<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;">Hi J</span><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;">iangn !</span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;"><br data-mce-bogus="1"></span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;">I did some modifications in the script ProtExcluder1.2/mspesl-sfetch.pl by replacing :</span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;"><br data-mce-bogus="1"></span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;">"esl-sfetch --index $ARGV[0] " by "samtools faidx $ARGV[0]" </span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;">and</span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;">"esl-sfetch -c $from..$to $ARGV[0] $line[7] >> $ARGV[3]" by "samtools faidx $ARGV[0] $line[7]:$from-$to >> $ARGV[3]"</span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;"><br data-mce-bogus="1"></span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;">it works fine know and the script can extract the subsequences correctly.</span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;"><br data-mce-bogus="1"></span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;">Best regard,</span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; float: none; display: inline !important;">Amine</span></div><div><br></div><hr id="zwchr" data-marker="__DIVIDER__"><div data-marker="__HEADERS__"><b>De: </b>"chebbi mohamed amine" <mohamed.amine.chebbi@univ-poitiers.fr><br><b>À: </b>"jiangn" <jiangn@msu.edu><br><b>Envoyé: </b>Vendredi 4 Novembre 2016 01:03:40<br><b>Objet: </b>Re: [maker-devel] ProtExcluder1.2 Error<br></div><div><br></div><div data-marker="__QUOTED_TEXT__"><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000;" data-mce-style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000;"><div>Hi J<span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;">iangn</span></div><br><div>In fact, this sequence has a size of <span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;">19031 bases.</span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;">When I try the command /hmmer-3.1b2-linux-intel-x86_64/binaries/esl-sfetch -c 1242..19031 all-te.lib rnd-4_family-1731#DNA I get the error , however by testing with coordiantes inferior to 19031 it works fine. I think that it's a related problem to hmmer. I will try to add manualy the subsequence to the file .fnolowm50seq.</span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;"><br></span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;">Thank you</span></div><div><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;">Amine</span></div><hr id="zwchr"><div><b>De: </b>"jiangn" <jiangn@msu.edu><br><b>À: </b>"chebbi mohamed amine" <mohamed.amine.chebbi@univ-poitiers.fr><br><b>Cc: </b>"Prashant S Hosmani" <psh65@cornell.edu>, "Michael Campbell" <michael.s.campbell1@gmail.com><br><b>Envoyé: </b>Vendredi 4 Novembre 2016 00:54:09<br><b>Objet: </b>Re: [maker-devel] ProtExcluder1.2 Error<br></div><br><div><div><p>Hi Amine,<br> <br> I don't have this kind of experience. If only one sequence failed, I would suspect there might be some format issue for that specific sequence.<br> <br> Regards,<br> <br> Ning<br> <br> Quoting chebbi mohamed amine <mohamed.amine.chebbi@univ-poitiers.fr>:<br> <br> ><br> > Hi !<br> ><br> > Thank you Prashant for sharing your experience. Indeed using the same<br> > blast version 2.2.29 for makeblastdb seems to resolve the problem. It<br> > is looking to work fine for all the sequences except one as I have<br> > the message above:<br> ><br> > Fatal exception (source file ../../easel/esl_sqio_ascii.c, line 2001):<br> > Failed to fetch subsequence residues -- corrupt coords?<br> > sh: line 1: 46520 Aborted (core dumped)<br> > /hmmer-3.1b2-linux-intel-x86_64/binaries/esl-sfetch -c 1242..19031<br> > all-te.lib rnd-4_family-1731#DNA >><br> > blastx_results-all-te.txt.fnolowm50seq<br> ><br> > Did you encounter this problem before?<br> ><br> > Thank you for your help.<br> ><br> > Amine<br> ><br> ><br> > De: jiangn@msu.edu<br> > À: "Prashant S Hosmani" <psh65@cornell.edu><br> > Cc: "Michael Campbell" <michael.s.campbell1@gmail.com>, "Mohamed<br> > Amine Chebbi" <mohamed.amine.chebbi@univ-poitiers.fr><br> > Envoyé: Jeudi 3 Novembre 2016 23:54:05<br> > Objet: Re: [maker-devel] ProtExcluder1.2 Error<br> ><br> ><br> ><br> > Hi Prashant,<br> ><br> > Thank you so much for sharing your experience. It is important to<br> > keep everything in the same version. I will remind users about this<br> > when we update it and I may need to bother you then.<br> ><br> > Best regards,<br> ><br> > Ning<br> ><br> > Quoting Prashant S Hosmani <psh65@cornell.edu>:<br> ><br> >> Hi Amine,<br> >><br> >> I was getting similar error. You need to be careful with the blast<br> >> versions. Try using the same blast version for makeblastdb. I was<br> >> using BLAST 2.2.29+. After recreating new blast database with same<br> >> version, it worked for me.<br> >><br> >> Hope this helps.<br> >> Prashant<br> >><br> >><br> >> Prashant Hosmani<br> >> Sol Genomics Network<br> >> Boyce Thompson Institute, Ithaca, NY, USA<br> >><br> >><br> >><br> >> On Nov 3, 2016, at 1:57 PM, Michael Campbell<br> >> <michael.s.campbell1@gmail.com<mailto:michael.s.campbell1@gmail.com>><br> >> wrote:<br> >><br> >> Hi Amine,<br> >><br> >> That script is maintained by Ning Jiang and Kevin Childs. They know<br> >> best what this script is expecting. I?ve ccd them on this email in<br> >> the hope that they can provide some direction.<br> >><br> >> Thanks,<br> >> Mike<br> >> On Nov 2, 2016, at 2:09 PM, Mohamed Amine Chebbi<br> >> <mohamed.amine.chebbi@univ-poitiers.fr<mailto:mohamed.amine.chebbi@univ-poitiers.fr>><br> >> wrote:<br> >><br> >> Hi!<br> >><br> >> I am working on creating a custom repeat library and I want to use<br> >> ProtExcluder1.2 to trim potential genes from my repeat sequences.<br> >> My blast version is BLAST 2.2.30+<br> >><br> >> I get this message error :<br> >><br> >> Can not open the seqfile test.lib_blast_results.txt.fnolowm50seq<br> >> mergeunmatchedregion.pl seqfile<br> >> Illegal division by zero at ProtExcluder1.2/GCcontent.pl line 122.<br> >><br> >> I wonder if you can help me to fix this.<br> >><br> >> Thank you.<br> >><br> >> Amine<br> >> _______________________________________________<br> >> maker-devel mailing list<br> >> maker-devel@box290.bluehost.com<mailto:maker-devel@box290.bluehost.com><br> >> <a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank" data-mce-href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br> >><br> >> _______________________________________________<br> >> maker-devel mailing list<br> >> maker-devel@box290.bluehost.com<mailto:maker-devel@box290.bluehost.com><br> >> <a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank" data-mce-href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br> >><br> >><br> ><br> ><br></p></div></div></div><br></div><div><br></div></div></body></html>