<html><head><base href="x-msg://161/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I think this thread accidentally got moved to the lab mailing list, so I'm forwarding it back to the maker mailing list.<div><br></div><div>Barry<br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">cwilks <<a href="mailto:cwilks@stanford.edu">cwilks@stanford.edu</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">October 7, 2009 10:13:16 PM MDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Carson Holt <<a href="mailto:carson.holt@genetics.utah.edu">carson.holt@genetics.utah.edu</a>>, "<a href="mailto:lab@yandell-lab.org">lab@yandell-lab.org</a>" <<a href="mailto:lab@yandell-lab.org">lab@yandell-lab.org</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: [Lab] maker question</b><br></span></div><br><span class="Apple-style-span" style="border-collapse: separate; font-family: Arial; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div bgcolor="#ffffff"><div><font face="Arial" size="2">Hi Carson,</font></div><div><font face="Arial" size="2"></font> </div><div><font face="Arial" size="2">Thanks for the quick response. We're definitely using Bioperl 1.6 (we followed the quick 'n dirty instructions in the maker readme). As for the maker version, we downloaded the 001 version, which appears to be still the current one, however, the one I just downloaded (after I got your email) appears to be [slightly?] different, so I'm currently re-running the data I referred to below again with that one. I'll let you know if and when it finishes.</font></div><div><font face="Arial" size="2"></font> </div><div><font face="Arial" size="2">Thanks again,</font></div><div><font face="Arial" size="2">Chris</font></div><div><font face="Arial" size="2"></font> </div><blockquote dir="ltr" style="padding-right: 0px; padding-left: 5px; margin-left: 5px; border-left-color: rgb(0, 0, 0); border-left-width: 2px; border-left-style: solid; margin-right: 0px; "><div style="font: normal normal normal 10pt/normal arial; ">----- Original Message -----</div><div style="background-image: initial; background-repeat: initial; background-attachment: initial; -webkit-background-clip: initial; -webkit-background-origin: initial; background-color: rgb(228, 228, 228); font: normal normal normal 10pt/normal arial; background-position: initial initial; "><b>From:</b><span class="Apple-converted-space"> </span><a title="carson.holt@genetics.utah.edu" href="mailto:carson.holt@genetics.utah.edu">Carson Holt</a></div><div style="font: normal normal normal 10pt/normal arial; "><b>To:</b><span class="Apple-converted-space"> </span><a title="cwilks@stanford.edu" href="mailto:cwilks@stanford.edu">cwilks</a><span class="Apple-converted-space"> </span>;<span class="Apple-converted-space"> </span><a title="lab@yandell-lab.org" href="mailto:lab@yandell-lab.org">lab@yandell-lab.org</a></div><div style="font: normal normal normal 10pt/normal arial; "><b>Sent:</b><span class="Apple-converted-space"> </span>Wednesday, October 07, 2009 11:28 AM</div><div style="font: normal normal normal 10pt/normal arial; "><b>Subject:</b><span class="Apple-converted-space"> </span>Re: maker question</div><div><br></div><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size: 11pt; ">Could you check two things for me. First, make sure your using BioPerl 1.6 and not 1.5. MAKER fails with 1.5. Second make sure you have the most recent version of MAKER downloaded and installed from our lab website (<span class="Apple-converted-space"> </span><a href="http://www.yandell-lab.org">http://www.yandell-lab.org</a><span class="Apple-converted-space"> </span>). I’ll take a look at the data in the ftp link you sent.<br><br>Thanks,<br>Carson<br><br><br>On 10/6/09 7:37 PM, "cwilks" <<a href="mailto:cwilks@stanford.edu">cwilks@stanford.edu</a>> wrote:<br><br></span></font><blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size: 11pt; ">Hi Carson,<br><br>We're attempting to use Maker to possibly supplement our annotation<br>process here at The Arabipdopsis Information resource (TAIR) and we've<br>run into an issue and hoping you might be able to help us out.<br><br>We've got some files (shown below, they're accessible if you want to run<br>them yourself), which are partial versions of our chromosome 2<br>annotation (they're partial because we tried on the whole chromosome<br>first and that failed as well). We keep getting the error shown below,<br>although when we tried it on a very small (<=10,000 bps) start region of<br>chromosome 2, it worked, but when we tried ~half of chromosome 2 we got<br>the same error as doing the whole thing.<br><br>Let me know if you need anything else, we would be grateful for any help<br>you can offer.<br><br>Thanks,<br>Chris Wilks<br>TAIR<br><br><br><a href="ftp://ftp.arabidopsis.org/home/tair/User_Requests/maker">ftp://ftp.arabidopsis.org/home/tair/User_Requests/maker</a>:<br><br>Three files:<br>ATH2_partial2.fas = contig file (1)<br>tair9w.cdnas.chr2.txt.fas.partial2 = est file<br>tair9w.proteins.chr2.txt.fas.partial2 = protein seq file<br><br><br>tail end of the STDOUT of the maker run on those files.<br><br>Choosing best annotations<br>re reading blast report.<br>/var/opt/oracle/short_reads/maker_arab_test/ATH2_partial2.maker.output/ATH2_partial2_datastore/Chr2/theVoid.Chr2/Chr2.67.tair9w.cdnas.chr2.txt.fas.partial2.blastn<br>deleted:8 hits<br>re reading blast report.<br>/var/opt/oracle/short_reads/maker_arab_test/ATH2_partial2.maker.output/ATH2_partial2_datastore/Chr2/theVoid.Chr2/Chr2.67.tair9w.proteins.chr2.txt.fas.partial2.blastx<br>deleted:0 hits<br>merging blast reports...<br>...finished<br>re-running blast against gi|17980420|gb|AF417474|AF417474...<br>#----------------------<br>FATAL: failed!!<br>#----------------------<br>Can't use string ("Chr2.6699345.6720856") as a HASH ref while "strict<br>refs" in use<br>ERROR: Failed while processing the chunk divide!!<br><br>ERROR: Chunk failed at level 13<br><br><br><br><br>--Next Contig--<br><br>Processing run.log file...<br>#---------------------------------------------------------------------<br>The contig failed 2 time!!<br>Maker will not try again!!<br>The contig will be stored in a fasta file that you can use for debugging.<br>SeqID: Chr2<br>Length: 9874921<br>FASTA:<br>/var/opt/oracle/short_reads/maker_arab_test/ATH2_partial2.maker.output/ATH2_partial2_datastore/Chr2/Chr2.died.fasta<br>#---------------------------------------------------------------------<br><br><br></span></font></blockquote></blockquote>_______________________________________________<br>Lab mailing list<br><a href="mailto:Lab@yandell-lab.org">Lab@yandell-lab.org</a><br><a href="http://yandell-lab.org/mailman/listinfo/lab_yandell-lab.org">http://yandell-lab.org/mailman/listinfo/lab_yandell-lab.org</a><br></div></span></blockquote></div><br></div></body></html>