<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Yes. That's ok, but you would get better performance by installing MPI and using that. Alternatively just start maker several times in the same directory without splitting the input fasta. You can usually start about 10-15 concurrent maker processes safely, but would still get better performance with MPI.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Diana LeDuc <<a href="mailto:diana_leduc@eva.mpg.de">diana_leduc@eva.mpg.de</a>><br><span style="font-weight:bold">Reply-To: </span> Diana LeDuc <<a href="mailto:diana_leduc@eva.mpg.de">diana_leduc@eva.mpg.de</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 28 May, 2013 8:16 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Gabriel Renaud <<a href="mailto:gabriel_renaud@eva.mpg.de">gabriel_renaud@eva.mpg.de</a>>, Janet Kelso <<a href="mailto:kelso@eva.mpg.de">kelso@eva.mpg.de</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Maker consensus<br></div><div><br></div><div xmlns="http://www.w3.org/1999/xhtml">
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Hi Carson,
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I have now restarted maker with specification of augustus path and species. I am trying to run it separately on each scaffold just to parallelise the process and speed it up. It happens that some of the scaffolds which run ok in the complete datatset now fail. Do you have any idea why this happens?
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Is it ok to have a separate directory for each of the scaffolds and run maker in each of them?
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Thank you for the help.
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Best regards,
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Diana
<br>On May 10, 2013 at 8:29 PM Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:
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You can use any species augustus already has. If it doesn't then you train it yourself. The species folder is pointed to by the AUGUSTUS_CONFIG_PATH environmental variable, and is usually …/augusts/config/species
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Thanks,
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Carson
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<span style="font-weight: bold;">From: </span> Diana LeDuc <
<a href="mailto:diana_leduc@eva.mpg.de">diana_leduc@eva.mpg.de</a>>
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<span style="font-weight: bold;">Reply-To: </span> Diana LeDuc <
<a href="mailto:diana_leduc@eva.mpg.de">diana_leduc@eva.mpg.de</a>>
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<span style="font-weight: bold;">Date: </span> Friday, 10 May, 2013 2:16 PM
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<span style="font-weight: bold;">To: </span> <
<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>, Carson Holt <
<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>
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<span style="font-weight: bold;">Cc: </span> Torsten Schoeneberg <
<a href="mailto:torsten.schoeneberg@medizin.uni-leipzig.de">torsten.schoeneberg@medizin.uni-leipzig.de</a>>, Gabriel Renaud <
<a href="mailto:gabriel_renaud@eva.mpg.de">gabriel_renaud@eva.mpg.de</a>>, Janet Kelso <
<a href="mailto:kelso@eva.mpg.de">kelso@eva.mpg.de</a>>
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<span style="font-weight: bold;">Subject: </span> Re: [maker-devel] Maker consensus
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Hi Carson,
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In maker_exe.ctl I would have to provide the path to augustus. Augustus has a training set for chicken that I would use. Is it possible to specify the species i want to use, or the only way is training Augustus myself?
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Thank you!
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Best,
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Diana
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On May 10, 2013 at 7:51 PM Carson Holt <
<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:
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Ok. You just ran the evidence and didn't give a gene predictor. You need to provide an HMM file for SNAP a species for augustus, or for rough annotations you can set protein3genome=1 and est2genome=1. This will try and generate models direct from the alignments.
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If you provide a gene predictor, then MAKER can talk to it about the evidence alignments so it can make a best gene call for the region. Then there will be gene/mRNA/exon model in the GFF3 file and entires in the proteins.fasta and transcripts.fasta. If you need to train a predictor, you can train SNAP using the maker2zff script and the SNAP documentation or maker GMOD tutorial. If you want to train augustus Jason Stajich wrote an excellent explanation as well as tools in a previous list message.
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list msg -
<a href="http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html">http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html</a>
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Script is in this github repo -
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<span style="font-family: Calibri; font-size: medium;" class="Apple-style-span"><a href="https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl">https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl</a></span>
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Thanks,
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Carson
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<span style="font-weight: bold;">From: </span> Diana LeDuc <
<a href="mailto:diana_leduc@eva.mpg.de">diana_leduc@eva.mpg.de</a>>
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<span style="font-weight: bold;">Reply-To: </span> Diana LeDuc <
<a href="mailto:diana_leduc@eva.mpg.de">diana_leduc@eva.mpg.de</a>>
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<span style="font-weight: bold;">Date: </span> Friday, 10 May, 2013 1:41 PM
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<span style="font-weight: bold;">To: </span> <
<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>, Carson Holt <
<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>
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<span style="font-weight: bold;">Cc: </span> Torsten Schoeneberg <
<a href="mailto:torsten.schoeneberg@medizin.uni-leipzig.de">torsten.schoeneberg@medizin.uni-leipzig.de</a>>, Gabriel Renaud <
<a href="mailto:gabriel_renaud@eva.mpg.de">gabriel_renaud@eva.mpg.de</a>>, Janet Kelso <
<a href="mailto:kelso@eva.mpg.de">kelso@eva.mpg.de</a>>
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<span style="font-weight: bold;">Subject: </span> Re: [maker-devel] Maker consensus
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Hi Carson,
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Thank you for the quick answer.
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I ran gff3_merge to merge all the gff files and this resulted in a gff file, which has these type of fields:
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scaffold32239 blastx protein_match 22905 34500 174 + . ID=scaffold32239:hit:976144;Name=ENSTGUG00000000198|ENSTGUT00000000219|DSCAML1-2039;
<br>scaffold32239 blastx match_part 22905 23045 174 + . ID=scaffold32239:hsp:2806529;Parent=scaffold32239:hit:976144;Name=ENSTGUG00000000198|ENSTGUT00000000219|DSCAML1-2039;Target=ENSTGUG00000000198|ENSTGUT00000000219|DSCAML1-2039 172 218;Gap=M47;
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In comparison to the dpp_contig test file, I am missing est2genome evidence, most probably because my est data set is pretty poor. I have blastx and protein2genome evidence though.
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My goal is to extract the genes that could be annotated on the scaffolds. In the gff files the hits overlap most of the times, I can visualize this properly in apollo: for example one scaffold hits DSCAML gene in both zebrafinch and chicken, but extracting the coordinates between which this scaffold fits this annotated gene is difficult from the gff. Manually curating the genes is also not an option, since I am trying to do this for a 1.7Gb genome.
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I hope this explains better what we are after.
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Thank you once again.
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Best regards,
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Diana
<br>On May 10, 2013 at 6:13 PM Carson Holt <
<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:
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I'm sorry I don’t' understand question 1. You are you missing resulting fasta files, correct? Did your resulting GFF3 file have any features of type "gene"? Did you run fasta_merge after running gff3_merge?
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Could you give me more details on what you are trying to do, so I can take a stab at question 2 as well.
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Thanks,
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Carson
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<span style="font-weight: bold;">From: </span> Diana LeDuc <
<a href="mailto:diana_leduc@eva.mpg.de">diana_leduc@eva.mpg.de</a>>
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<span style="font-weight: bold;">Reply-To: </span> Diana LeDuc <
<a href="mailto:diana_leduc@eva.mpg.de">diana_leduc@eva.mpg.de</a>>
<br>
<span style="font-weight: bold;">Date: </span> Friday, 10 May, 2013 10:44 AM
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<span style="font-weight: bold;">To: </span> <
<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>
<br>
<span style="font-weight: bold;">Cc: </span> Gabriel Renaud <
<a href="mailto:gabriel_renaud@eva.mpg.de">gabriel_renaud@eva.mpg.de</a>>, Janet Kelso <
<a href="mailto:kelso@eva.mpg.de">kelso@eva.mpg.de</a>>, Torsten Schoeneberg <
<a href="mailto:torsten.schoeneberg@medizin.uni-leipzig.de">torsten.schoeneberg@medizin.uni-leipzig.de</a>>
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<span style="font-weight: bold;">Subject: </span> [maker-devel] Maker consensus
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<p>Dear maker developers,</p>
<p>I am a phD student working on de novo assembly and annotation of a bird genome. I used Maker as annotation pipeline, which ran very well, and I obtained different annotations with evidence from Augustus gene predictor, small EST dataset from my organism and protein sequences from chicken, turkey and zebrafinch. I could combine the different gff files from different scaffolds into one gff file with annotations for the entire genome.</p>
<p>I now have two questions:</p>
<p>1. What could be the reason that I haven't gotten the protein.fasta and trancript.fasta files</p>
<p>2. How can I obtain a consensus gene list of different evidences from maker? What I would actually need is the scaffold, coordinates and annotation (gene name) according to the 3 other bird species.</p> Thank you in advance.
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Best regards,
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Diana Le Duc
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--
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<br>Max Planck Institute for Evolutionary Anthropology
<br>Department of Evolutionary Genetics
<br>Deutscher Platz 6
<br>D-04103 Leipzig
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<br>Phone +49 (0)341-3550-554
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<a target="_blank" href="http://www.eva.mpg.de">www.eva.mpg.de</a>
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