<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Passing from Perl 5.10.1 to 5.16.3 seems to have fixed the <span class="" style="color: rgb(255, 255, 255); font-family: Menlo; background-color: rgb(43, 102, 201);">substr outside of string at PhatHit_utils.pm line 850.</span> issue.<div class=""><br class=""></div><div class="">Thank you again for your help.<br class=""><div class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">/Jacques</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></div></div></div></div></div></div></div></div></div></div></div></div></div>
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<div><br class=""><blockquote type="cite" class=""><div class="">On 17 Apr 2018, at 17:58, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">It runs fine to completion for me (on both 3.01.01 and 3.01.02). Since I’m using your output, no external tools are called, it just parses the reports already written in the directory and finishes.<div class=""><br class=""></div><div class="">This suggests that any issue is either with your version of Perl or a component MAKER is using (such as BioPerl). I am using Perl 5.16.3 and BioPerl 1.007002 (the CPAN version).</div><div class=""><br class=""></div><div class="">Note if you are using BioPerl live or the GitHub release it still shows version 1.007002 but will not necessarily match the CPAN version as the GitHub version counter does not get iterated with each commit. So make sure you are not accidentally using BioPerl live from GitHub (only use CPAN or let MAKER do the install of BioPerl if it’s not system wide). Also you are using Exonerate 2.4 instead of the stable 2.2 release. That shouldn’t make any difference since I am just parsing your output that is already in the folder and not running exonerate. But it may be worth an off chance look.</div><div class=""><br class=""></div><div class="">Finally what you may want to do is download a new version of Perl, then install that and run MAKER with that version just to make sure Perl or something installed inside your Perl is not generating thee issue.</div><div class=""><br class=""></div><div class="">I would try the current stable release of perl (since it comes all ready to go - no compiling needed). Alternatively you can also try perlbrew to get a specific version (but it will have to compile against local libraries).</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Apr 17, 2018, at 6:54 AM, Jacques Dainat <<a href="mailto:jacques.dainat@nbis.se" class="">jacques.dainat@nbis.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">I tried with the last version 3.01.02-beta, still the same error.<div class=""><br class=""><div class="">I agree that it could be something wrong with the input GFF3 file, but I don’t find what it could be.</div><div class=""><br class=""></div><div class="">I have loaded the whole folder as user guest_5602.</div><div class=""><br class=""></div><div class="">I’m looking forward to hearing from you.</div><div class=""><br class=""><div class="">
<div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">/Jacques</div></div></div></div></div></div></div></div></div></div></div></div></div>
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">On 16 Apr 2018, at 22:11, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">I can’t replicate your failure. Normally this error indicates there is something wrong with the input GFF3 file.<div class=""><br class=""></div><div class="">If you want, you can run this on your own machine to generate the failure, then tarball up the complete maker directory for the failure and upload it here —> <a href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi" class="">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi</a></div><div class=""><br class=""></div><div class="">Also try the most current version of MAKER (3.01.02 - October 2017). See if it happens for you there.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Apr 13, 2018, at 6:52 AM, Jacques Dainat <<a href="mailto:jacques.dainat@nbis.se" class="">jacques.dainat@nbis.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Carson,<div class=""><br class=""></div><div class="">I come back to you still with the same problem: <span style="color: rgb(255, 255, 255); font-family: Menlo; background-color: rgb(43, 102, 201);" class="">substr outside of string at /sw/bioinfo/maker/3.01.1-beta-OMPI/bin/../lib/PhatHit_utils.pm line 850.</span></div><div class="">Since our last conversation in January I have seen in the MAKER mailing list that one more person (seoanezonjic) had this issue.</div><div class="">In January, the only way I found to avoid the problem was to remove the gff files that were related to the issue.</div><div class=""><br class=""></div><div class="">I have again the problem for a new annotation project. On the 6 `EST` gff files I’m using (produced in the same way, with Stringtie and converted in gff3 alignment style), 2 of them are raising the error.</div><div class="">To try to better get where the problem come from I have minimise the tools used within MAKER. So no repeat masking and abinitio tools activated, only protein in fasta format and one EST file in gff format.</div><div class="">Using only the gff est file with est2genome=1 works</div><div class="">Using only protein in fasta with protein2genome works</div><div class="">Using the gff EST file and the protein in fasta format with protein2genome and est2genome or only protein2genome <b class="">doesn’t work </b></div><div class=""><br class=""></div><div class="">The problem occurs when protein alignments try to be extended by the EST information.</div><div class="">I tried using the same tool versions as you (BioPerl 1.007002, BLAST+ 2.7.1, Exonerate 2.2.0) but still the same problem.</div><div class="">One of the interesting thing is that the problem does not occur when I used the protein in gff format.</div><div class=""><br class=""></div><div class="">Here is one gff file raising the error. If you want to try in the same conditions you will have to use/dowmload the swissprot database (uniprot rewieved only).</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""></div></div><span id="cid:137DBF83-7F56-43AC-A5D4-6FFCC85F3E69@genetics.utah.edu" class=""><9529.1.136329.CGATGT.gff3></span><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><meta http-equiv="Content-Type" content="text/html; charset=us-ascii" class=""><div class=""></div></div><span id="cid:D50DC10C-1EE6-4216-A375-B6FFF170EAA1@genetics.utah.edu" class=""><scaffold_1017.fa></span><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""></div><div class=""><br class=""></div><div class="">I hope we will finish to find a solution to this problem…</div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""></div><div class="">Jacques<br class=""><div class="">
<div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">-------------------------------------------------</div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Jacques Dainat, Ph.D.</div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">NBIS (National Bioinformatics Infrastructure Sweden)</div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Genome Annotation Service</div><div class=""><a href="http://nbis.se/about/staff/jacques-dainat/" class="">http://nbis.se/about/staff/jacques-dainat/</a></div><div class=""><a href="http://nbis.se/" class="">http://nbis.se</a></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><u class="">Address:</u></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Uppsala University, Biomedicinska Centrum<br class="">Department of Medical Biochemistry Microbiology, Genomics</div>Husargatan 3, box 582</div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">S-75123 Uppsala Sweden</div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Phone: +46 18 471 46 25</div></div></div></div></div></div></div></div></div></div></div></div>
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