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Thanks Carson,</div>
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I think I see the problem now. Here's what I'm getting:</div>
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STATUS: Parsing control files...
<div>STATUS: Processing and indexing input FASTA files...</div>
<div>STATUS: Setting up database for any GFF3 input...</div>
<div>A data structure will be created for you at:</div>
<div>/home/wirenia/Desktop/2021-08-11_MAKER_Dreissena_rostriformis/PGA_assembly_shortened_headers.fasta.maker.output/PGA_assembly_shortened_headers.fasta_datastore</div>
<div><br>
</div>
<div>To access files for individual sequences use the datastore index:</div>
<div>/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</div>
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<div>STATUS: Now running MAKER...</div>
<div>examining contents of the fasta file and run log</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>--Next Contig--</div>
<div><br>
</div>
<div>Processing run.log file...</div>
<div>#---------------------------------------------------------------------</div>
<div>Now retrying the contig!!</div>
<div>SeqID: PGA_scaffold0</div>
<div>Length: 141759199</div>
<div>Tries: 5!!</div>
<div>#---------------------------------------------------------------------</div>
<div><br>
</div>
<div><br>
</div>
<div>setting up GFF3 output and fasta chunks</div>
<div>prepare section files</div>
<div>Gathering GFF3 input into hits - chunk:0</div>
<div>ERROR: Non-unique top level ID for match.19561.56</div>
<div>While this is technically legal in GFF3, it usually</div>
<div>indicates a poorly fomatted GFF3 file (perhaps you</div>
<div>tried to merge two GFF3 files without accounting for</div>
<div>unique IDs). MAKER will not handle these correctly.</div>
<div><br>
</div>
<div>--> rank=NA, hostname=wirenia</div>
<div>ERROR: Failed while prepare section files</div>
<div>ERROR: Chunk failed at level:12, tier_type:3</div>
<div>FAILED CONTIG:PGA_scaffold0</div>
<div><br>
</div>
<div>ERROR: Chunk failed at level:4, tier_type:0</div>
<div>FAILED CONTIG:PGA_scaffold0</div>
<div><br>
</div>
<div>examining contents of the fasta file and run log</div>
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<div>It looks like maker doesn't like the format of the exonerate gff3 I am using. I tried 'fixing' it with agat_convert_sp_gxf2gxf.pl, 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?<br>
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<div>Thanks!</div>
<div>Kevin<br>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Carson Holt <carsonhh@gmail.com><br>
<b>Sent:</b> Monday, September 20, 2021 8:06 AM<br>
<b>To:</b> Kevin Kocot <kmkocot@ua.edu><br>
<b>Cc:</b> maker-devel@yandell-lab.org <maker-devel@yandell-lab.org><br>
<b>Subject:</b> [EXTERNAL] Re: [maker-devel] Troubleshooting Maker failure</font>
<div> </div>
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<div dir="auto">Hi Kevin,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>—Carson <br>
<br>
<div dir="ltr">Sent from my iPhone</div>
<div dir="ltr"><br>
<blockquote type="cite">On Sep 20, 2021, at 4:56 AM, Kevin Kocot <kmkocot@ua.edu> wrote:<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Thanks Carson! I've uploaded that file here:</div>
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<a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/round1_run_maker_try2.log" id="LPlnk439129">http://genomes.ua.edu/Kocot/2021-09-10_Maker/round1_run_maker_try2.log</a><br>
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<br>
<hr tabindex="-1" style="display:inline-block; width:98%">
<b>From:</b> Carson Holt<br>
<b>Sent:</b> Tuesday, September 14, 2021 9:51 PM<br>
<b>To:</b> Kevin Kocot<br>
<b>Cc:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> [EXTERNAL] Re: [maker-devel] Troubleshooting Maker failure
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<div class="x_rps_346f">
<div class="" style="word-wrap:break-word; line-break:after-white-space">What I really need is the captured STDERR from the failed run.
<div class=""><br class="">
</div>
<div class="">—Carson<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Sep 10, 2021, at 9:19 AM, Kevin Kocot <<a href="mailto:kmkocot@ua.edu" target="_blank" rel="noopener noreferrer" class="">kmkocot@ua.edu</a>> wrote:</div>
<br class="x_x_Apple-interchange-newline">
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<span class="" style="font-size:12pt">Hi Carson and all,</span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt"> </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt">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></div>
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<span class="" style="font-size:12pt"> </span></div>
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<span class="" style="font-size:12pt">I’ve uploaded a<span class="" style=""><span class="x_x_Apple-converted-space"> </span>zipped sample output folder as well as my config files</span><span class="x_x_Apple-converted-space"> </span>and the datastore.log file
here:<span class="x_x_Apple-converted-space"> </span><a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/" target="_blank" rel="noopener noreferrer" class="" style="color:rgb(5,99,193); text-decoration:underline">http://genomes.ua.edu/Kocot/2021-09-10_Maker/</a><span class="" style=""></span></span></div>
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<span class="" style="font-size:12pt">Any guidance on what might be the issue would be greatly appreciated.</span></div>
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<span class="" style="font-size:12pt"> </span></div>
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<span class="" style="font-size:12pt">Thanks!</span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt">Kevin</span></div>
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</div>
<p class="x_x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;margin:7.5pt 0in 0in; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<b class=""><span class="" style="font-size:12pt; font-family:Helvetica,sans-serif; color:rgb(153,0,0)">Kevin M. Kocot<br class="">
</span></b><span class="" style="font-size:8pt; font-family:Helvetica,sans-serif">he/him/his</span><b class=""><span class="" style="font-size:12pt; font-family:Helvetica,sans-serif; color:rgb(153,0,0)"></span></b></p>
<p class="x_x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;margin:0in 0in 7.5pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:11.5pt; font-family:Helvetica,sans-serif">Associate Professor & Curator of Invertebrates<br class="">
Department of Biological Sciences & Alabama Museum of Natural History<br class="">
</span><span class="" style="font-size:10.5pt; font-family:Helvetica,sans-serif"><a href="https://www.ua.edu/" target="_blank" rel="noopener noreferrer" class="" style="color:rgb(5,99,193); text-decoration:underline"><span class="" style="color:maroon; text-decoration:none">The
University of Alabama</span></a> <br class="">
307 Mary Harmon Bryant Hall<br class="">
Box 870344<br class="">
Tuscaloosa, AL 35487<br class="">
phone <a href="tel:205-348-4052" target="_blank" rel="noopener noreferrer" class="" style="color:rgb(5,99,193); text-decoration:underline"><span class="" style="">205-348-4052</span></a><span class="x_x_Apple-converted-space"> </span></span><span class="" style="font-size:10.5pt; font-family:Helvetica,sans-serif; color:maroon">|</span><span class="" style="font-size:10.5pt; font-family:Helvetica,sans-serif"><span class="x_x_Apple-converted-space"> </span>fax
205-348-4039 <br class="">
<a href="mailto:kmkocot@ua.edu" target="_blank" rel="noopener noreferrer" class="" style="color:rgb(5,99,193); text-decoration:underline"><span class="" style="">kmkocot@ua.edu</span></a> </span><span class="" style="font-size:10.5pt; font-family:Helvetica,sans-serif; color:maroon">|</span><span class="" style="font-size:10.5pt; font-family:Helvetica,sans-serif"> <a href="https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kocotlab.com%2F&data=04%7C01%7Ckmkocot%40ua.edu%7C076240cd4e344ea3edca08d97c377b07%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637677400014541339%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ZaHL3%2FTQBgdYkf6B7N%2FUKwrwOObDQk%2Fh5O4sd%2FTkAoQ%3D&reserved=0" originalsrc="http://www.kocotlab.com/" shash="cjZdHSsFRMmTFCcGNApSP4OcPJH9lVoRWHcV6V8Fw2BiiKZtUpBCgvzjSxA5JHPPhIrwAkD8Ju/3PK/UmR17vioeU9BRiTna0BnFgmhdKt/vXokjRizHKXvzOcxi4PgvBzyHLHReY82/eRYLa0OCSbNZ5optxLba31nPAhO2Y68=" target="_blank" rel="noopener noreferrer" class="" style="color:rgb(5,99,193); text-decoration:underline"><span class="" style="">www.kocotlab.com</span></a><br class="">
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