From munholl at uwindsor.ca Fri Jan 11 12:11:40 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Fri, 11 Jan 2019 13:11:40 -0500 Subject: [maker-devel] Maker can't find snap Message-ID: Hello, I'm installing a new instance of maker and when I run Build.PL it can't find snap, though it is compiled and working properly. I can use ./Build snap to compile Maker, then redirect it to my installed snap in the ctl files, but that seems like a workaround and I don't know if something is happening on the back end that this might be breaking. Is there a way to point maker at my install during compile? Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Tue Jan 15 03:54:42 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Tue, 15 Jan 2019 09:54:42 +0000 Subject: [maker-devel] Maker crash with big protein evidence ? Message-ID: Hi, I run maker with mpi and default option. It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : in cluster::shadow_cluster... sorting hits in shadow cluster... j_size:3 current j:0 j_size:3 current j:1 j_size:3 current j:2 ...finished clustering. Did you already face something similar ? Thanks. Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From munholl at uwindsor.ca Wed Jan 16 10:43:48 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Wed, 16 Jan 2019 11:43:48 -0500 Subject: [maker-devel] tRNAscan-SE file already exists Message-ID: Hi Everyone, Just getting my latest Maker install running and I'm running into the following issue when it gets to tRNAscan-SE: running trnascan. #--------- command -------------# Widget::trnascan: /usr/local/bin/tRNAscan-SE -b -q /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_no mask.0 > /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_nomask.0.eukaryotic.trnasc an #-------------------------------# WARNING: -q exists already. (O)verwrite file, (A)ppend to file, or (Q)uit program? I have tRNAscan-SE-2.0 installed, which has a -b option for a bed output but needs a file to be specified. Do I need to roll back to a specific version or would it be easier to skip it and run tRNAscan-SE separately? Do the outputs get integrated later to adjsut Maker calls or are they stand alone? Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 15:27:36 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:27:36 -0700 Subject: [maker-devel] tRNAscan-SE file already exists In-Reply-To: References: Message-ID: <53237E1D-00BE-4AB5-A87A-2EBE359A11B4@gmail.com> You will need to downgrade. I know 1.3.1 works. I will have to update MAKER for the new tRNAscan. ?Carson > On Jan 16, 2019, at 9:43 AM, Seth Munholland wrote: > > Hi Everyone, > > Just getting my latest Maker install running and I'm running into the following issue when it gets to tRNAscan-SE: > > running trnascan. > #--------- command -------------# > Widget::trnascan: > /usr/local/bin/tRNAscan-SE -b -q /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_no > mask.0 > /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_nomask.0.eukaryotic.trnasc > an > #-------------------------------# > > WARNING: -q exists already. > > (O)verwrite file, (A)ppend to file, or (Q)uit program? > > I have tRNAscan-SE-2.0 installed, which has a -b option for a bed output but needs a file to be specified. Do I need to roll back to a specific version or would it be easier to skip it and run tRNAscan-SE separately? Do the outputs get integrated later to adjsut Maker calls or are they stand alone? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 <>_______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 15:31:17 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:31:17 -0700 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: References: Message-ID: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). ?Carson > On Jan 15, 2019, at 2:54 AM, Patrick Tran Van wrote: > > Hi, > > I run maker with mpi and default option. > It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : > > in cluster::shadow_cluster... > sorting hits in shadow cluster... > j_size:3 current j:0 > j_size:3 current j:1 > j_size:3 current j:2 > ...finished clustering. > > Did you already face something similar ? > > Thanks. > > Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 15:33:40 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:33:40 -0700 Subject: [maker-devel] Maker can't find snap In-Reply-To: References: Message-ID: If you are using ?sudo? to do the install you may be reseting the PATH environmental variable. Or snap was never in your PATH. The Build script searches the PATH to find the snap executable. Type ?which snap? on the command line to test. ?Carson > On Jan 11, 2019, at 11:11 AM, Seth Munholland wrote: > > Hello, > > I'm installing a new instance of maker and when I run Build.PL it can't find snap, though it is compiled and working properly. I can use ./Build snap to compile Maker, then redirect it to my installed snap in the ctl files, but that seems like a workaround and I don't know if something is happening on the back end that this might be breaking. Is there a way to point maker at my install during compile? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 <>_______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From munholl at uwindsor.ca Thu Jan 17 15:32:03 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Thu, 17 Jan 2019 16:32:03 -0500 Subject: [maker-devel] Maker can't find snap In-Reply-To: References: Message-ID: I was sudo installing. I'll update PATH. Thanks! Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 On Thu, Jan 17, 2019 at 4:33 PM Carson Holt wrote: > If you are using ?sudo? to do the install you may be reseting the PATH > environmental variable. Or snap was never in your PATH. The Build script > searches the PATH to find the snap executable. Type ?which snap? on the > command line to test. > > ?Carson > > > On Jan 11, 2019, at 11:11 AM, Seth Munholland wrote: > > Hello, > > I'm installing a new instance of maker and when I run Build.PL it can't > find snap, though it is compiled and working properly. I can use ./Build > snap to compile Maker, then redirect it to my installed snap in the ctl > files, but that seems like a workaround and I don't know if something is > happening on the back end that this might be breaking. Is there a way to > point maker at my install during compile? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Fri Jan 18 11:09:52 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Fri, 18 Jan 2019 17:09:52 +0000 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> References: , <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> Message-ID: <96ea2ea82c744683b4757f1aa01c676f@unil.ch> Thanks Carson. I thought also to use only swissprot at the beginning but I am working with a non model organism and I am scared that swissprot is not enough complete to capture all the gene prediction. but if I use nr and I select only gene with AED < 0.5, it should be good no ? or do you have an AED cut off to recommend ? Cheers. Patrick ________________________________ From: Carson Holt Sent: Thursday, January 17, 2019 10:31:17 PM To: Patrick Tran Van Cc: maker-devel at yandell-lab.org Subject: Re: Maker crash with big protein evidence ? You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). ?Carson On Jan 15, 2019, at 2:54 AM, Patrick Tran Van > wrote: Hi, I run maker with mpi and default option. It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : in cluster::shadow_cluster... sorting hits in shadow cluster... j_size:3 current j:0 j_size:3 current j:1 j_size:3 current j:2 ...finished clustering. Did you already face something similar ? Thanks. Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From scott at scottcain.net Wed Jan 23 12:25:07 2019 From: scott at scottcain.net (Scott Cain) Date: Wed, 23 Jan 2019 10:25:07 -0800 Subject: [maker-devel] Fwd: [GSoC 2019] [Open Genome Informatics] Google Summer of Code 2019 Participation In-Reply-To: References: Message-ID: ---------- Forwarded message --------- From: Robin Haw Date: Wed, Jan 23, 2019 at 10:20 AM Subject: [GSoC 2019] [Open Genome Informatics] Google Summer of Code 2019 Participation To: gmod-devel at lists.sourceforge.net Cc: Dannon Baker , Dave Clements < clements at galaxyproject.org>, Marc Gillespie , Scott Cain Dear All, The Open Genome Informatics team serves as an ?umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC) . Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others. Call for 2019 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year?s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here or this online form . For more information please refer to the Open Genome Informatics page . The mentoring organization application deadline with GSoC is February 6th, 2019 at 3 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions please let us know. Thanks, Robin, Marc, Dave, Dannon, and Scott. -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jan 24 09:36:24 2019 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 24 Jan 2019 15:36:24 +0000 Subject: [maker-devel] BioPerl and MAKER Message-ID: Hi Carson, I?ll be working over the next several months to push out a new stripped-down version of BioPerl (along with the help of Carne Draug) with the hopeful target goal of a CPAN release in April-May. I know MAKER still relies on a few BioPerl core modules, such as those related to codon tables, FASTA indexing, etc. Just from a quick grep through the latest release (2.31.10) I found the ones at the bottom of the email; I know the various Phat* modules are MAKER-specific, but can you think of any others that might be required? (I haven?t checked the 3.0 beta version yet) Thanks chris Bio::DB::Fasta Bio::DB::GFF Bio::FeatureIO::gff Bio::Search::HSP::GenericHSP Bio::Search::HSP::HSPFactory Bio::Search::HSP::PhatHSP::Base Bio::Search::HSP::PhatHSP::augustus Bio::Search::HSP::PhatHSP::blastn Bio::Search::HSP::PhatHSP::blastx Bio::Search::HSP::PhatHSP::cdna2genome Bio::Search::HSP::PhatHSP::est2genome Bio::Search::HSP::PhatHSP::fgenesh Bio::Search::HSP::PhatHSP::genemark Bio::Search::HSP::PhatHSP::gff3 Bio::Search::HSP::PhatHSP::protein2genome Bio::Search::HSP::PhatHSP::repeatmasker Bio::Search::HSP::PhatHSP::snap Bio::Search::HSP::PhatHSP::snoscan Bio::Search::HSP::PhatHSP::tblastx Bio::Search::HSP::PhatHSP::trnascan Bio::Search::Hit::GenericHit Bio::Search::Hit::HitFactory Bio::Search::Hit::PhatHit::Base Bio::Search::Hit::PhatHit::augustus Bio::Search::Hit::PhatHit::blastn Bio::Search::Hit::PhatHit::blastx Bio::Search::Hit::PhatHit::cdna2genome Bio::Search::Hit::PhatHit::est2genome Bio::Search::Hit::PhatHit::fgenesh Bio::Search::Hit::PhatHit::genemark Bio::Search::Hit::PhatHit::gff3 Bio::Search::Hit::PhatHit::protein2genome Bio::Search::Hit::PhatHit::repeatmasker Bio::Search::Hit::PhatHit::snap Bio::Search::Hit::PhatHit::snoscan Bio::Search::Hit::PhatHit::tblastx Bio::Search::Hit::PhatHit::trnascan Bio::Search::Result::ResultFactory Bio::SearchIO Bio::SeqIO Bio::Tools::CodonTable Bio::Tools::GFF -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Jan 25 17:06:22 2019 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 25 Jan 2019 16:06:22 -0700 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: <96ea2ea82c744683b4757f1aa01c676f@unil.ch> References: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> <96ea2ea82c744683b4757f1aa01c676f@unil.ch> Message-ID: <12D0A479-5FA3-43CA-B04F-5226258AC8E1@gmail.com> NR will likly create problems on more genes than it will help recover in comparison to swiss-prot. The AED cutoff can be a convenient way to remove models when you expect too much or poor quality evidence (but it?s more of a sledgehammer than a scalpel). So using NR to get better sensitivity and then using AED to reduce sensitivity will likely just make all models worse in general while not adding many missed models. ?Carson > On Jan 18, 2019, at 10:09 AM, Patrick Tran Van wrote: > > Thanks Carson. > I thought also to use only swissprot at the beginning but I am working with a non model organism and I am scared that swissprot is not enough complete to capture all the gene prediction. > > but if I use nr and I select only gene with AED < 0.5, it should be good no ? or do you have an AED cut off to recommend ? > > Cheers. > > Patrick > From: Carson Holt > > Sent: Thursday, January 17, 2019 10:31:17 PM > To: Patrick Tran Van > Cc: maker-devel at yandell-lab.org > Subject: Re: Maker crash with big protein evidence ? > > You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). > > ?Carson > > >> On Jan 15, 2019, at 2:54 AM, Patrick Tran Van > wrote: >> >> Hi, >> >> I run maker with mpi and default option. >> It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : >> >> in cluster::shadow_cluster... >> sorting hits in shadow cluster... >> j_size:3 current j:0 >> j_size:3 current j:1 >> j_size:3 current j:2 >> ...finished clustering. >> >> Did you already face something similar ? >> >> Thanks. >> >> Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From munholl at uwindsor.ca Fri Jan 11 11:11:40 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Fri, 11 Jan 2019 13:11:40 -0500 Subject: [maker-devel] Maker can't find snap Message-ID: Hello, I'm installing a new instance of maker and when I run Build.PL it can't find snap, though it is compiled and working properly. I can use ./Build snap to compile Maker, then redirect it to my installed snap in the ctl files, but that seems like a workaround and I don't know if something is happening on the back end that this might be breaking. Is there a way to point maker at my install during compile? Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Tue Jan 15 02:54:42 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Tue, 15 Jan 2019 09:54:42 +0000 Subject: [maker-devel] Maker crash with big protein evidence ? Message-ID: Hi, I run maker with mpi and default option. It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : in cluster::shadow_cluster... sorting hits in shadow cluster... j_size:3 current j:0 j_size:3 current j:1 j_size:3 current j:2 ...finished clustering. Did you already face something similar ? Thanks. Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From munholl at uwindsor.ca Wed Jan 16 09:43:48 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Wed, 16 Jan 2019 11:43:48 -0500 Subject: [maker-devel] tRNAscan-SE file already exists Message-ID: Hi Everyone, Just getting my latest Maker install running and I'm running into the following issue when it gets to tRNAscan-SE: running trnascan. #--------- command -------------# Widget::trnascan: /usr/local/bin/tRNAscan-SE -b -q /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_no mask.0 > /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_nomask.0.eukaryotic.trnasc an #-------------------------------# WARNING: -q exists already. (O)verwrite file, (A)ppend to file, or (Q)uit program? I have tRNAscan-SE-2.0 installed, which has a -b option for a bed output but needs a file to be specified. Do I need to roll back to a specific version or would it be easier to skip it and run tRNAscan-SE separately? Do the outputs get integrated later to adjsut Maker calls or are they stand alone? Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 14:27:36 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:27:36 -0700 Subject: [maker-devel] tRNAscan-SE file already exists In-Reply-To: References: Message-ID: <53237E1D-00BE-4AB5-A87A-2EBE359A11B4@gmail.com> You will need to downgrade. I know 1.3.1 works. I will have to update MAKER for the new tRNAscan. ?Carson > On Jan 16, 2019, at 9:43 AM, Seth Munholland wrote: > > Hi Everyone, > > Just getting my latest Maker install running and I'm running into the following issue when it gets to tRNAscan-SE: > > running trnascan. > #--------- command -------------# > Widget::trnascan: > /usr/local/bin/tRNAscan-SE -b -q /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_no > mask.0 > /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_nomask.0.eukaryotic.trnasc > an > #-------------------------------# > > WARNING: -q exists already. > > (O)verwrite file, (A)ppend to file, or (Q)uit program? > > I have tRNAscan-SE-2.0 installed, which has a -b option for a bed output but needs a file to be specified. Do I need to roll back to a specific version or would it be easier to skip it and run tRNAscan-SE separately? Do the outputs get integrated later to adjsut Maker calls or are they stand alone? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 <>_______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 14:31:17 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:31:17 -0700 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: References: Message-ID: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). ?Carson > On Jan 15, 2019, at 2:54 AM, Patrick Tran Van wrote: > > Hi, > > I run maker with mpi and default option. > It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : > > in cluster::shadow_cluster... > sorting hits in shadow cluster... > j_size:3 current j:0 > j_size:3 current j:1 > j_size:3 current j:2 > ...finished clustering. > > Did you already face something similar ? > > Thanks. > > Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 14:33:40 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:33:40 -0700 Subject: [maker-devel] Maker can't find snap In-Reply-To: References: Message-ID: If you are using ?sudo? to do the install you may be reseting the PATH environmental variable. Or snap was never in your PATH. The Build script searches the PATH to find the snap executable. Type ?which snap? on the command line to test. ?Carson > On Jan 11, 2019, at 11:11 AM, Seth Munholland wrote: > > Hello, > > I'm installing a new instance of maker and when I run Build.PL it can't find snap, though it is compiled and working properly. I can use ./Build snap to compile Maker, then redirect it to my installed snap in the ctl files, but that seems like a workaround and I don't know if something is happening on the back end that this might be breaking. Is there a way to point maker at my install during compile? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 <>_______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From munholl at uwindsor.ca Thu Jan 17 14:32:03 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Thu, 17 Jan 2019 16:32:03 -0500 Subject: [maker-devel] Maker can't find snap In-Reply-To: References: Message-ID: I was sudo installing. I'll update PATH. Thanks! Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 On Thu, Jan 17, 2019 at 4:33 PM Carson Holt wrote: > If you are using ?sudo? to do the install you may be reseting the PATH > environmental variable. Or snap was never in your PATH. The Build script > searches the PATH to find the snap executable. Type ?which snap? on the > command line to test. > > ?Carson > > > On Jan 11, 2019, at 11:11 AM, Seth Munholland wrote: > > Hello, > > I'm installing a new instance of maker and when I run Build.PL it can't > find snap, though it is compiled and working properly. I can use ./Build > snap to compile Maker, then redirect it to my installed snap in the ctl > files, but that seems like a workaround and I don't know if something is > happening on the back end that this might be breaking. Is there a way to > point maker at my install during compile? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Fri Jan 18 10:09:52 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Fri, 18 Jan 2019 17:09:52 +0000 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> References: , <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> Message-ID: <96ea2ea82c744683b4757f1aa01c676f@unil.ch> Thanks Carson. I thought also to use only swissprot at the beginning but I am working with a non model organism and I am scared that swissprot is not enough complete to capture all the gene prediction. but if I use nr and I select only gene with AED < 0.5, it should be good no ? or do you have an AED cut off to recommend ? Cheers. Patrick ________________________________ From: Carson Holt Sent: Thursday, January 17, 2019 10:31:17 PM To: Patrick Tran Van Cc: maker-devel at yandell-lab.org Subject: Re: Maker crash with big protein evidence ? You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). ?Carson On Jan 15, 2019, at 2:54 AM, Patrick Tran Van > wrote: Hi, I run maker with mpi and default option. It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : in cluster::shadow_cluster... sorting hits in shadow cluster... j_size:3 current j:0 j_size:3 current j:1 j_size:3 current j:2 ...finished clustering. Did you already face something similar ? Thanks. Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From scott at scottcain.net Wed Jan 23 11:25:07 2019 From: scott at scottcain.net (Scott Cain) Date: Wed, 23 Jan 2019 10:25:07 -0800 Subject: [maker-devel] Fwd: [GSoC 2019] [Open Genome Informatics] Google Summer of Code 2019 Participation In-Reply-To: References: Message-ID: ---------- Forwarded message --------- From: Robin Haw Date: Wed, Jan 23, 2019 at 10:20 AM Subject: [GSoC 2019] [Open Genome Informatics] Google Summer of Code 2019 Participation To: gmod-devel at lists.sourceforge.net Cc: Dannon Baker , Dave Clements < clements at galaxyproject.org>, Marc Gillespie , Scott Cain Dear All, The Open Genome Informatics team serves as an ?umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC) . Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others. Call for 2019 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year?s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here or this online form . For more information please refer to the Open Genome Informatics page . The mentoring organization application deadline with GSoC is February 6th, 2019 at 3 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions please let us know. Thanks, Robin, Marc, Dave, Dannon, and Scott. -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jan 24 08:36:24 2019 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 24 Jan 2019 15:36:24 +0000 Subject: [maker-devel] BioPerl and MAKER Message-ID: Hi Carson, I?ll be working over the next several months to push out a new stripped-down version of BioPerl (along with the help of Carne Draug) with the hopeful target goal of a CPAN release in April-May. I know MAKER still relies on a few BioPerl core modules, such as those related to codon tables, FASTA indexing, etc. Just from a quick grep through the latest release (2.31.10) I found the ones at the bottom of the email; I know the various Phat* modules are MAKER-specific, but can you think of any others that might be required? (I haven?t checked the 3.0 beta version yet) Thanks chris Bio::DB::Fasta Bio::DB::GFF Bio::FeatureIO::gff Bio::Search::HSP::GenericHSP Bio::Search::HSP::HSPFactory Bio::Search::HSP::PhatHSP::Base Bio::Search::HSP::PhatHSP::augustus Bio::Search::HSP::PhatHSP::blastn Bio::Search::HSP::PhatHSP::blastx Bio::Search::HSP::PhatHSP::cdna2genome Bio::Search::HSP::PhatHSP::est2genome Bio::Search::HSP::PhatHSP::fgenesh Bio::Search::HSP::PhatHSP::genemark Bio::Search::HSP::PhatHSP::gff3 Bio::Search::HSP::PhatHSP::protein2genome Bio::Search::HSP::PhatHSP::repeatmasker Bio::Search::HSP::PhatHSP::snap Bio::Search::HSP::PhatHSP::snoscan Bio::Search::HSP::PhatHSP::tblastx Bio::Search::HSP::PhatHSP::trnascan Bio::Search::Hit::GenericHit Bio::Search::Hit::HitFactory Bio::Search::Hit::PhatHit::Base Bio::Search::Hit::PhatHit::augustus Bio::Search::Hit::PhatHit::blastn Bio::Search::Hit::PhatHit::blastx Bio::Search::Hit::PhatHit::cdna2genome Bio::Search::Hit::PhatHit::est2genome Bio::Search::Hit::PhatHit::fgenesh Bio::Search::Hit::PhatHit::genemark Bio::Search::Hit::PhatHit::gff3 Bio::Search::Hit::PhatHit::protein2genome Bio::Search::Hit::PhatHit::repeatmasker Bio::Search::Hit::PhatHit::snap Bio::Search::Hit::PhatHit::snoscan Bio::Search::Hit::PhatHit::tblastx Bio::Search::Hit::PhatHit::trnascan Bio::Search::Result::ResultFactory Bio::SearchIO Bio::SeqIO Bio::Tools::CodonTable Bio::Tools::GFF -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Jan 25 16:06:22 2019 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 25 Jan 2019 16:06:22 -0700 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: <96ea2ea82c744683b4757f1aa01c676f@unil.ch> References: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> <96ea2ea82c744683b4757f1aa01c676f@unil.ch> Message-ID: <12D0A479-5FA3-43CA-B04F-5226258AC8E1@gmail.com> NR will likly create problems on more genes than it will help recover in comparison to swiss-prot. The AED cutoff can be a convenient way to remove models when you expect too much or poor quality evidence (but it?s more of a sledgehammer than a scalpel). So using NR to get better sensitivity and then using AED to reduce sensitivity will likely just make all models worse in general while not adding many missed models. ?Carson > On Jan 18, 2019, at 10:09 AM, Patrick Tran Van wrote: > > Thanks Carson. > I thought also to use only swissprot at the beginning but I am working with a non model organism and I am scared that swissprot is not enough complete to capture all the gene prediction. > > but if I use nr and I select only gene with AED < 0.5, it should be good no ? or do you have an AED cut off to recommend ? > > Cheers. > > Patrick > From: Carson Holt > > Sent: Thursday, January 17, 2019 10:31:17 PM > To: Patrick Tran Van > Cc: maker-devel at yandell-lab.org > Subject: Re: Maker crash with big protein evidence ? > > You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). > > ?Carson > > >> On Jan 15, 2019, at 2:54 AM, Patrick Tran Van > wrote: >> >> Hi, >> >> I run maker with mpi and default option. >> It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : >> >> in cluster::shadow_cluster... >> sorting hits in shadow cluster... >> j_size:3 current j:0 >> j_size:3 current j:1 >> j_size:3 current j:2 >> ...finished clustering. >> >> Did you already face something similar ? >> >> Thanks. >> >> Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From munholl at uwindsor.ca Fri Jan 11 11:11:40 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Fri, 11 Jan 2019 13:11:40 -0500 Subject: [maker-devel] Maker can't find snap Message-ID: Hello, I'm installing a new instance of maker and when I run Build.PL it can't find snap, though it is compiled and working properly. I can use ./Build snap to compile Maker, then redirect it to my installed snap in the ctl files, but that seems like a workaround and I don't know if something is happening on the back end that this might be breaking. Is there a way to point maker at my install during compile? Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Tue Jan 15 02:54:42 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Tue, 15 Jan 2019 09:54:42 +0000 Subject: [maker-devel] Maker crash with big protein evidence ? Message-ID: Hi, I run maker with mpi and default option. It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : in cluster::shadow_cluster... sorting hits in shadow cluster... j_size:3 current j:0 j_size:3 current j:1 j_size:3 current j:2 ...finished clustering. Did you already face something similar ? Thanks. Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From munholl at uwindsor.ca Wed Jan 16 09:43:48 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Wed, 16 Jan 2019 11:43:48 -0500 Subject: [maker-devel] tRNAscan-SE file already exists Message-ID: Hi Everyone, Just getting my latest Maker install running and I'm running into the following issue when it gets to tRNAscan-SE: running trnascan. #--------- command -------------# Widget::trnascan: /usr/local/bin/tRNAscan-SE -b -q /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_no mask.0 > /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_nomask.0.eukaryotic.trnasc an #-------------------------------# WARNING: -q exists already. (O)verwrite file, (A)ppend to file, or (Q)uit program? I have tRNAscan-SE-2.0 installed, which has a -b option for a bed output but needs a file to be specified. Do I need to roll back to a specific version or would it be easier to skip it and run tRNAscan-SE separately? Do the outputs get integrated later to adjsut Maker calls or are they stand alone? Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 14:27:36 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:27:36 -0700 Subject: [maker-devel] tRNAscan-SE file already exists In-Reply-To: References: Message-ID: <53237E1D-00BE-4AB5-A87A-2EBE359A11B4@gmail.com> You will need to downgrade. I know 1.3.1 works. I will have to update MAKER for the new tRNAscan. ?Carson > On Jan 16, 2019, at 9:43 AM, Seth Munholland wrote: > > Hi Everyone, > > Just getting my latest Maker install running and I'm running into the following issue when it gets to tRNAscan-SE: > > running trnascan. > #--------- command -------------# > Widget::trnascan: > /usr/local/bin/tRNAscan-SE -b -q /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_no > mask.0 > /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_nomask.0.eukaryotic.trnasc > an > #-------------------------------# > > WARNING: -q exists already. > > (O)verwrite file, (A)ppend to file, or (Q)uit program? > > I have tRNAscan-SE-2.0 installed, which has a -b option for a bed output but needs a file to be specified. Do I need to roll back to a specific version or would it be easier to skip it and run tRNAscan-SE separately? Do the outputs get integrated later to adjsut Maker calls or are they stand alone? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 <>_______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 14:31:17 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:31:17 -0700 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: References: Message-ID: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). ?Carson > On Jan 15, 2019, at 2:54 AM, Patrick Tran Van wrote: > > Hi, > > I run maker with mpi and default option. > It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : > > in cluster::shadow_cluster... > sorting hits in shadow cluster... > j_size:3 current j:0 > j_size:3 current j:1 > j_size:3 current j:2 > ...finished clustering. > > Did you already face something similar ? > > Thanks. > > Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 14:33:40 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:33:40 -0700 Subject: [maker-devel] Maker can't find snap In-Reply-To: References: Message-ID: If you are using ?sudo? to do the install you may be reseting the PATH environmental variable. Or snap was never in your PATH. The Build script searches the PATH to find the snap executable. Type ?which snap? on the command line to test. ?Carson > On Jan 11, 2019, at 11:11 AM, Seth Munholland wrote: > > Hello, > > I'm installing a new instance of maker and when I run Build.PL it can't find snap, though it is compiled and working properly. I can use ./Build snap to compile Maker, then redirect it to my installed snap in the ctl files, but that seems like a workaround and I don't know if something is happening on the back end that this might be breaking. Is there a way to point maker at my install during compile? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 <>_______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From munholl at uwindsor.ca Thu Jan 17 14:32:03 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Thu, 17 Jan 2019 16:32:03 -0500 Subject: [maker-devel] Maker can't find snap In-Reply-To: References: Message-ID: I was sudo installing. I'll update PATH. Thanks! Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 On Thu, Jan 17, 2019 at 4:33 PM Carson Holt wrote: > If you are using ?sudo? to do the install you may be reseting the PATH > environmental variable. Or snap was never in your PATH. The Build script > searches the PATH to find the snap executable. Type ?which snap? on the > command line to test. > > ?Carson > > > On Jan 11, 2019, at 11:11 AM, Seth Munholland wrote: > > Hello, > > I'm installing a new instance of maker and when I run Build.PL it can't > find snap, though it is compiled and working properly. I can use ./Build > snap to compile Maker, then redirect it to my installed snap in the ctl > files, but that seems like a workaround and I don't know if something is > happening on the back end that this might be breaking. Is there a way to > point maker at my install during compile? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Fri Jan 18 10:09:52 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Fri, 18 Jan 2019 17:09:52 +0000 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> References: , <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> Message-ID: <96ea2ea82c744683b4757f1aa01c676f@unil.ch> Thanks Carson. I thought also to use only swissprot at the beginning but I am working with a non model organism and I am scared that swissprot is not enough complete to capture all the gene prediction. but if I use nr and I select only gene with AED < 0.5, it should be good no ? or do you have an AED cut off to recommend ? Cheers. Patrick ________________________________ From: Carson Holt Sent: Thursday, January 17, 2019 10:31:17 PM To: Patrick Tran Van Cc: maker-devel at yandell-lab.org Subject: Re: Maker crash with big protein evidence ? You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). ?Carson On Jan 15, 2019, at 2:54 AM, Patrick Tran Van > wrote: Hi, I run maker with mpi and default option. It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : in cluster::shadow_cluster... sorting hits in shadow cluster... j_size:3 current j:0 j_size:3 current j:1 j_size:3 current j:2 ...finished clustering. Did you already face something similar ? Thanks. Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From scott at scottcain.net Wed Jan 23 11:25:07 2019 From: scott at scottcain.net (Scott Cain) Date: Wed, 23 Jan 2019 10:25:07 -0800 Subject: [maker-devel] Fwd: [GSoC 2019] [Open Genome Informatics] Google Summer of Code 2019 Participation In-Reply-To: References: Message-ID: ---------- Forwarded message --------- From: Robin Haw Date: Wed, Jan 23, 2019 at 10:20 AM Subject: [GSoC 2019] [Open Genome Informatics] Google Summer of Code 2019 Participation To: gmod-devel at lists.sourceforge.net Cc: Dannon Baker , Dave Clements < clements at galaxyproject.org>, Marc Gillespie , Scott Cain Dear All, The Open Genome Informatics team serves as an ?umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC) . Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others. Call for 2019 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year?s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here or this online form . For more information please refer to the Open Genome Informatics page . The mentoring organization application deadline with GSoC is February 6th, 2019 at 3 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions please let us know. Thanks, Robin, Marc, Dave, Dannon, and Scott. -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jan 24 08:36:24 2019 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 24 Jan 2019 15:36:24 +0000 Subject: [maker-devel] BioPerl and MAKER Message-ID: Hi Carson, I?ll be working over the next several months to push out a new stripped-down version of BioPerl (along with the help of Carne Draug) with the hopeful target goal of a CPAN release in April-May. I know MAKER still relies on a few BioPerl core modules, such as those related to codon tables, FASTA indexing, etc. Just from a quick grep through the latest release (2.31.10) I found the ones at the bottom of the email; I know the various Phat* modules are MAKER-specific, but can you think of any others that might be required? (I haven?t checked the 3.0 beta version yet) Thanks chris Bio::DB::Fasta Bio::DB::GFF Bio::FeatureIO::gff Bio::Search::HSP::GenericHSP Bio::Search::HSP::HSPFactory Bio::Search::HSP::PhatHSP::Base Bio::Search::HSP::PhatHSP::augustus Bio::Search::HSP::PhatHSP::blastn Bio::Search::HSP::PhatHSP::blastx Bio::Search::HSP::PhatHSP::cdna2genome Bio::Search::HSP::PhatHSP::est2genome Bio::Search::HSP::PhatHSP::fgenesh Bio::Search::HSP::PhatHSP::genemark Bio::Search::HSP::PhatHSP::gff3 Bio::Search::HSP::PhatHSP::protein2genome Bio::Search::HSP::PhatHSP::repeatmasker Bio::Search::HSP::PhatHSP::snap Bio::Search::HSP::PhatHSP::snoscan Bio::Search::HSP::PhatHSP::tblastx Bio::Search::HSP::PhatHSP::trnascan Bio::Search::Hit::GenericHit Bio::Search::Hit::HitFactory Bio::Search::Hit::PhatHit::Base Bio::Search::Hit::PhatHit::augustus Bio::Search::Hit::PhatHit::blastn Bio::Search::Hit::PhatHit::blastx Bio::Search::Hit::PhatHit::cdna2genome Bio::Search::Hit::PhatHit::est2genome Bio::Search::Hit::PhatHit::fgenesh Bio::Search::Hit::PhatHit::genemark Bio::Search::Hit::PhatHit::gff3 Bio::Search::Hit::PhatHit::protein2genome Bio::Search::Hit::PhatHit::repeatmasker Bio::Search::Hit::PhatHit::snap Bio::Search::Hit::PhatHit::snoscan Bio::Search::Hit::PhatHit::tblastx Bio::Search::Hit::PhatHit::trnascan Bio::Search::Result::ResultFactory Bio::SearchIO Bio::SeqIO Bio::Tools::CodonTable Bio::Tools::GFF -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Jan 25 16:06:22 2019 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 25 Jan 2019 16:06:22 -0700 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: <96ea2ea82c744683b4757f1aa01c676f@unil.ch> References: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> <96ea2ea82c744683b4757f1aa01c676f@unil.ch> Message-ID: <12D0A479-5FA3-43CA-B04F-5226258AC8E1@gmail.com> NR will likly create problems on more genes than it will help recover in comparison to swiss-prot. The AED cutoff can be a convenient way to remove models when you expect too much or poor quality evidence (but it?s more of a sledgehammer than a scalpel). So using NR to get better sensitivity and then using AED to reduce sensitivity will likely just make all models worse in general while not adding many missed models. ?Carson > On Jan 18, 2019, at 10:09 AM, Patrick Tran Van wrote: > > Thanks Carson. > I thought also to use only swissprot at the beginning but I am working with a non model organism and I am scared that swissprot is not enough complete to capture all the gene prediction. > > but if I use nr and I select only gene with AED < 0.5, it should be good no ? or do you have an AED cut off to recommend ? > > Cheers. > > Patrick > From: Carson Holt > > Sent: Thursday, January 17, 2019 10:31:17 PM > To: Patrick Tran Van > Cc: maker-devel at yandell-lab.org > Subject: Re: Maker crash with big protein evidence ? > > You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). > > ?Carson > > >> On Jan 15, 2019, at 2:54 AM, Patrick Tran Van > wrote: >> >> Hi, >> >> I run maker with mpi and default option. >> It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : >> >> in cluster::shadow_cluster... >> sorting hits in shadow cluster... >> j_size:3 current j:0 >> j_size:3 current j:1 >> j_size:3 current j:2 >> ...finished clustering. >> >> Did you already face something similar ? >> >> Thanks. >> >> Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From munholl at uwindsor.ca Fri Jan 11 11:11:40 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Fri, 11 Jan 2019 13:11:40 -0500 Subject: [maker-devel] Maker can't find snap Message-ID: Hello, I'm installing a new instance of maker and when I run Build.PL it can't find snap, though it is compiled and working properly. I can use ./Build snap to compile Maker, then redirect it to my installed snap in the ctl files, but that seems like a workaround and I don't know if something is happening on the back end that this might be breaking. Is there a way to point maker at my install during compile? Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Tue Jan 15 02:54:42 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Tue, 15 Jan 2019 09:54:42 +0000 Subject: [maker-devel] Maker crash with big protein evidence ? Message-ID: Hi, I run maker with mpi and default option. It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : in cluster::shadow_cluster... sorting hits in shadow cluster... j_size:3 current j:0 j_size:3 current j:1 j_size:3 current j:2 ...finished clustering. Did you already face something similar ? Thanks. Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From munholl at uwindsor.ca Wed Jan 16 09:43:48 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Wed, 16 Jan 2019 11:43:48 -0500 Subject: [maker-devel] tRNAscan-SE file already exists Message-ID: Hi Everyone, Just getting my latest Maker install running and I'm running into the following issue when it gets to tRNAscan-SE: running trnascan. #--------- command -------------# Widget::trnascan: /usr/local/bin/tRNAscan-SE -b -q /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_no mask.0 > /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_nomask.0.eukaryotic.trnasc an #-------------------------------# WARNING: -q exists already. (O)verwrite file, (A)ppend to file, or (Q)uit program? I have tRNAscan-SE-2.0 installed, which has a -b option for a bed output but needs a file to be specified. Do I need to roll back to a specific version or would it be easier to skip it and run tRNAscan-SE separately? Do the outputs get integrated later to adjsut Maker calls or are they stand alone? Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 14:27:36 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:27:36 -0700 Subject: [maker-devel] tRNAscan-SE file already exists In-Reply-To: References: Message-ID: <53237E1D-00BE-4AB5-A87A-2EBE359A11B4@gmail.com> You will need to downgrade. I know 1.3.1 works. I will have to update MAKER for the new tRNAscan. ?Carson > On Jan 16, 2019, at 9:43 AM, Seth Munholland wrote: > > Hi Everyone, > > Just getting my latest Maker install running and I'm running into the following issue when it gets to tRNAscan-SE: > > running trnascan. > #--------- command -------------# > Widget::trnascan: > /usr/local/bin/tRNAscan-SE -b -q /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_no > mask.0 > /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_nomask.0.eukaryotic.trnasc > an > #-------------------------------# > > WARNING: -q exists already. > > (O)verwrite file, (A)ppend to file, or (Q)uit program? > > I have tRNAscan-SE-2.0 installed, which has a -b option for a bed output but needs a file to be specified. Do I need to roll back to a specific version or would it be easier to skip it and run tRNAscan-SE separately? Do the outputs get integrated later to adjsut Maker calls or are they stand alone? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 <>_______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 14:31:17 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:31:17 -0700 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: References: Message-ID: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). ?Carson > On Jan 15, 2019, at 2:54 AM, Patrick Tran Van wrote: > > Hi, > > I run maker with mpi and default option. > It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : > > in cluster::shadow_cluster... > sorting hits in shadow cluster... > j_size:3 current j:0 > j_size:3 current j:1 > j_size:3 current j:2 > ...finished clustering. > > Did you already face something similar ? > > Thanks. > > Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jan 17 14:33:40 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 17 Jan 2019 14:33:40 -0700 Subject: [maker-devel] Maker can't find snap In-Reply-To: References: Message-ID: If you are using ?sudo? to do the install you may be reseting the PATH environmental variable. Or snap was never in your PATH. The Build script searches the PATH to find the snap executable. Type ?which snap? on the command line to test. ?Carson > On Jan 11, 2019, at 11:11 AM, Seth Munholland wrote: > > Hello, > > I'm installing a new instance of maker and when I run Build.PL it can't find snap, though it is compiled and working properly. I can use ./Build snap to compile Maker, then redirect it to my installed snap in the ctl files, but that seems like a workaround and I don't know if something is happening on the back end that this might be breaking. Is there a way to point maker at my install during compile? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 <>_______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From munholl at uwindsor.ca Thu Jan 17 14:32:03 2019 From: munholl at uwindsor.ca (Seth Munholland) Date: Thu, 17 Jan 2019 16:32:03 -0500 Subject: [maker-devel] Maker can't find snap In-Reply-To: References: Message-ID: I was sudo installing. I'll update PATH. Thanks! Seth Munholland, Ph.D. Candidate Intern, International Society for Computational Biology VP, Finance & Extracurricular Affairs, DBGSA Department of Biological Sciences Rm. 306 Biology Building University of Windsor 401 Sunset Ave. N9B 3P4 T: (519) 253-3000 Ext: 4755 On Thu, Jan 17, 2019 at 4:33 PM Carson Holt wrote: > If you are using ?sudo? to do the install you may be reseting the PATH > environmental variable. Or snap was never in your PATH. The Build script > searches the PATH to find the snap executable. Type ?which snap? on the > command line to test. > > ?Carson > > > On Jan 11, 2019, at 11:11 AM, Seth Munholland wrote: > > Hello, > > I'm installing a new instance of maker and when I run Build.PL it can't > find snap, though it is compiled and working properly. I can use ./Build > snap to compile Maker, then redirect it to my installed snap in the ctl > files, but that seems like a workaround and I don't know if something is > happening on the back end that this might be breaking. Is there a way to > point maker at my install during compile? > > Seth Munholland, Ph.D. Candidate > Intern, International Society for Computational Biology > VP, Finance & Extracurricular Affairs, DBGSA > Department of Biological Sciences > Rm. 306 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Fri Jan 18 10:09:52 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Fri, 18 Jan 2019 17:09:52 +0000 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> References: , <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> Message-ID: <96ea2ea82c744683b4757f1aa01c676f@unil.ch> Thanks Carson. I thought also to use only swissprot at the beginning but I am working with a non model organism and I am scared that swissprot is not enough complete to capture all the gene prediction. but if I use nr and I select only gene with AED < 0.5, it should be good no ? or do you have an AED cut off to recommend ? Cheers. Patrick ________________________________ From: Carson Holt Sent: Thursday, January 17, 2019 10:31:17 PM To: Patrick Tran Van Cc: maker-devel at yandell-lab.org Subject: Re: Maker crash with big protein evidence ? You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). ?Carson On Jan 15, 2019, at 2:54 AM, Patrick Tran Van > wrote: Hi, I run maker with mpi and default option. It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : in cluster::shadow_cluster... sorting hits in shadow cluster... j_size:3 current j:0 j_size:3 current j:1 j_size:3 current j:2 ...finished clustering. Did you already face something similar ? Thanks. Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From scott at scottcain.net Wed Jan 23 11:25:07 2019 From: scott at scottcain.net (Scott Cain) Date: Wed, 23 Jan 2019 10:25:07 -0800 Subject: [maker-devel] Fwd: [GSoC 2019] [Open Genome Informatics] Google Summer of Code 2019 Participation In-Reply-To: References: Message-ID: ---------- Forwarded message --------- From: Robin Haw Date: Wed, Jan 23, 2019 at 10:20 AM Subject: [GSoC 2019] [Open Genome Informatics] Google Summer of Code 2019 Participation To: gmod-devel at lists.sourceforge.net Cc: Dannon Baker , Dave Clements < clements at galaxyproject.org>, Marc Gillespie , Scott Cain Dear All, The Open Genome Informatics team serves as an ?umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC) . Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others. Call for 2019 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year?s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here or this online form . For more information please refer to the Open Genome Informatics page . The mentoring organization application deadline with GSoC is February 6th, 2019 at 3 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions please let us know. Thanks, Robin, Marc, Dave, Dannon, and Scott. -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jan 24 08:36:24 2019 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 24 Jan 2019 15:36:24 +0000 Subject: [maker-devel] BioPerl and MAKER Message-ID: Hi Carson, I?ll be working over the next several months to push out a new stripped-down version of BioPerl (along with the help of Carne Draug) with the hopeful target goal of a CPAN release in April-May. I know MAKER still relies on a few BioPerl core modules, such as those related to codon tables, FASTA indexing, etc. Just from a quick grep through the latest release (2.31.10) I found the ones at the bottom of the email; I know the various Phat* modules are MAKER-specific, but can you think of any others that might be required? (I haven?t checked the 3.0 beta version yet) Thanks chris Bio::DB::Fasta Bio::DB::GFF Bio::FeatureIO::gff Bio::Search::HSP::GenericHSP Bio::Search::HSP::HSPFactory Bio::Search::HSP::PhatHSP::Base Bio::Search::HSP::PhatHSP::augustus Bio::Search::HSP::PhatHSP::blastn Bio::Search::HSP::PhatHSP::blastx Bio::Search::HSP::PhatHSP::cdna2genome Bio::Search::HSP::PhatHSP::est2genome Bio::Search::HSP::PhatHSP::fgenesh Bio::Search::HSP::PhatHSP::genemark Bio::Search::HSP::PhatHSP::gff3 Bio::Search::HSP::PhatHSP::protein2genome Bio::Search::HSP::PhatHSP::repeatmasker Bio::Search::HSP::PhatHSP::snap Bio::Search::HSP::PhatHSP::snoscan Bio::Search::HSP::PhatHSP::tblastx Bio::Search::HSP::PhatHSP::trnascan Bio::Search::Hit::GenericHit Bio::Search::Hit::HitFactory Bio::Search::Hit::PhatHit::Base Bio::Search::Hit::PhatHit::augustus Bio::Search::Hit::PhatHit::blastn Bio::Search::Hit::PhatHit::blastx Bio::Search::Hit::PhatHit::cdna2genome Bio::Search::Hit::PhatHit::est2genome Bio::Search::Hit::PhatHit::fgenesh Bio::Search::Hit::PhatHit::genemark Bio::Search::Hit::PhatHit::gff3 Bio::Search::Hit::PhatHit::protein2genome Bio::Search::Hit::PhatHit::repeatmasker Bio::Search::Hit::PhatHit::snap Bio::Search::Hit::PhatHit::snoscan Bio::Search::Hit::PhatHit::tblastx Bio::Search::Hit::PhatHit::trnascan Bio::Search::Result::ResultFactory Bio::SearchIO Bio::SeqIO Bio::Tools::CodonTable Bio::Tools::GFF -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Jan 25 16:06:22 2019 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 25 Jan 2019 16:06:22 -0700 Subject: [maker-devel] Maker crash with big protein evidence ? In-Reply-To: <96ea2ea82c744683b4757f1aa01c676f@unil.ch> References: <6CE6D674-5A9A-4433-B29F-BF6F6E7FABD8@gmail.com> <96ea2ea82c744683b4757f1aa01c676f@unil.ch> Message-ID: <12D0A479-5FA3-43CA-B04F-5226258AC8E1@gmail.com> NR will likly create problems on more genes than it will help recover in comparison to swiss-prot. The AED cutoff can be a convenient way to remove models when you expect too much or poor quality evidence (but it?s more of a sledgehammer than a scalpel). So using NR to get better sensitivity and then using AED to reduce sensitivity will likely just make all models worse in general while not adding many missed models. ?Carson > On Jan 18, 2019, at 10:09 AM, Patrick Tran Van wrote: > > Thanks Carson. > I thought also to use only swissprot at the beginning but I am working with a non model organism and I am scared that swissprot is not enough complete to capture all the gene prediction. > > but if I use nr and I select only gene with AED < 0.5, it should be good no ? or do you have an AED cut off to recommend ? > > Cheers. > > Patrick > From: Carson Holt > > Sent: Thursday, January 17, 2019 10:31:17 PM > To: Patrick Tran Van > Cc: maker-devel at yandell-lab.org > Subject: Re: Maker crash with big protein evidence ? > > You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It?s not curated to the extent swiss-prot is, so you will get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out). > > ?Carson > > >> On Jan 15, 2019, at 2:54 AM, Patrick Tran Van > wrote: >> >> Hi, >> >> I run maker with mpi and default option. >> It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this : >> >> in cluster::shadow_cluster... >> sorting hits in shadow cluster... >> j_size:3 current j:0 >> j_size:3 current j:1 >> j_size:3 current j:2 >> ...finished clustering. >> >> Did you already face something similar ? >> >> Thanks. >> >> Patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: