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<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you again for the help! This solved my issue with the file formatting and I was able to successfully run Maker on a test scaffold. I have the full run going now.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks again!<o:p></o:p></p>
<p class="MsoNormal">Kevin<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b> Jacques Dainat <jacques.dainat@gmail.com> <br>
<b>Sent:</b> Friday, September 24, 2021 3:42 AM<br>
<b>To:</b> Kevin Kocot <kmkocot@ua.edu><br>
<b>Cc:</b> carsonhh@gmail.com; maker-devel@yandell-lab.org<br>
<b>Subject:</b> [EXTERNAL] Re: [maker-devel] Troubleshooting Maker failure<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">Hi Kevin,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I have checked the 2 files.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">About <a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/pasa_predictions.gff3" target="_blank">
pasa_predictions.gff3</a>:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">It is parsed without any problem with <a href="https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fagat_convert_sp_gxf2gxf.pl%2F&data=04%7C01%7Ckmkocot%40ua.edu%7C85529bc2cc9f4ce1e64508d97f372ea8%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637680698957862360%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=8SBdAHgiK3i5dB0Xe2rn2QCiORIY5eQbTTZosvj%2FR2M%3D&reserved=0" target="_blank">
agat_convert_sp_gxf2gxf.pl</a> in about 10 mins. MAKER (>=v3) should be able to use it like that, but you might prefer to convert it into match/match_part style using the
<a href="https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fagat_sp_alignment_output_style.pl%2F&data=04%7C01%7Ckmkocot%40ua.edu%7C85529bc2cc9f4ce1e64508d97f372ea8%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637680698957872355%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=TEyTxhyWI5PtFAkw4oyNVa4VuGXqH4tGLDfXym8M0Jg%3D&reserved=0" target="_blank">
agat_sp_alignment_output_style.p</a>l. The match/match_part style works in all of MAKER version.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">About <a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/protein_alignments.gff3" target="_blank">
protein_alignments.gff3</a>: <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">This file is more problematic, it contains only 1 feature type, which is level1 in AGAT (i.e. like a gene), and in the current state is expecting sub-features. On top of that, the ID attribute is confusing because it is supposed to be unique,
and it is not. So here the commands you should launch to get a proper file for MAKER:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">First<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">```<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">sed 's/nucleotide_to_protein_match/match_part/' protein_alignments.gff3 | sed 's/ID=/Parent=/' > protein_alignments_repared.gff3<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">```<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Then<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">```<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><a href="https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fagat_convert_sp_gxf2gxf.pl%2F&data=04%7C01%7Ckmkocot%40ua.edu%7C85529bc2cc9f4ce1e64508d97f372ea8%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637680698957872355%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=0kJ7q77pRXQdMvvq4wPxlO8gc74LCVuZeVHaQ1%2FaciU%3D&reserved=0">agat_convert_sp_gxf2gxf.pl</a>
--gff protein_alignments_repared.gff3 -o protein_alignments_clean.gff3 <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">```<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Then you should be good with a proper match/match_part file.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Best,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">/Jacques<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal"> <o:p></o:p></p>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Hi Carson and Jacques,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Thank you both very much for the help. It looks like my PASA and exonerate (via Funannotate) gff3 files are not correctly formatted for maker. I've uploaded them here just in case it might be
helpful for you to see them, but I will try to figure out how to reformat them correctly following Jacques's advice.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/pasa_predictions.gff3" target="_blank">http://genomes.ua.edu/Kocot/2021-09-10_Maker/pasa_predictions.gff3</a><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/protein_alignments.gff3" target="_blank">http://genomes.ua.edu/Kocot/2021-09-10_Maker/protein_alignments.gff3</a><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Is there a standalone tool or Maker feature I'm not seeing that can assess whether a gff3 file is correctly formatted for Maker?<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Thank you again!<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Kevin<o:p></o:p></span></p>
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<div class="MsoNormal" align="center" style="text-align:center">
<hr size="2" width="98%" align="center">
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<div id="gmail-m_-3511602195170912938divRplyFwdMsg">
<p class="MsoNormal"><b><span style="color:black">From:</span></b><span style="color:black"> Jacques Dainat <<a href="mailto:jacques.dainat@nbis.se" target="_blank">jacques.dainat@nbis.se</a>><br>
<b>Sent:</b> Wednesday, September 22, 2021 2:09 PM<br>
<b>To:</b> Kevin Kocot <<a href="mailto:kmkocot@ua.edu" target="_blank">kmkocot@ua.edu</a>><br>
<b>Cc:</b> <a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a> <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>>; Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br>
<b>Subject:</b> [EXTERNAL] Re: [maker-devel] Troubleshooting Maker failure</span>
<o:p></o:p></p>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">Hi Kevin, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">About using AGAT (<a href="https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fagat_convert_sp_gxf2gxf.pl%2F&data=04%7C01%7Ckmkocot%40ua.edu%7C85529bc2cc9f4ce1e64508d97f372ea8%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637680698957882353%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=mgqfdOJ1WFyDpTfzCJhJXCR%2BzE7gpSXMKdpxKw7bU7c%3D&reserved=0" target="_blank">agat_convert_sp_gxf2gxf.pl</a>),
two reasons to get empty output files.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">I) The feature types (3rd column) are not yet handled by AGAT. You can inform AGAT how to deal with it <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">See <a href="https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fagat.readthedocs.io%2Fen%2Flatest%2Ftroubleshooting.html%23agat-throws-features-out-because-the-feature-type-is-not-yet-taken-into-account&data=04%7C01%7Ckmkocot%40ua.edu%7C85529bc2cc9f4ce1e64508d97f372ea8%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637680698957882353%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=fw9tT6EEjFCol8hnEtwqhVBOrW%2Fikg%2FTyuAvyd%2F%2B8wg%3D&reserved=0" target="_blank">https://agat.readthedocs.io/en/latest/troubleshooting.html#agat-throws-features-out-because-the-feature-type-is-not-yet-taken-into-account</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">II) The features are thrown by AGAT because child feature are missing <span style="color:black">(e.g. gene feature expect at least one transcript linked to it)</span>. See
<a href="https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fagat.readthedocs.io%2Fen%2Flatest%2Ftroubleshooting.html%23agat-throws-features-out-because-child-features-are-not-provided&data=04%7C01%7Ckmkocot%40ua.edu%7C85529bc2cc9f4ce1e64508d97f372ea8%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637680698957892346%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=93e0pFslVN4PkKv660M0cBxpwuMgQik7c%2BLL9sej0RI%3D&reserved=0" target="_blank">
https://agat.readthedocs.io/en/latest/troubleshooting.html#agat-throws-features-out-because-child-features-are-not-provided</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I invite you to open an issue in the AGAT GitHub repository.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Once the file is parsed correctly you can use the script <a href="https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fagat_sp_alignment_output_style.pl%2F&data=04%7C01%7Ckmkocot%40ua.edu%7C85529bc2cc9f4ce1e64508d97f372ea8%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637680698957902343%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=tSctIFDYhbO97GAYSExqE9qfmwVVQofA6r5%2FsyS971Q%3D&reserved=0" target="_blank">
agat_sp_alignment_output_style.pl</a> to turn level1 feature types (e.g. gene) and level2 feature types (e.g. mRNA) into match and match_part features respectively as it can be preferred by MAKER.<o:p></o:p></p>
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<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
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<p class="MsoNormal"><span style="color:black">Best regards,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:black"><br>
Jacques Dainat, Ph.D.<o:p></o:p></span></p>
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</div>
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</div>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 22 Sep 2021, at 18:21, Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">I’d have to see the GFF, but in general you should organize sequence alignments as match/match_part features.
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Here is n example from the GFF3 format specification:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:Courier">ctg123 . cDNA_match 1200 9000 . . . ID=cDNA00001</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:Courier">ctg123 . match_part 1200 3200 2.2e-30 + . ID=match00002;Parent=cDNA00001;Target=mjm1123.5 5 506;Gap=M301 D1499 M201</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:Courier">ctg123 . match_part 7000 9000 7.4e-32 - . ID=match00003;Parent=cDNA00001;Target=mjm1123.3 1 502;Gap=M101 D1499 M401</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Also make sure you are not inadvertently using GFF2 or GTF. They are not backwards compatible with GFF3.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">—Carson<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Sep 22, 2021, at 8:06 AM, Kevin Kocot <<a href="mailto:kmkocot@ua.edu" target="_blank">kmkocot@ua.edu</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Thanks Carson,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">I think I see the problem now. Here's what I'm getting:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">-----<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt">STATUS: Parsing control files...
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">STATUS: Processing and indexing input FASTA files...<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt">STATUS: Setting up database for any GFF3 input...<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt">A data structure will be created for you at:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">/home/wirenia/Desktop/2021-08-11_MAKER_Dreissena_rostriformis/PGA_assembly_shortened_headers.fasta.maker.output/PGA_assembly_shortened_headers.fasta_datastore<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt">To access files for individual sequences use the datastore index:<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt">/home/wirenia/Desktop/2021-08-11_MAKER_Dreissena_rostriformis/PGA_assembly_shortened_headers.fasta.maker.output/PGA_assembly_shortened_headers.fasta_master_datastore_index.log<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt">STATUS: Now running MAKER...<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt">examining contents of the fasta file and run log<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">--Next Contig--<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Processing run.log file...<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">#---------------------------------------------------------------------<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Now retrying the contig!!<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">SeqID: PGA_scaffold0<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Length: 141759199<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Tries: 5!!<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">#---------------------------------------------------------------------<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">setting up GFF3 output and fasta chunks<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">prepare section files<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Gathering GFF3 input into hits - chunk:0<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">ERROR: Non-unique top level ID for match.19561.56<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">While this is technically legal in GFF3, it usually<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">indicates a poorly fomatted GFF3 file (perhaps you<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">tried to merge two GFF3 files without accounting for<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">unique IDs). MAKER will not handle these correctly.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">--> rank=NA, hostname=wirenia<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">ERROR: Failed while prepare section files<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">ERROR: Chunk failed at level:12, tier_type:3<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">FAILED CONTIG:PGA_scaffold0<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">ERROR: Chunk failed at level:4, tier_type:0<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">FAILED CONTIG:PGA_scaffold0<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">examining contents of the fasta file and run log<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt">-----<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">It looks like maker doesn't like the format of the exonerate gff3 I am using. I tried 'fixing' it with
<a href="https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fagat_convert_sp_gxf2gxf.pl%2F&data=04%7C01%7Ckmkocot%40ua.edu%7C85529bc2cc9f4ce1e64508d97f372ea8%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637680698957902343%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=B0rz4C4QHRD6CKNShj0asmj7Ryjwg9pY8561f3u1QY4%3D&reserved=0" target="_blank">
agat_convert_sp_gxf2gxf.pl</a>, which seemed to work on my Braker output, but that just produced an empty gff3 file for both my exonerate and PASA gff3 files. Any advice on how to prepare exonerate or PASA gff3 files for Maker?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">Thanks!<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">Kevin<o:p></o:p></span></p>
<div class="MsoNormal" align="center" style="text-align:center"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">
<hr size="2" width="1440" style="width:15.0in" align="center">
</span></div>
<div id="gmail-m_-3511602195170912938x_divRplyFwdMsg">
<p class="MsoNormal"><b>From:</b> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br>
<b>Sent:</b> Monday, September 20, 2021 8:06 AM<br>
<b>To:</b> Kevin Kocot <<a href="mailto:kmkocot@ua.edu" target="_blank">kmkocot@ua.edu</a>><br>
<b>Cc:</b> <a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a> <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<b>Subject:</b> [EXTERNAL] Re: [maker-devel] Troubleshooting Maker failure<span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"> <o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">Hi Kevin,
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">The files are already being skipped because of previous failures. Can you increase the try count (-t on the command line) to something like 6, and send me the STDERR after
it generates a new failure.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">—Carson <o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">Sent from my iPhone<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">On Sep 20, 2021, at 4:56 AM, Kevin Kocot <<a href="mailto:kmkocot@ua.edu" target="_blank">kmkocot@ua.edu</a>> wrote:<o:p></o:p></span></p>
</blockquote>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Tahoma",sans-serif"></span><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Thanks Carson! I've uploaded that file here:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/round1_run_maker_try2.log" target="_blank">http://genomes.ua.edu/Kocot/2021-09-10_Maker/round1_run_maker_try2.log</a><o:p></o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<div class="MsoNormal" align="center" style="text-align:center"><span style="font-size:12.0pt">
<hr size="2" width="1440" style="width:15.0in" align="center">
</span></div>
<p class="MsoNormal"><b><span style="font-size:12.0pt">From:</span></b><span style="font-size:12.0pt"> Carson Holt<br>
<b>Sent:</b> Tuesday, September 14, 2021 9:51 PM<br>
<b>To:</b> Kevin Kocot<br>
<b>Cc:</b> <a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br>
<b>Subject:</b> [EXTERNAL] Re: [maker-devel] Troubleshooting Maker failure <o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">What I really need is the captured STDERR from the failed run.
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">—Carson<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">On Sep 10, 2021, at 9:19 AM, Kevin Kocot <<a href="mailto:kmkocot@ua.edu" target="_blank">kmkocot@ua.edu</a>> wrote:<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Hi Carson and all,</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">I ran Maker 3.01.03 on a chromosome-level mollusc genome assembly using some evidence I previously generated with Funannotate and BRAKER2, but Maker is not completing successfully. Every scaffold in the datastore_index.log
file has both STARTED and FAILED statuses. I can't figure out where the problem lies, though. Running ./Build status indicates all the dependencies are there (I’m not using MPI). The run.log files just ends with "DIED RANK 0" and "DIED COUNT 3." Is there a
way to tell which (if any) of the dependencies is misbehaving here (they all seem to run fine independently) or if my evidence .gff3 files are not correctly formatted?</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">I’ve uploaded a zipped sample output folder as well as my config files and the datastore.log file here: <a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/" target="_blank"><span style="color:#0563C1">http://genomes.ua.edu/Kocot/2021-09-10_Maker/</span></a></span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Any guidance on what might be the issue would be greatly appreciated.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Thanks!</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Kevin</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p style="mso-margin-top-alt:7.5pt;margin-right:0in;margin-bottom:0in;margin-left:0in;background:white">
<b><span style="font-size:12.0pt;font-family:"Helvetica",sans-serif;color:#990000">Kevin M. Kocot<br>
</span></b><span style="font-size:8.0pt;font-family:"Helvetica",sans-serif;color:black">he/him/his</span><o:p></o:p></p>
<p style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:7.5pt;margin-left:0in;background:white">
<span style="font-size:11.5pt;font-family:"Helvetica",sans-serif;color:black">Associate Professor & Curator of Invertebrates<br>
Department of Biological Sciences & Alabama Museum of Natural History<br>
</span><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:black"><a href="https://www.ua.edu/" target="_blank"><span style="color:maroon;text-decoration:none">The University of Alabama</span></a> <br>
307 Mary Harmon Bryant Hall<br>
Box 870344<br>
Tuscaloosa, AL 35487<br>
phone <a href="tel:205-348-4052" target="_blank"><span style="color:#0563C1">205-348-4052</span></a> </span><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:maroon">|</span><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:black"> fax
205-348-4039 <br>
<a href="mailto:kmkocot@ua.edu" target="_blank"><span style="color:#0563C1">kmkocot@ua.edu</span></a> </span><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:maroon">|</span><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:black"> <a href="https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kocotlab.com%2F&data=04%7C01%7Ckmkocot%40ua.edu%7C85529bc2cc9f4ce1e64508d97f372ea8%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637680698957912339%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=FeO70rdCHrVvvb5U2LGq8mKGyxTyLkFmUYtgkqCNpS0%3D&reserved=0" target="_blank">www.kocotlab.com</a><br>
</span><span style="font-family:"Helvetica",sans-serif;color:black"><a href="https://uasystem.zoom.us/j/3755490727" target="_blank"><span style="color:#0563C1">https://uasystem.zoom.us/j/3755490727</span></a></span><o:p></o:p></p>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
maker-devel mailing list<br>
<a href="mailto:maker-devel@yandell-lab.org" target="_blank"><span style="color:#0563C1">maker-devel@yandell-lab.org</span></a><br>
<a href="https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fyandell-lab.org%2Fmailman%2Flistinfo%2Fmaker-devel_yandell-lab.org&data=04%7C01%7Ckmkocot%40ua.edu%7C85529bc2cc9f4ce1e64508d97f372ea8%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637680698957912339%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rvorqh%2BD%2F7wdmEOxgzJPpawKx8%2BSfJd4TprNQsrW5%2Bk%3D&reserved=0" target="_blank">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a><o:p></o:p></span></p>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
<p class="MsoNormal">_______________________________________________<br>
maker-devel mailing list<br>
<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br>
<a href="https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fyandell-lab.org%2Fmailman%2Flistinfo%2Fmaker-devel_yandell-lab.org&data=04%7C01%7Ckmkocot%40ua.edu%7C85529bc2cc9f4ce1e64508d97f372ea8%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637680698957922331%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=cBQCSaxMVhTsdrN4W4O6l9ZPtc4OV8OlRVyS4a3aCr4%3D&reserved=0" target="_blank">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a><o:p></o:p></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
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</div>
</blockquote>
</div>
</blockquote>
</div>
<p class="MsoNormal"><br clear="all">
<br>
-- <o:p></o:p></p>
<div>
<p class="MsoNormal">Jacques Dainat<o:p></o:p></p>
</div>
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