiv836316177OLK_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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