<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>You can pre-mask the genome, convert the RepaetMasker results to GFF3 and pass them in, or just run the ./configure script in the RepeatMasker directory to configure wublast to be the default.</div><div><br></div><div>You can also let MAKER install it's own separate installation of RepeatMasker using rmblast. Just go to the maker/src/ directory and run this command --> ./Build repeatmasker</div><div><br></div><div>MAKER will use that installation preferentially if you let it install that.</div><div><br></div><div>Thanks,</div><div>Carson</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> padioleau ismaël <<a href="mailto:ismpadioleau@gmail.com">ismpadioleau@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Fri, 13 Apr 2012 17:42:20 +0200<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] Huge memory usage<br></div><div><br></div>Dear Carson,<br><br>I have a problem with RepeatMasker on my cluster. It work with wublast but not with Crossmatch. As maker try to run RepeatMasker with default I can not successfully run maker.<br><br>I wanted to know if I can provide to maker the genome already masked (if I run with wublast externally), I though it was possible but I can't found in the configuration files where I should provide it i.e : In maker_opts.ctl, should I provide the result from RepeatMasker to 'genome_gff:' and set 'rm_pass' to 1, or set rm_gff in the 'Repeat Masking' part of the file?<br>
Or maybe I should provide directly the masked fasta as genome reference.<br><br>An other solution could be to ask maker to run RepeatMasker with the option '-e wublast'.<br><br>Is it possible to use one of these solutions?<br><br>Thanks,<br><br>Ismael<br><br><div class="gmail_quote">2012/4/5 padioleau ismaël <span dir="ltr"><<a href="mailto:ismpadioleau@gmail.com">ismpadioleau@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Carson,<br><br>Thank you for your very quick answering.<br><br>I realised that I missed some error messages and the problem seems to be linked to the DB_file package as you suggested. The person in charge of installation told me that he will recover the configuration.<br><br>I will test it after the Easter weekend and come back to you if we have other issues.<br><br>Have a nice Easter weekend,<br><br>Ismael<br><br>Here Is the error message:<br>Use of uninitialized value $DB_File::db_version in numeric ge (>=) at /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-linux-thread-multi/DB_File.pm line 276.<br>
Use of uninitialized value $DB_File::db_version in numeric gt (>) at /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-linux-thread-multi/DB_File.pm line 280.<br>Deep recursion on subroutine "DB_File::AUTOLOAD" at /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-linux-thread-multi/DB_File.pm line 235.<div><div class="h5"><br><br><br><div class="gmail_quote">2012/4/5 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
The test should not use up more then a few megabytes of RAM. Even on very<br>
large datasets you should never really use more that 1 or 2 gig of RAM<br>
perl MAKER instance<br><br>
It's possible that their may be other perl modules that are broken need to<br>
be reinstalled on your system. This can happen when perl gets updated,<br>
but you are pointing to modules built for a different perl version with<br>the PERL5LIB environmental variable. Make sure you you have the latest<br>
version of MAKER and run with --debug set. Collect that output and send<br>
it to me (the --debug option does some dependancy checking).<br><br>
I know there is an issue on Macs with updating perl's DB_File module that<br>
causes it to gobble up big sections of the hard drive (it will eventually<br>
fill the drive if you let it). It's not a memory issue but just one<br>
example of how broken modules can cause weird behavior.<br><br>
Thanks,<br>
Carson<br><br><br><br><br>
On 12-04-05 10:14 AM, "<a href="mailto:pingouinandsheep@gmail.com" target="_blank">pingouinandsheep@gmail.com</a>"<br>
<<a href="mailto:pingouinandsheep@gmail.com" target="_blank">pingouinandsheep@gmail.com</a>> wrote:<br><br>
>Hello,<br>
><br>
>When I try to run the test provided with maker2, maker start to use a<br>
>huge amount of memory. I stoped it after it reach ~100go of memory<br>
>used. I believe the test should not use that amount of memory.<br>
><br>
>In an other message someone suggest that the bioperl version installed<br>
>could be the cause of the problem, but the bioperl installed on my<br>
>cluster is already at version 1.6.<br>
><br>
>perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'<br>
>1.006901<br>
><br>
>Unfortunately I don't have an error message to provide, that could<br>
>clarify my problem.<br>
><br>
>But maybe it is a recurrent problem and you know a few things I should<br>
>check.<br>
><br>
>Thanks,<br>
><br>
>Ismael<br>
><br>
>_______________________________________________<br>
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><a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><br>
><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br><br><br></blockquote></div><br><br clear="all"><br></div></div>-- <br>Ismaël Padioleau<br>Evgeny Zdobnov Group (Computational Evolutionary Genomics Group)<br>Emmanouil Dermitzakis Group<br>Dpt de Médecine Génétique et Développement<br>
Université de Genève - Faculté de Médecine<br>
CMU - Rue Michel-Servet 1<br>CH 1211 Genève 4<br>Tel: 0041 22 379 59 74<br><a href="mailto:ismael.padioleau@unige.ch" target="_blank">ismael.padioleau@unige.ch</a><br><br>--<br>Tel. <span style="border-collapse: collapse; font-size: 13px; font-family: arial, sans-serif; ">0041 78 77 69 561</span><br><a href="mailto:ismpadioleau@gmail.com" target="_blank">ismpadioleau@gmail.com</a><br></blockquote></div><br><br clear="all"><br>-- <br>Ismaël Padioleau<br>Evgeny Zdobnov Group (Computational Evolutionary Genomics Group)<br>Emmanouil Dermitzakis Group<br>Dpt de Médecine Génétique et Développement<br>Université de Genève - Faculté de Médecine<br>
CMU - Rue Michel-Servet 1<br>CH 1211 Genève 4<br>Tel: 0041 22 379 59 74<br><a href="mailto:ismael.padioleau@unige.ch" target="_blank">ismael.padioleau@unige.ch</a><br><br>--<br>Tel. <span style="border-collapse: collapse; font-size: 13px; font-family: arial, sans-serif; ">0041 78 77 69 561</span><br><a href="mailto:ismpadioleau@gmail.com" target="_blank">ismpadioleau@gmail.com</a><br></span></body></html>