From Cedric.Cabau at inra.fr Fri Sep 6 08:48:25 2019 From: Cedric.Cabau at inra.fr (=?UTF-8?Q?C=c3=a9dric_Cabau?=) Date: Fri, 6 Sep 2019 15:48:25 +0200 Subject: [maker-devel] Trouble with EVM and evidence from external GFF3 Message-ID: Hi, I use Maker 3.01.02-beta in mpi mode to merge data from gene models and cdna/protein evidence. I run Maker with entries est_gff, protein_gff and pred_gff in run_evm=1, est2genome=0 and protein2genome=0 mode. Being surprised by the amount of RAM required for some EVM jobs, I wanted to reproduce the execution of EVM commands outside of Maker. I commented the line 1819 inside maker/lib/GI.pm to keep the EVM command input files inside my temporary directory. By doing this, I noticed that the *.protein_for_evm.gff files generated for each chunk were systematically empty (only the gff3 header is written in the file) unlike the *.ests_for_evm.gff and *.preds_for_evm_gene.gff files. The formatting of my protein_gff input file does not seem to cause this because I find protein evidence in my output file *.all.maker.gff. Evidence files are therefore well taken into account by Maker but the protein evidence does not seem to have been passed on to EVM. Have you ever notice this before? Is this due to a misuse of Maker of my own? Thank you in advance for your answer. est_gff file 1??? Cufflinks??? match??? 6706??? 11762??? 3194.685322??? - .??? ID=1:CUFF.4.1;Name=1:CUFF.4.1; 1??? Cufflinks??? match_part??? 6706??? 6760??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-1;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 1 55 +; 1??? Cufflinks??? match_part??? 6892??? 6955??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-2;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 56 119 +; 1??? Cufflinks??? match_part??? 9558??? 9694??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-3;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 120 256 +; 1??? Cufflinks??? match_part??? 10081??? 10191??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-4;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 257 367 +; 1??? Cufflinks??? match_part??? 11550??? 11625??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-5;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 368 443 +; 1??? Cufflinks??? match_part??? 11751??? 11762??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-6;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 444 455 +; protein_gff file 5??? exonerate??? protein_match??? 8111679??? 8145811??? . -??? .??? ID=5:1;Target=ENSAMXP00000000017.1 5??? exonerate??? match??? 8111679??? 8111886??? 83.57??? - .??? ID=5:1:exon-1;Parent=5:1;Target=ENSAMXP00000000017.1 1 69 5??? exonerate??? match??? 8120294??? 8120428??? 83.57??? - .??? ID=5:1:exon-2;Parent=5:1;Target=ENSAMXP00000000017.1 70 84 5??? exonerate??? match??? 8125321??? 8125515??? 83.57??? - .??? ID=5:1:exon-3;Parent=5:1;Target=ENSAMXP00000000017.1 84 174 5??? exonerate??? match??? 8128007??? 8128240??? 83.57??? - .??? ID=5:1:exon-4;Parent=5:1;Target=ENSAMXP00000000017.1 175 252 5??? exonerate??? match??? 8138856??? 8139127??? 83.57??? - .??? ID=5:1:exon-5;Parent=5:1;Target=ENSAMXP00000000017.1 253 317 maker_evm.log #-----Transcript weights evmtrans=10 #default weight for source unspecified est/alt_est alignments evmtrans:blastn=0 #weight for blastn sourced alignments evmtrans:est2genome=10 #weight for est2genome sourced alignments evmtrans:tblastx=0 #weight for tblastx sourced alignments evmtrans:cdna2genome=7 #weight for cdna2genome sourced alignments evmtrans:est_gff:cufflinks=30 #weight for est_gff:cufflinks sourced alignments #-----Protein weights evmprot=10 #default weight for source unspecified protein alignments evmprot:blastx=2 #weight for blastx sourced alignments evmprot:protein2genome=15 #weight for protein2genome sourced alignments evmprot:protein_gff:exonerate=15 #weight for protein_gff:exonerate sourced alignments #-----Abinitio Prediction weights evmab=10 #default weight for source unspecified ab initio predictions evmab:snap=10 #weight for snap sourced predictions evmab:augustus=10 #weight for augustus sourced predictions evmab:fgenesh=10 #weight for fgenesh sourced predictions evmab:genemark=7 #weight for genemark sourced predictions evmab:pred_gff:augustus=10 #weight for pred_gff:augustus sourced predictions -------------- next part -------------- An HTML attachment was scrubbed... URL: From qlian003 at ucr.edu Fri Sep 27 17:45:31 2019 From: qlian003 at ucr.edu (Qihua Liang) Date: Fri, 27 Sep 2019 15:45:31 -0700 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins Message-ID: Dear Maker Dev Team: I am using Maker for gene annotations and I separate different tracks in the GFF to visualize a genomic region in a genome browser. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? I also examine another genomic region where Augustus and SNAP predict a gene; there is no EST hit, but one protein hit. At this case, Maker does not annotate a gene at this region. Is it because a protein hit is not enough for annotating a region and it always requires EST hit? Thanks Qihua From qlian003 at ucr.edu Mon Sep 23 12:00:55 2019 From: qlian003 at ucr.edu (Qihua Liang) Date: Mon, 23 Sep 2019 11:00:55 -0700 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins Message-ID: Dear Maker Dev Team: I am using Maker for gene annotations and I separate different tracks in the GFF to visualize in a genome browser. As in the attached picture, there is a very long Maker gene ?maker-chr9-augustus-gene-102.77?. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? Thanks Qihua -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PastedGraphic-1.png Type: image/png Size: 220052 bytes Desc: not available URL: From katherine.balasingham at mail.utoronto.ca Sat Sep 28 16:08:04 2019 From: katherine.balasingham at mail.utoronto.ca (Katherine Balasingham) Date: Sat, 28 Sep 2019 22:08:04 +0000 Subject: [maker-devel] Maker installation fails for MacOSX Message-ID: Hello! I hope I am contacting the correct email - I have been trying to install Maker for a few days now on my Mac OSX version 10.14 Mojave. It fails at the first few steps where it cannot install RepeatMasker, SNAP, or Exonerate. I have even tried to install these programs manually but Maker continues to fail to detect these packages or fails to install them properly. I did try using ./build package-name as well but to no avail. I ran ./Build installexes and ./Build installdeps but they constantly fail for those three programs only and I cannot find a solution online. Could you provide me with the proper code to manually install these three programs so I can use Maker? I have checked online sources for these programs but then I run into the issue where configuring Maker does not seem to find these three programs if I install it separately, so I am stuck at this step. Sorry for the long email I wanted to be explicit as I could be! The error message I always get is: ERROR: Failed installing RepeatMasker, now cleaning installation path... You may need to install RepeatMasker manually. Checking external program dependencies... requires: ! Exonerate is not installed ! SNAP is not installed ! RepeatMasker is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the programs indicated above before proceeding with this installation. Run 'Build installexes' to install missing prerequisites. Sincerely, Katherine Balasingham PS: I have never installed these programs before at all so I do not have older versions interfering with Maker. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eennadi at gmail.com Sun Sep 29 17:51:53 2019 From: eennadi at gmail.com (Emmanuel Nnadi) Date: Mon, 30 Sep 2019 00:51:53 +0100 Subject: [maker-devel] /perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck Message-ID: Hello I compiled Maker on a cluster using MPI, attempting to run maker i got this error. /home/emmanuel/miniconda3/bin/perl: symbol lookup error: /home/emmanuel/maker/bin/../perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck Can you help? Thanks Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:00:57 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:00:57 -0600 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins In-Reply-To: References: Message-ID: > I am using Maker for gene annotations and I separate different tracks in the GFF to visualize a genomic region in a genome browser. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? MAKER just provides hints to the gene predictors (i.e. and set or protein increases the probability that awn exon/intron should exist where indicated), the predictor then identifies if the hint is workable or not. You can manually curate where you thing incorrect evidence tipped the scales in favor of an incorrect models probability using Apollo. You can also try EVM post processing where you can specify different weights to give to specific evidence types. > I also examine another genomic region where Augustus and SNAP predict a gene; there is no EST hit, but one protein hit. At this case, Maker does not annotate a gene at this region. Is it because a protein hit is not enough for annotating a region and it always requires EST hit? The protein hit may not be in the same reading frame as the gene predictions (in which case it does not count as evidence support) or it may be too small a fraction of the original protein in which case it may be filtered out as a spurious low complexity alignment. ?Carson From carsonhh at gmail.com Mon Sep 30 11:04:54 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:04:54 -0600 Subject: [maker-devel] /perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck In-Reply-To: References: Message-ID: <33C71B74-9551-413F-959C-688523959743@gmail.com> ?symbol lookup error? means that you are running with a different version of perl than the one used to install a program. Sao you might have installed with /usr/bin/perl but are running with /home/emmanuel/miniconda3/bin/perl or vice versa. You can run /home/emmanuel/miniconda3/bin/cpan (if it exists there) and manually install Acme::Damn just for that perl installation. You may also need to reinstall MAKER for the version of perl you are using. ?Carson > On Sep 29, 2019, at 5:51 PM, Emmanuel Nnadi wrote: > > Hello > > I compiled Maker on a cluster using MPI, > attempting to run maker i got this error. > > > /home/emmanuel/miniconda3/bin/perl: symbol lookup error: /home/emmanuel/maker/bin/../perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck > > > Can you help? > > Thanks > > Nnadi Nnaemeka Emmanuel,Ph.D > Department of Microbiology, > Faculty of Natural and Applied Science, > Plateau State University, Bokkos, Plateau State, Nigeria. > +2348068124819 > Publications: > https://www.researchgate.net/profile/Emmanuel_Nnadi/publications _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:10:00 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:10:00 -0600 Subject: [maker-devel] Maker installation fails for MacOSX In-Reply-To: References: Message-ID: <4BF52BB3-BE2C-4697-AD1F-CA3F01BF70B6@gmail.com> The problem is OSX. It has gradually moved out of compatibility with other Linux distributions over the years. You will need to install developer tools like Xcode, and perhaps even try homebrew to try and get around certain differences in OSX behavior.. Homebrew ?> https://brew.sh Brewsci/bio (science packages) -> https://github.com/brewsci/homebrew-bio After that 'brew install maker? might work (cross your fingers). ?Carson > On Sep 28, 2019, at 4:08 PM, Katherine Balasingham wrote: > > Hello! > > I hope I am contacting the correct email - I have been trying to install Maker for a few days now on my Mac OSX version 10.14 Mojave. > > It fails at the first few steps where it cannot install RepeatMasker, SNAP, or Exonerate. I have even tried to install these programs manually but Maker continues to fail to detect these packages or fails to install them properly. I did try using ./build package-name as well but to no avail. I ran ./Build installexes and ./Build installdeps but they constantly fail for those three programs only and I cannot find a solution online. > > Could you provide me with the proper code to manually install these three programs so I can use Maker? I have checked online sources for these programs but then I run into the issue where configuring Maker does not seem to find these three programs if I install it separately, so I am stuck at this step. > > Sorry for the long email I wanted to be explicit as I could be! > > The error message I always get is: > > ERROR: Failed installing RepeatMasker, now cleaning installation path... > You may need to install RepeatMasker manually. > > Checking external program dependencies... > requires: > ! Exonerate is not installed > ! SNAP is not installed > ! RepeatMasker is not installed > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the programs > indicated above before proceeding with this installation. > Run 'Build installexes' to install missing prerequisites. > > > Sincerely, > > Katherine Balasingham > > PS: I have never installed these programs before at all so I do not have older versions interfering with Maker. > > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:16:16 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:16:16 -0600 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins In-Reply-To: References: Message-ID: <3B38F9B0-4AC6-4038-B397-763728F2B33F@gmail.com> Try looking at this in Apollo instead. You do not seem to get intron/exon/utr differentiation with this viewer, ?Carson > On Sep 23, 2019, at 12:00 PM, Qihua Liang wrote: > > Dear Maker Dev Team: > > I am using Maker for gene annotations and I separate different tracks in the GFF to visualize in a genome browser. As in the attached picture, there is a very long Maker gene ?maker-chr9-augustus-gene-102.77?. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? > > Thanks > Qihua > > > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org From Cedric.Cabau at inra.fr Fri Sep 6 07:48:25 2019 From: Cedric.Cabau at inra.fr (=?UTF-8?Q?C=c3=a9dric_Cabau?=) Date: Fri, 6 Sep 2019 15:48:25 +0200 Subject: [maker-devel] Trouble with EVM and evidence from external GFF3 Message-ID: Hi, I use Maker 3.01.02-beta in mpi mode to merge data from gene models and cdna/protein evidence. I run Maker with entries est_gff, protein_gff and pred_gff in run_evm=1, est2genome=0 and protein2genome=0 mode. Being surprised by the amount of RAM required for some EVM jobs, I wanted to reproduce the execution of EVM commands outside of Maker. I commented the line 1819 inside maker/lib/GI.pm to keep the EVM command input files inside my temporary directory. By doing this, I noticed that the *.protein_for_evm.gff files generated for each chunk were systematically empty (only the gff3 header is written in the file) unlike the *.ests_for_evm.gff and *.preds_for_evm_gene.gff files. The formatting of my protein_gff input file does not seem to cause this because I find protein evidence in my output file *.all.maker.gff. Evidence files are therefore well taken into account by Maker but the protein evidence does not seem to have been passed on to EVM. Have you ever notice this before? Is this due to a misuse of Maker of my own? Thank you in advance for your answer. est_gff file 1??? Cufflinks??? match??? 6706??? 11762??? 3194.685322??? - .??? ID=1:CUFF.4.1;Name=1:CUFF.4.1; 1??? Cufflinks??? match_part??? 6706??? 6760??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-1;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 1 55 +; 1??? Cufflinks??? match_part??? 6892??? 6955??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-2;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 56 119 +; 1??? Cufflinks??? match_part??? 9558??? 9694??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-3;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 120 256 +; 1??? Cufflinks??? match_part??? 10081??? 10191??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-4;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 257 367 +; 1??? Cufflinks??? match_part??? 11550??? 11625??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-5;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 368 443 +; 1??? Cufflinks??? match_part??? 11751??? 11762??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-6;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 444 455 +; protein_gff file 5??? exonerate??? protein_match??? 8111679??? 8145811??? . -??? .??? ID=5:1;Target=ENSAMXP00000000017.1 5??? exonerate??? match??? 8111679??? 8111886??? 83.57??? - .??? ID=5:1:exon-1;Parent=5:1;Target=ENSAMXP00000000017.1 1 69 5??? exonerate??? match??? 8120294??? 8120428??? 83.57??? - .??? ID=5:1:exon-2;Parent=5:1;Target=ENSAMXP00000000017.1 70 84 5??? exonerate??? match??? 8125321??? 8125515??? 83.57??? - .??? ID=5:1:exon-3;Parent=5:1;Target=ENSAMXP00000000017.1 84 174 5??? exonerate??? match??? 8128007??? 8128240??? 83.57??? - .??? ID=5:1:exon-4;Parent=5:1;Target=ENSAMXP00000000017.1 175 252 5??? exonerate??? match??? 8138856??? 8139127??? 83.57??? - .??? ID=5:1:exon-5;Parent=5:1;Target=ENSAMXP00000000017.1 253 317 maker_evm.log #-----Transcript weights evmtrans=10 #default weight for source unspecified est/alt_est alignments evmtrans:blastn=0 #weight for blastn sourced alignments evmtrans:est2genome=10 #weight for est2genome sourced alignments evmtrans:tblastx=0 #weight for tblastx sourced alignments evmtrans:cdna2genome=7 #weight for cdna2genome sourced alignments evmtrans:est_gff:cufflinks=30 #weight for est_gff:cufflinks sourced alignments #-----Protein weights evmprot=10 #default weight for source unspecified protein alignments evmprot:blastx=2 #weight for blastx sourced alignments evmprot:protein2genome=15 #weight for protein2genome sourced alignments evmprot:protein_gff:exonerate=15 #weight for protein_gff:exonerate sourced alignments #-----Abinitio Prediction weights evmab=10 #default weight for source unspecified ab initio predictions evmab:snap=10 #weight for snap sourced predictions evmab:augustus=10 #weight for augustus sourced predictions evmab:fgenesh=10 #weight for fgenesh sourced predictions evmab:genemark=7 #weight for genemark sourced predictions evmab:pred_gff:augustus=10 #weight for pred_gff:augustus sourced predictions -------------- next part -------------- An HTML attachment was scrubbed... URL: From qlian003 at ucr.edu Fri Sep 27 16:45:31 2019 From: qlian003 at ucr.edu (Qihua Liang) Date: Fri, 27 Sep 2019 15:45:31 -0700 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins Message-ID: Dear Maker Dev Team: I am using Maker for gene annotations and I separate different tracks in the GFF to visualize a genomic region in a genome browser. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? I also examine another genomic region where Augustus and SNAP predict a gene; there is no EST hit, but one protein hit. At this case, Maker does not annotate a gene at this region. Is it because a protein hit is not enough for annotating a region and it always requires EST hit? Thanks Qihua From qlian003 at ucr.edu Mon Sep 23 12:00:55 2019 From: qlian003 at ucr.edu (Qihua Liang) Date: Mon, 23 Sep 2019 11:00:55 -0700 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins Message-ID: Dear Maker Dev Team: I am using Maker for gene annotations and I separate different tracks in the GFF to visualize in a genome browser. As in the attached picture, there is a very long Maker gene ?maker-chr9-augustus-gene-102.77?. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? Thanks Qihua -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PastedGraphic-1.png Type: image/png Size: 220052 bytes Desc: not available URL: From katherine.balasingham at mail.utoronto.ca Sat Sep 28 16:08:04 2019 From: katherine.balasingham at mail.utoronto.ca (Katherine Balasingham) Date: Sat, 28 Sep 2019 22:08:04 +0000 Subject: [maker-devel] Maker installation fails for MacOSX Message-ID: Hello! I hope I am contacting the correct email - I have been trying to install Maker for a few days now on my Mac OSX version 10.14 Mojave. It fails at the first few steps where it cannot install RepeatMasker, SNAP, or Exonerate. I have even tried to install these programs manually but Maker continues to fail to detect these packages or fails to install them properly. I did try using ./build package-name as well but to no avail. I ran ./Build installexes and ./Build installdeps but they constantly fail for those three programs only and I cannot find a solution online. Could you provide me with the proper code to manually install these three programs so I can use Maker? I have checked online sources for these programs but then I run into the issue where configuring Maker does not seem to find these three programs if I install it separately, so I am stuck at this step. Sorry for the long email I wanted to be explicit as I could be! The error message I always get is: ERROR: Failed installing RepeatMasker, now cleaning installation path... You may need to install RepeatMasker manually. Checking external program dependencies... requires: ! Exonerate is not installed ! SNAP is not installed ! RepeatMasker is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the programs indicated above before proceeding with this installation. Run 'Build installexes' to install missing prerequisites. Sincerely, Katherine Balasingham PS: I have never installed these programs before at all so I do not have older versions interfering with Maker. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eennadi at gmail.com Sun Sep 29 17:51:53 2019 From: eennadi at gmail.com (Emmanuel Nnadi) Date: Mon, 30 Sep 2019 00:51:53 +0100 Subject: [maker-devel] /perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck Message-ID: Hello I compiled Maker on a cluster using MPI, attempting to run maker i got this error. /home/emmanuel/miniconda3/bin/perl: symbol lookup error: /home/emmanuel/maker/bin/../perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck Can you help? Thanks Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:00:57 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:00:57 -0600 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins In-Reply-To: References: Message-ID: > I am using Maker for gene annotations and I separate different tracks in the GFF to visualize a genomic region in a genome browser. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? MAKER just provides hints to the gene predictors (i.e. and set or protein increases the probability that awn exon/intron should exist where indicated), the predictor then identifies if the hint is workable or not. You can manually curate where you thing incorrect evidence tipped the scales in favor of an incorrect models probability using Apollo. You can also try EVM post processing where you can specify different weights to give to specific evidence types. > I also examine another genomic region where Augustus and SNAP predict a gene; there is no EST hit, but one protein hit. At this case, Maker does not annotate a gene at this region. Is it because a protein hit is not enough for annotating a region and it always requires EST hit? The protein hit may not be in the same reading frame as the gene predictions (in which case it does not count as evidence support) or it may be too small a fraction of the original protein in which case it may be filtered out as a spurious low complexity alignment. ?Carson From carsonhh at gmail.com Mon Sep 30 11:04:54 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:04:54 -0600 Subject: [maker-devel] /perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck In-Reply-To: References: Message-ID: <33C71B74-9551-413F-959C-688523959743@gmail.com> ?symbol lookup error? means that you are running with a different version of perl than the one used to install a program. Sao you might have installed with /usr/bin/perl but are running with /home/emmanuel/miniconda3/bin/perl or vice versa. You can run /home/emmanuel/miniconda3/bin/cpan (if it exists there) and manually install Acme::Damn just for that perl installation. You may also need to reinstall MAKER for the version of perl you are using. ?Carson > On Sep 29, 2019, at 5:51 PM, Emmanuel Nnadi wrote: > > Hello > > I compiled Maker on a cluster using MPI, > attempting to run maker i got this error. > > > /home/emmanuel/miniconda3/bin/perl: symbol lookup error: /home/emmanuel/maker/bin/../perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck > > > Can you help? > > Thanks > > Nnadi Nnaemeka Emmanuel,Ph.D > Department of Microbiology, > Faculty of Natural and Applied Science, > Plateau State University, Bokkos, Plateau State, Nigeria. > +2348068124819 > Publications: > https://www.researchgate.net/profile/Emmanuel_Nnadi/publications _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:10:00 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:10:00 -0600 Subject: [maker-devel] Maker installation fails for MacOSX In-Reply-To: References: Message-ID: <4BF52BB3-BE2C-4697-AD1F-CA3F01BF70B6@gmail.com> The problem is OSX. It has gradually moved out of compatibility with other Linux distributions over the years. You will need to install developer tools like Xcode, and perhaps even try homebrew to try and get around certain differences in OSX behavior.. Homebrew ?> https://brew.sh Brewsci/bio (science packages) -> https://github.com/brewsci/homebrew-bio After that 'brew install maker? might work (cross your fingers). ?Carson > On Sep 28, 2019, at 4:08 PM, Katherine Balasingham wrote: > > Hello! > > I hope I am contacting the correct email - I have been trying to install Maker for a few days now on my Mac OSX version 10.14 Mojave. > > It fails at the first few steps where it cannot install RepeatMasker, SNAP, or Exonerate. I have even tried to install these programs manually but Maker continues to fail to detect these packages or fails to install them properly. I did try using ./build package-name as well but to no avail. I ran ./Build installexes and ./Build installdeps but they constantly fail for those three programs only and I cannot find a solution online. > > Could you provide me with the proper code to manually install these three programs so I can use Maker? I have checked online sources for these programs but then I run into the issue where configuring Maker does not seem to find these three programs if I install it separately, so I am stuck at this step. > > Sorry for the long email I wanted to be explicit as I could be! > > The error message I always get is: > > ERROR: Failed installing RepeatMasker, now cleaning installation path... > You may need to install RepeatMasker manually. > > Checking external program dependencies... > requires: > ! Exonerate is not installed > ! SNAP is not installed > ! RepeatMasker is not installed > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the programs > indicated above before proceeding with this installation. > Run 'Build installexes' to install missing prerequisites. > > > Sincerely, > > Katherine Balasingham > > PS: I have never installed these programs before at all so I do not have older versions interfering with Maker. > > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:16:16 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:16:16 -0600 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins In-Reply-To: References: Message-ID: <3B38F9B0-4AC6-4038-B397-763728F2B33F@gmail.com> Try looking at this in Apollo instead. You do not seem to get intron/exon/utr differentiation with this viewer, ?Carson > On Sep 23, 2019, at 12:00 PM, Qihua Liang wrote: > > Dear Maker Dev Team: > > I am using Maker for gene annotations and I separate different tracks in the GFF to visualize in a genome browser. As in the attached picture, there is a very long Maker gene ?maker-chr9-augustus-gene-102.77?. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? > > Thanks > Qihua > > > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org From Cedric.Cabau at inra.fr Fri Sep 6 07:48:25 2019 From: Cedric.Cabau at inra.fr (=?UTF-8?Q?C=c3=a9dric_Cabau?=) Date: Fri, 6 Sep 2019 15:48:25 +0200 Subject: [maker-devel] Trouble with EVM and evidence from external GFF3 Message-ID: Hi, I use Maker 3.01.02-beta in mpi mode to merge data from gene models and cdna/protein evidence. I run Maker with entries est_gff, protein_gff and pred_gff in run_evm=1, est2genome=0 and protein2genome=0 mode. Being surprised by the amount of RAM required for some EVM jobs, I wanted to reproduce the execution of EVM commands outside of Maker. I commented the line 1819 inside maker/lib/GI.pm to keep the EVM command input files inside my temporary directory. By doing this, I noticed that the *.protein_for_evm.gff files generated for each chunk were systematically empty (only the gff3 header is written in the file) unlike the *.ests_for_evm.gff and *.preds_for_evm_gene.gff files. The formatting of my protein_gff input file does not seem to cause this because I find protein evidence in my output file *.all.maker.gff. Evidence files are therefore well taken into account by Maker but the protein evidence does not seem to have been passed on to EVM. Have you ever notice this before? Is this due to a misuse of Maker of my own? Thank you in advance for your answer. est_gff file 1??? Cufflinks??? match??? 6706??? 11762??? 3194.685322??? - .??? ID=1:CUFF.4.1;Name=1:CUFF.4.1; 1??? Cufflinks??? match_part??? 6706??? 6760??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-1;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 1 55 +; 1??? Cufflinks??? match_part??? 6892??? 6955??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-2;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 56 119 +; 1??? Cufflinks??? match_part??? 9558??? 9694??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-3;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 120 256 +; 1??? Cufflinks??? match_part??? 10081??? 10191??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-4;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 257 367 +; 1??? Cufflinks??? match_part??? 11550??? 11625??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-5;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 368 443 +; 1??? Cufflinks??? match_part??? 11751??? 11762??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-6;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 444 455 +; protein_gff file 5??? exonerate??? protein_match??? 8111679??? 8145811??? . -??? .??? ID=5:1;Target=ENSAMXP00000000017.1 5??? exonerate??? match??? 8111679??? 8111886??? 83.57??? - .??? ID=5:1:exon-1;Parent=5:1;Target=ENSAMXP00000000017.1 1 69 5??? exonerate??? match??? 8120294??? 8120428??? 83.57??? - .??? ID=5:1:exon-2;Parent=5:1;Target=ENSAMXP00000000017.1 70 84 5??? exonerate??? match??? 8125321??? 8125515??? 83.57??? - .??? ID=5:1:exon-3;Parent=5:1;Target=ENSAMXP00000000017.1 84 174 5??? exonerate??? match??? 8128007??? 8128240??? 83.57??? - .??? ID=5:1:exon-4;Parent=5:1;Target=ENSAMXP00000000017.1 175 252 5??? exonerate??? match??? 8138856??? 8139127??? 83.57??? - .??? ID=5:1:exon-5;Parent=5:1;Target=ENSAMXP00000000017.1 253 317 maker_evm.log #-----Transcript weights evmtrans=10 #default weight for source unspecified est/alt_est alignments evmtrans:blastn=0 #weight for blastn sourced alignments evmtrans:est2genome=10 #weight for est2genome sourced alignments evmtrans:tblastx=0 #weight for tblastx sourced alignments evmtrans:cdna2genome=7 #weight for cdna2genome sourced alignments evmtrans:est_gff:cufflinks=30 #weight for est_gff:cufflinks sourced alignments #-----Protein weights evmprot=10 #default weight for source unspecified protein alignments evmprot:blastx=2 #weight for blastx sourced alignments evmprot:protein2genome=15 #weight for protein2genome sourced alignments evmprot:protein_gff:exonerate=15 #weight for protein_gff:exonerate sourced alignments #-----Abinitio Prediction weights evmab=10 #default weight for source unspecified ab initio predictions evmab:snap=10 #weight for snap sourced predictions evmab:augustus=10 #weight for augustus sourced predictions evmab:fgenesh=10 #weight for fgenesh sourced predictions evmab:genemark=7 #weight for genemark sourced predictions evmab:pred_gff:augustus=10 #weight for pred_gff:augustus sourced predictions -------------- next part -------------- An HTML attachment was scrubbed... URL: From qlian003 at ucr.edu Fri Sep 27 16:45:31 2019 From: qlian003 at ucr.edu (Qihua Liang) Date: Fri, 27 Sep 2019 15:45:31 -0700 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins Message-ID: Dear Maker Dev Team: I am using Maker for gene annotations and I separate different tracks in the GFF to visualize a genomic region in a genome browser. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? I also examine another genomic region where Augustus and SNAP predict a gene; there is no EST hit, but one protein hit. At this case, Maker does not annotate a gene at this region. Is it because a protein hit is not enough for annotating a region and it always requires EST hit? Thanks Qihua From qlian003 at ucr.edu Mon Sep 23 12:00:55 2019 From: qlian003 at ucr.edu (Qihua Liang) Date: Mon, 23 Sep 2019 11:00:55 -0700 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins Message-ID: Dear Maker Dev Team: I am using Maker for gene annotations and I separate different tracks in the GFF to visualize in a genome browser. As in the attached picture, there is a very long Maker gene ?maker-chr9-augustus-gene-102.77?. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? Thanks Qihua -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PastedGraphic-1.png Type: image/png Size: 220052 bytes Desc: not available URL: From katherine.balasingham at mail.utoronto.ca Sat Sep 28 16:08:04 2019 From: katherine.balasingham at mail.utoronto.ca (Katherine Balasingham) Date: Sat, 28 Sep 2019 22:08:04 +0000 Subject: [maker-devel] Maker installation fails for MacOSX Message-ID: Hello! I hope I am contacting the correct email - I have been trying to install Maker for a few days now on my Mac OSX version 10.14 Mojave. It fails at the first few steps where it cannot install RepeatMasker, SNAP, or Exonerate. I have even tried to install these programs manually but Maker continues to fail to detect these packages or fails to install them properly. I did try using ./build package-name as well but to no avail. I ran ./Build installexes and ./Build installdeps but they constantly fail for those three programs only and I cannot find a solution online. Could you provide me with the proper code to manually install these three programs so I can use Maker? I have checked online sources for these programs but then I run into the issue where configuring Maker does not seem to find these three programs if I install it separately, so I am stuck at this step. Sorry for the long email I wanted to be explicit as I could be! The error message I always get is: ERROR: Failed installing RepeatMasker, now cleaning installation path... You may need to install RepeatMasker manually. Checking external program dependencies... requires: ! Exonerate is not installed ! SNAP is not installed ! RepeatMasker is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the programs indicated above before proceeding with this installation. Run 'Build installexes' to install missing prerequisites. Sincerely, Katherine Balasingham PS: I have never installed these programs before at all so I do not have older versions interfering with Maker. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eennadi at gmail.com Sun Sep 29 17:51:53 2019 From: eennadi at gmail.com (Emmanuel Nnadi) Date: Mon, 30 Sep 2019 00:51:53 +0100 Subject: [maker-devel] /perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck Message-ID: Hello I compiled Maker on a cluster using MPI, attempting to run maker i got this error. /home/emmanuel/miniconda3/bin/perl: symbol lookup error: /home/emmanuel/maker/bin/../perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck Can you help? Thanks Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:00:57 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:00:57 -0600 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins In-Reply-To: References: Message-ID: > I am using Maker for gene annotations and I separate different tracks in the GFF to visualize a genomic region in a genome browser. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? MAKER just provides hints to the gene predictors (i.e. and set or protein increases the probability that awn exon/intron should exist where indicated), the predictor then identifies if the hint is workable or not. You can manually curate where you thing incorrect evidence tipped the scales in favor of an incorrect models probability using Apollo. You can also try EVM post processing where you can specify different weights to give to specific evidence types. > I also examine another genomic region where Augustus and SNAP predict a gene; there is no EST hit, but one protein hit. At this case, Maker does not annotate a gene at this region. Is it because a protein hit is not enough for annotating a region and it always requires EST hit? The protein hit may not be in the same reading frame as the gene predictions (in which case it does not count as evidence support) or it may be too small a fraction of the original protein in which case it may be filtered out as a spurious low complexity alignment. ?Carson From carsonhh at gmail.com Mon Sep 30 11:04:54 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:04:54 -0600 Subject: [maker-devel] /perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck In-Reply-To: References: Message-ID: <33C71B74-9551-413F-959C-688523959743@gmail.com> ?symbol lookup error? means that you are running with a different version of perl than the one used to install a program. Sao you might have installed with /usr/bin/perl but are running with /home/emmanuel/miniconda3/bin/perl or vice versa. You can run /home/emmanuel/miniconda3/bin/cpan (if it exists there) and manually install Acme::Damn just for that perl installation. You may also need to reinstall MAKER for the version of perl you are using. ?Carson > On Sep 29, 2019, at 5:51 PM, Emmanuel Nnadi wrote: > > Hello > > I compiled Maker on a cluster using MPI, > attempting to run maker i got this error. > > > /home/emmanuel/miniconda3/bin/perl: symbol lookup error: /home/emmanuel/maker/bin/../perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck > > > Can you help? > > Thanks > > Nnadi Nnaemeka Emmanuel,Ph.D > Department of Microbiology, > Faculty of Natural and Applied Science, > Plateau State University, Bokkos, Plateau State, Nigeria. > +2348068124819 > Publications: > https://www.researchgate.net/profile/Emmanuel_Nnadi/publications _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:10:00 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:10:00 -0600 Subject: [maker-devel] Maker installation fails for MacOSX In-Reply-To: References: Message-ID: <4BF52BB3-BE2C-4697-AD1F-CA3F01BF70B6@gmail.com> The problem is OSX. It has gradually moved out of compatibility with other Linux distributions over the years. You will need to install developer tools like Xcode, and perhaps even try homebrew to try and get around certain differences in OSX behavior.. Homebrew ?> https://brew.sh Brewsci/bio (science packages) -> https://github.com/brewsci/homebrew-bio After that 'brew install maker? might work (cross your fingers). ?Carson > On Sep 28, 2019, at 4:08 PM, Katherine Balasingham wrote: > > Hello! > > I hope I am contacting the correct email - I have been trying to install Maker for a few days now on my Mac OSX version 10.14 Mojave. > > It fails at the first few steps where it cannot install RepeatMasker, SNAP, or Exonerate. I have even tried to install these programs manually but Maker continues to fail to detect these packages or fails to install them properly. I did try using ./build package-name as well but to no avail. I ran ./Build installexes and ./Build installdeps but they constantly fail for those three programs only and I cannot find a solution online. > > Could you provide me with the proper code to manually install these three programs so I can use Maker? I have checked online sources for these programs but then I run into the issue where configuring Maker does not seem to find these three programs if I install it separately, so I am stuck at this step. > > Sorry for the long email I wanted to be explicit as I could be! > > The error message I always get is: > > ERROR: Failed installing RepeatMasker, now cleaning installation path... > You may need to install RepeatMasker manually. > > Checking external program dependencies... > requires: > ! Exonerate is not installed > ! SNAP is not installed > ! RepeatMasker is not installed > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the programs > indicated above before proceeding with this installation. > Run 'Build installexes' to install missing prerequisites. > > > Sincerely, > > Katherine Balasingham > > PS: I have never installed these programs before at all so I do not have older versions interfering with Maker. > > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:16:16 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:16:16 -0600 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins In-Reply-To: References: Message-ID: <3B38F9B0-4AC6-4038-B397-763728F2B33F@gmail.com> Try looking at this in Apollo instead. You do not seem to get intron/exon/utr differentiation with this viewer, ?Carson > On Sep 23, 2019, at 12:00 PM, Qihua Liang wrote: > > Dear Maker Dev Team: > > I am using Maker for gene annotations and I separate different tracks in the GFF to visualize in a genome browser. As in the attached picture, there is a very long Maker gene ?maker-chr9-augustus-gene-102.77?. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? > > Thanks > Qihua > > > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org From Cedric.Cabau at inra.fr Fri Sep 6 07:48:25 2019 From: Cedric.Cabau at inra.fr (=?UTF-8?Q?C=c3=a9dric_Cabau?=) Date: Fri, 6 Sep 2019 15:48:25 +0200 Subject: [maker-devel] Trouble with EVM and evidence from external GFF3 Message-ID: Hi, I use Maker 3.01.02-beta in mpi mode to merge data from gene models and cdna/protein evidence. I run Maker with entries est_gff, protein_gff and pred_gff in run_evm=1, est2genome=0 and protein2genome=0 mode. Being surprised by the amount of RAM required for some EVM jobs, I wanted to reproduce the execution of EVM commands outside of Maker. I commented the line 1819 inside maker/lib/GI.pm to keep the EVM command input files inside my temporary directory. By doing this, I noticed that the *.protein_for_evm.gff files generated for each chunk were systematically empty (only the gff3 header is written in the file) unlike the *.ests_for_evm.gff and *.preds_for_evm_gene.gff files. The formatting of my protein_gff input file does not seem to cause this because I find protein evidence in my output file *.all.maker.gff. Evidence files are therefore well taken into account by Maker but the protein evidence does not seem to have been passed on to EVM. Have you ever notice this before? Is this due to a misuse of Maker of my own? Thank you in advance for your answer. est_gff file 1??? Cufflinks??? match??? 6706??? 11762??? 3194.685322??? - .??? ID=1:CUFF.4.1;Name=1:CUFF.4.1; 1??? Cufflinks??? match_part??? 6706??? 6760??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-1;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 1 55 +; 1??? Cufflinks??? match_part??? 6892??? 6955??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-2;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 56 119 +; 1??? Cufflinks??? match_part??? 9558??? 9694??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-3;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 120 256 +; 1??? Cufflinks??? match_part??? 10081??? 10191??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-4;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 257 367 +; 1??? Cufflinks??? match_part??? 11550??? 11625??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-5;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 368 443 +; 1??? Cufflinks??? match_part??? 11751??? 11762??? 3194.685322 -??? . ID=1:CUFF.4.1:exon-6;Name=1:CUFF.4.1;Parent=1:CUFF.4.1;Target=1:CUFF.4.1 444 455 +; protein_gff file 5??? exonerate??? protein_match??? 8111679??? 8145811??? . -??? .??? ID=5:1;Target=ENSAMXP00000000017.1 5??? exonerate??? match??? 8111679??? 8111886??? 83.57??? - .??? ID=5:1:exon-1;Parent=5:1;Target=ENSAMXP00000000017.1 1 69 5??? exonerate??? match??? 8120294??? 8120428??? 83.57??? - .??? ID=5:1:exon-2;Parent=5:1;Target=ENSAMXP00000000017.1 70 84 5??? exonerate??? match??? 8125321??? 8125515??? 83.57??? - .??? ID=5:1:exon-3;Parent=5:1;Target=ENSAMXP00000000017.1 84 174 5??? exonerate??? match??? 8128007??? 8128240??? 83.57??? - .??? ID=5:1:exon-4;Parent=5:1;Target=ENSAMXP00000000017.1 175 252 5??? exonerate??? match??? 8138856??? 8139127??? 83.57??? - .??? ID=5:1:exon-5;Parent=5:1;Target=ENSAMXP00000000017.1 253 317 maker_evm.log #-----Transcript weights evmtrans=10 #default weight for source unspecified est/alt_est alignments evmtrans:blastn=0 #weight for blastn sourced alignments evmtrans:est2genome=10 #weight for est2genome sourced alignments evmtrans:tblastx=0 #weight for tblastx sourced alignments evmtrans:cdna2genome=7 #weight for cdna2genome sourced alignments evmtrans:est_gff:cufflinks=30 #weight for est_gff:cufflinks sourced alignments #-----Protein weights evmprot=10 #default weight for source unspecified protein alignments evmprot:blastx=2 #weight for blastx sourced alignments evmprot:protein2genome=15 #weight for protein2genome sourced alignments evmprot:protein_gff:exonerate=15 #weight for protein_gff:exonerate sourced alignments #-----Abinitio Prediction weights evmab=10 #default weight for source unspecified ab initio predictions evmab:snap=10 #weight for snap sourced predictions evmab:augustus=10 #weight for augustus sourced predictions evmab:fgenesh=10 #weight for fgenesh sourced predictions evmab:genemark=7 #weight for genemark sourced predictions evmab:pred_gff:augustus=10 #weight for pred_gff:augustus sourced predictions -------------- next part -------------- An HTML attachment was scrubbed... URL: From qlian003 at ucr.edu Fri Sep 27 16:45:31 2019 From: qlian003 at ucr.edu (Qihua Liang) Date: Fri, 27 Sep 2019 15:45:31 -0700 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins Message-ID: Dear Maker Dev Team: I am using Maker for gene annotations and I separate different tracks in the GFF to visualize a genomic region in a genome browser. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? I also examine another genomic region where Augustus and SNAP predict a gene; there is no EST hit, but one protein hit. At this case, Maker does not annotate a gene at this region. Is it because a protein hit is not enough for annotating a region and it always requires EST hit? Thanks Qihua From qlian003 at ucr.edu Mon Sep 23 12:00:55 2019 From: qlian003 at ucr.edu (Qihua Liang) Date: Mon, 23 Sep 2019 11:00:55 -0700 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins Message-ID: Dear Maker Dev Team: I am using Maker for gene annotations and I separate different tracks in the GFF to visualize in a genome browser. As in the attached picture, there is a very long Maker gene ?maker-chr9-augustus-gene-102.77?. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? Thanks Qihua -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PastedGraphic-1.png Type: image/png Size: 220052 bytes Desc: not available URL: From katherine.balasingham at mail.utoronto.ca Sat Sep 28 16:08:04 2019 From: katherine.balasingham at mail.utoronto.ca (Katherine Balasingham) Date: Sat, 28 Sep 2019 22:08:04 +0000 Subject: [maker-devel] Maker installation fails for MacOSX Message-ID: Hello! I hope I am contacting the correct email - I have been trying to install Maker for a few days now on my Mac OSX version 10.14 Mojave. It fails at the first few steps where it cannot install RepeatMasker, SNAP, or Exonerate. I have even tried to install these programs manually but Maker continues to fail to detect these packages or fails to install them properly. I did try using ./build package-name as well but to no avail. I ran ./Build installexes and ./Build installdeps but they constantly fail for those three programs only and I cannot find a solution online. Could you provide me with the proper code to manually install these three programs so I can use Maker? I have checked online sources for these programs but then I run into the issue where configuring Maker does not seem to find these three programs if I install it separately, so I am stuck at this step. Sorry for the long email I wanted to be explicit as I could be! The error message I always get is: ERROR: Failed installing RepeatMasker, now cleaning installation path... You may need to install RepeatMasker manually. Checking external program dependencies... requires: ! Exonerate is not installed ! SNAP is not installed ! RepeatMasker is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the programs indicated above before proceeding with this installation. Run 'Build installexes' to install missing prerequisites. Sincerely, Katherine Balasingham PS: I have never installed these programs before at all so I do not have older versions interfering with Maker. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eennadi at gmail.com Sun Sep 29 17:51:53 2019 From: eennadi at gmail.com (Emmanuel Nnadi) Date: Mon, 30 Sep 2019 00:51:53 +0100 Subject: [maker-devel] /perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck Message-ID: Hello I compiled Maker on a cluster using MPI, attempting to run maker i got this error. /home/emmanuel/miniconda3/bin/perl: symbol lookup error: /home/emmanuel/maker/bin/../perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck Can you help? Thanks Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:00:57 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:00:57 -0600 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins In-Reply-To: References: Message-ID: > I am using Maker for gene annotations and I separate different tracks in the GFF to visualize a genomic region in a genome browser. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? MAKER just provides hints to the gene predictors (i.e. and set or protein increases the probability that awn exon/intron should exist where indicated), the predictor then identifies if the hint is workable or not. You can manually curate where you thing incorrect evidence tipped the scales in favor of an incorrect models probability using Apollo. You can also try EVM post processing where you can specify different weights to give to specific evidence types. > I also examine another genomic region where Augustus and SNAP predict a gene; there is no EST hit, but one protein hit. At this case, Maker does not annotate a gene at this region. Is it because a protein hit is not enough for annotating a region and it always requires EST hit? The protein hit may not be in the same reading frame as the gene predictions (in which case it does not count as evidence support) or it may be too small a fraction of the original protein in which case it may be filtered out as a spurious low complexity alignment. ?Carson From carsonhh at gmail.com Mon Sep 30 11:04:54 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:04:54 -0600 Subject: [maker-devel] /perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck In-Reply-To: References: Message-ID: <33C71B74-9551-413F-959C-688523959743@gmail.com> ?symbol lookup error? means that you are running with a different version of perl than the one used to install a program. Sao you might have installed with /usr/bin/perl but are running with /home/emmanuel/miniconda3/bin/perl or vice versa. You can run /home/emmanuel/miniconda3/bin/cpan (if it exists there) and manually install Acme::Damn just for that perl installation. You may also need to reinstall MAKER for the version of perl you are using. ?Carson > On Sep 29, 2019, at 5:51 PM, Emmanuel Nnadi wrote: > > Hello > > I compiled Maker on a cluster using MPI, > attempting to run maker i got this error. > > > /home/emmanuel/miniconda3/bin/perl: symbol lookup error: /home/emmanuel/maker/bin/../perl/lib/auto/Acme/Damn/Damn.so: undefined symbol: Perl_xs_apiversion_bootcheck > > > Can you help? > > Thanks > > Nnadi Nnaemeka Emmanuel,Ph.D > Department of Microbiology, > Faculty of Natural and Applied Science, > Plateau State University, Bokkos, Plateau State, Nigeria. > +2348068124819 > Publications: > https://www.researchgate.net/profile/Emmanuel_Nnadi/publications _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:10:00 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:10:00 -0600 Subject: [maker-devel] Maker installation fails for MacOSX In-Reply-To: References: Message-ID: <4BF52BB3-BE2C-4697-AD1F-CA3F01BF70B6@gmail.com> The problem is OSX. It has gradually moved out of compatibility with other Linux distributions over the years. You will need to install developer tools like Xcode, and perhaps even try homebrew to try and get around certain differences in OSX behavior.. Homebrew ?> https://brew.sh Brewsci/bio (science packages) -> https://github.com/brewsci/homebrew-bio After that 'brew install maker? might work (cross your fingers). ?Carson > On Sep 28, 2019, at 4:08 PM, Katherine Balasingham wrote: > > Hello! > > I hope I am contacting the correct email - I have been trying to install Maker for a few days now on my Mac OSX version 10.14 Mojave. > > It fails at the first few steps where it cannot install RepeatMasker, SNAP, or Exonerate. I have even tried to install these programs manually but Maker continues to fail to detect these packages or fails to install them properly. I did try using ./build package-name as well but to no avail. I ran ./Build installexes and ./Build installdeps but they constantly fail for those three programs only and I cannot find a solution online. > > Could you provide me with the proper code to manually install these three programs so I can use Maker? I have checked online sources for these programs but then I run into the issue where configuring Maker does not seem to find these three programs if I install it separately, so I am stuck at this step. > > Sorry for the long email I wanted to be explicit as I could be! > > The error message I always get is: > > ERROR: Failed installing RepeatMasker, now cleaning installation path... > You may need to install RepeatMasker manually. > > Checking external program dependencies... > requires: > ! Exonerate is not installed > ! SNAP is not installed > ! RepeatMasker is not installed > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the programs > indicated above before proceeding with this installation. > Run 'Build installexes' to install missing prerequisites. > > > Sincerely, > > Katherine Balasingham > > PS: I have never installed these programs before at all so I do not have older versions interfering with Maker. > > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 30 11:16:16 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Sep 2019 11:16:16 -0600 Subject: [maker-devel] Maker decision of genes when having a long transcript over several proteins In-Reply-To: References: Message-ID: <3B38F9B0-4AC6-4038-B397-763728F2B33F@gmail.com> Try looking at this in Apollo instead. You do not seem to get intron/exon/utr differentiation with this viewer, ?Carson > On Sep 23, 2019, at 12:00 PM, Qihua Liang wrote: > > Dear Maker Dev Team: > > I am using Maker for gene annotations and I separate different tracks in the GFF to visualize in a genome browser. As in the attached picture, there is a very long Maker gene ?maker-chr9-augustus-gene-102.77?. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the ?correct? way, is it any settings I should change instead of removing the EST evidence? > > Thanks > Qihua > > > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org