From carsonhh at gmail.com Mon Dec 2 11:42:31 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 2 Dec 2019 11:42:31 -0700 Subject: [maker-devel] Apply old maker gff to new assembly In-Reply-To: References: Message-ID: Here is an archived post that covers this topic ?> https://groups.google.com/forum/#!searchin/maker-devel/est_forward%7Csort:date/maker-devel/gDbvTknuep4/gDiGCMgjCQAJ This will help map old structural models to new coordinates. Moving functional data may take some additional work. You might even want to rerun domain finders like interproscan rather than just copying old domain coordinates. ?Carson > On Nov 15, 2019, at 2:26 PM, Boyher, Adam wrote: > > Hi > I'm a bit unsure of how to apply a previous maker annotation to a new > assembly. I just want a quick annotation, so just taking the genes that > are already in the annotation file with their functional annotations > and naming schemes and find those genes in the new assembly. Which > settings should i use in maker_opts.ctl? > > Thanks > Adam > _______________________________________________ > 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 ABoyher at danforthcenter.org Mon Dec 2 12:50:38 2019 From: ABoyher at danforthcenter.org (Boyher, Adam) Date: Mon, 2 Dec 2019 19:50:38 +0000 Subject: [maker-devel] Apply old maker gff to new assembly In-Reply-To: References:

Message-ID: <40cc33637943737f719d77e2b2fb09cd1077d6a7.camel@danforthcenter.org> Thank you Carson. That helps. Can I ask another question in this thread? I have a phased genome (i.e. haplotype specific chromosomes of a diploid organism). I'm debating on the best way to annotate. Does it make sense to annotate both phases together, or separately? I've previously annotated them separately, and found some genes that exist on both phases are only annotated on one. I thought by annotating them together, the second/third iterations using augustus and snap would help annotate those missing genes. Another question I have is about creating a "global" gene naming scheme. Meaning, I want genes that exist on both phases to be named the same on both annotations, global_0001 for instance, and genes that only exist on one phase to be named a different way, phase0_0001. Do you have ideas on the best way to do that? Thanks for your help and time! Adam On Mon, 2019-12-02 at 11:42 -0700, Carson Holt wrote: > Here is an archived post that covers this topic ?> > https://groups.google.com/forum/#!searchin/maker-devel/est_forward%7Csort:date/maker-devel/gDbvTknuep4/gDiGCMgjCQAJ > > This will help map old structural models to new coordinates. Moving > functional data may take some additional work. You might even want to > rerun domain finders like interproscan rather than just copying old > domain coordinates. > > ?Carson > > > > On Nov 15, 2019, at 2:26 PM, Boyher, Adam < > > ABoyher at danforthcenter.org> wrote: > > > > Hi > > I'm a bit unsure of how to apply a previous maker annotation to a > > new > > assembly. I just want a quick annotation, so just taking the genes > > that > > are already in the annotation file with their functional > > annotations > > and naming schemes and find those genes in the new assembly. Which > > settings should i use in maker_opts.ctl? > > > > Thanks > > Adam > > _______________________________________________ > > maker-devel mailing list > > maker-devel at yandell-lab.org > > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org > > From carsonhh at gmail.com Mon Dec 2 13:03:28 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 2 Dec 2019 13:03:28 -0700 Subject: [maker-devel] Apply old maker gff to new assembly In-Reply-To: <40cc33637943737f719d77e2b2fb09cd1077d6a7.camel@danforthcenter.org> References:

<40cc33637943737f719d77e2b2fb09cd1077d6a7.camel@danforthcenter.org> Message-ID: <1C086510-9190-4D94-B369-C79C143C55F8@gmail.com> Either separate or together will probably result in near identical results. In GFF3 format ID= has to be unique but Name= does not. So you can name them the same by, setting Name= in the GFF3 file. I think map_gff_ids can do that for you if you provide a two column, tab delimited, text file (old-name new-name). Naming them the same thing in the fasta files will result in confusion though (unless the transcript has identical sequence), so while the genes can have the same name, keep the mRNA names different with a suffix (i.e. something like -RA, -RB, etc). As far as identifying who goes with who, reciprocal best blast hits might be the best staring point (i.e. each model is each others best scoring BLAST hit - both ways). Just beware of historical genomic duplications that might make this difficult. ?Carson > On Dec 2, 2019, at 12:50 PM, Boyher, Adam wrote: > > Thank you Carson. That helps. > > Can I ask another question in this thread? > I have a phased genome (i.e. haplotype specific chromosomes of a > diploid organism). I'm debating on the best way to annotate. Does it > make sense to annotate both phases together, or separately? I've > previously annotated them separately, and found some genes that exist > on both phases are only annotated on one. I thought by annotating them > together, the second/third iterations using augustus and snap would > help annotate those missing genes. Another question I have is about > creating a "global" gene naming scheme. Meaning, I want genes that > exist on both phases to be named the same on both annotations, > global_0001 for instance, and genes that only exist on one phase to be > named a different way, phase0_0001. Do you have ideas on the best way > to do that? > > Thanks for your help and time! > Adam > > > > On Mon, 2019-12-02 at 11:42 -0700, Carson Holt wrote: >> Here is an archived post that covers this topic ?> >> https://groups.google.com/forum/#!searchin/maker-devel/est_forward%7Csort:date/maker-devel/gDbvTknuep4/gDiGCMgjCQAJ >> >> This will help map old structural models to new coordinates. Moving >> functional data may take some additional work. You might even want to >> rerun domain finders like interproscan rather than just copying old >> domain coordinates. >> >> ?Carson >> >> >>> On Nov 15, 2019, at 2:26 PM, Boyher, Adam < >>> ABoyher at danforthcenter.org> wrote: >>> >>> Hi >>> I'm a bit unsure of how to apply a previous maker annotation to a >>> new >>> assembly. I just want a quick annotation, so just taking the genes >>> that >>> are already in the annotation file with their functional >>> annotations >>> and naming schemes and find those genes in the new assembly. Which >>> settings should i use in maker_opts.ctl? >>> >>> Thanks >>> Adam >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at yandell-lab.org >>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org >> >> From robert.king at rothamsted.ac.uk Thu Dec 12 14:42:46 2019 From: robert.king at rothamsted.ac.uk (Robert King) Date: Thu, 12 Dec 2019 21:42:46 +0000 Subject: [maker-devel] est_forward option and low or incorrect orientation transfer Message-ID: I am using the est_forward=1 #reserve flag for map2assembly option to transfer a transcriptome to the genome and create directly gene models from it. This usually works ok but on a larger genome I only have a transfer rate of 44% from busco score of cds (gffread extracted). I?m not sure if it?s just transferred 50% as wrong orientation so UTR instead which sometimes happens but not to that scale, or just not transferred because of snps. What settings can I change to test some things out to improve transfer of transcriptome to genome? Sent from Mail for Windows 10 Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038. -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Wed Dec 18 07:19:26 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Wed, 18 Dec 2019 14:19:26 +0000 Subject: [maker-devel] Multiple UTR ? Message-ID: Hi Carson, I have seen something strange in my annotation: multiple UTR. How can we explain this ? Thanks! Scaffold maker mRNA 12117462 12128433 . - . ID=GENE_02395-RA;Parent=GENE_02395;Name=GENE_02395-RA;Alias=maker-Scaffold-augustus-gene-40.12-mRNA-3;_AED=0.02;_QI=5383|1|1|1|0.88|0.9|10|247|238;_eAED=0.02;Note=Protein of unknown function; Scaffold maker exon 12128112 12128433 . - . ID=GENE_02395-RA:exon:571;Parent=GENE_02395-RA; Scaffold maker exon 12117462 12118046 . - . ID=GENE_02395-RB:exon:569;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA; Scaffold maker exon 12118141 12118301 . - . ID=GENE_02395-RB:exon:568;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA; Scaffold maker exon 12118386 12118539 . - . ID=GENE_02395-RB:exon:567;Parent=GENE_02395-RB,GENE_02395-RA; Scaffold maker exon 12118818 12122493 . - . ID=GENE_02395-RB:exon:566;Parent=GENE_02395-RB,GENE_02395-RA; Scaffold maker exon 12123591 12123893 . - . ID=GENE_02395-RB:exon:565;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA; Scaffold maker exon 12123995 12124303 . - . ID=GENE_02395-RB:exon:564;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA; Scaffold maker exon 12125119 12125418 . - . ID=GENE_02395-RB:exon:563;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA; Scaffold maker exon 12126005 12126313 . - . ID=GENE_02395-RB:exon:562;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA; Scaffold maker exon 12127460 12127687 . - . ID=GENE_02395-RB:exon:561;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA; Scaffold maker five_prime_UTR 12128112 12128433 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA; Scaffold maker five_prime_UTR 12127460 12127687 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA; Scaffold maker five_prime_UTR 12126005 12126313 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA; Scaffold maker five_prime_UTR 12125119 12125418 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA; Scaffold maker five_prime_UTR 12123995 12124303 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA; Scaffold maker five_prime_UTR 12123591 12123893 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA; Scaffold maker five_prime_UTR 12118882 12122493 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA; Scaffold maker CDS 12118818 12118881 . - 0 ID=GENE_02395-RA:cds;Parent=GENE_02395-RA; Scaffold maker CDS 12118386 12118539 . - 2 ID=GENE_02395-RA:cds;Parent=GENE_02395-RA; Scaffold maker CDS 12118141 12118301 . - 1 ID=GENE_02395-RA:cds;Parent=GENE_02395-RA; Scaffold maker CDS 12117709 12118046 . - 2 ID=GENE_02395-RA:cds;Parent=GENE_02395-RA; Scaffold maker three_prime_UTR 12117462 12117708 . - . ID=GENE_02395-RA:three_prime_utr;Parent=GENE_02395-RA; Patrick Tran Van Bioinformatician: Lab Chapuisat & Schwander Department of Ecology and Evolution University of Lausanne Lausanne - Switzerland Office 3206 -------------- next part -------------- An HTML attachment was scrubbed... URL: From peachandolives at gmail.com Sun Dec 29 15:03:44 2019 From: peachandolives at gmail.com (Linnie Linnie) Date: Sun, 29 Dec 2019 17:03:44 -0500 Subject: [maker-devel] Maker installation-RepeatMasker (or running RepeatMasker outside maker) Message-ID: Dear Maker team, I am analyzing a number of genomes in a cluster. I had previously installed RepeatMasker and RepeatModeler independently without problem in order to obtain the repeat libraries that are required by maker. This installation runs perfectly. However, when I install maker, it does not recognize that a successful installation of RepeatMasker is already available. How can tell maker where RepeatMasker is already located? I have alternatively tried to install RepeatMasker from within maker and then try to run maker. But it gives me the following error: Unrecognized character \x7F; marked by <-- HERE after <-- HERE near column 1 at /data1/home/maker/exe/RepeatMasker/TRF.pm line 1. Compilation failed in require at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339. BEGIN failed--compilation aborted at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339. ERROR: RepeatMasker failed --> rank=NA, hostname=loma ERROR: Failed while doing repeat masking ERROR: Chunk failed at level:0, tier_type:1 FAILED CONTIG:NQYS01000001.1 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:NQYS01000001.1 examining contents of the fasta file and run log As a last option, I think I could run RepeatMasker with the installation I already have and then pass its .gff file to maker. In this case, which parameters should I pass in the maker_opts.ctl file? Thank you so much for all your help (and Happy New Year to everyone!) L. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lmeunier at uliege.be Mon Dec 2 08:45:37 2019 From: lmeunier at uliege.be (=?UTF-8?B?TG/Dr2M=?=) Date: Mon, 02 Dec 2019 15:45:37 -0000 Subject: [maker-devel] Is Maker running without progressing? Message-ID: <38a0eda4-043a-d40e-2062-f7df4e77184c@uliege.be> Hello, I am running MAKER for 3 weeks on a large plant genome with a significant evidence dataset, my job seems in appearance to be running properly as it uses the allocated CPUs and the run folder is actualized every minute. However, MAKER stopped writing in the logfile after one day (in the middle of a step, see below). It is actually the second time I have the problem, I killed a first time the job as the logfile didn't change in a week and launched back the annotation based on the previous run repository. As it has been three weeks since it runs without visible results, would it be possible that the process is running without making any progress? Is there a way to assess the annotation state? Logfile end: ... total clusters:2 now processing 0 ?...processing 0 of 3 ?...processing 1 of 3 ?...processing 2 of 3 total clusters:2 now processing 0 ?...processing 0 of 2 ?...processing 1 of 2 Could you help me? Here are the logfiles of the two analysis: https://edc.ulg.ac.be/merci/maker_run_logs_4af3cd16577f3e870597_.zip Thank you for reading this message. Best regards, Lo?c Meunier -------------- next part -------------- An HTML attachment was scrubbed... URL: From guerrer at uni-duesseldorf.de Fri Dec 27 07:42:03 2019 From: guerrer at uni-duesseldorf.de (Ricardo Guerreiro) Date: Fri, 27 Dec 2019 15:42:03 +0100 Subject: [maker-devel] Maker with alternative Ests only Message-ID: Dear Maker developers, Is it possible to run maker with alternative ESTs only? I have tried it but have an error: > ERROR: You must provide some form of EST evidence to use est2genome as > a predictor. Should I run maker with est2genome=0? But then is it using the altest I provided? Wish you a happy new year, Ricardo From carsonhh at gmail.com Mon Dec 2 11:42:31 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 2 Dec 2019 11:42:31 -0700 Subject: [maker-devel] Apply old maker gff to new assembly In-Reply-To: References: Message-ID: Here is an archived post that covers this topic ?> https://groups.google.com/forum/#!searchin/maker-devel/est_forward%7Csort:date/maker-devel/gDbvTknuep4/gDiGCMgjCQAJ This will help map old structural models to new coordinates. Moving functional data may take some additional work. You might even want to rerun domain finders like interproscan rather than just copying old domain coordinates. ?Carson > On Nov 15, 2019, at 2:26 PM, Boyher, Adam wrote: > > Hi > I'm a bit unsure of how to apply a previous maker annotation to a new > assembly. I just want a quick annotation, so just taking the genes that > are already in the annotation file with their functional annotations > and naming schemes and find those genes in the new assembly. Which > settings should i use in maker_opts.ctl? > > Thanks > Adam > _______________________________________________ > 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 ABoyher at danforthcenter.org Mon Dec 2 12:50:38 2019 From: ABoyher at danforthcenter.org (Boyher, Adam) Date: Mon, 2 Dec 2019 19:50:38 +0000 Subject: [maker-devel] Apply old maker gff to new assembly In-Reply-To: References: