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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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<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="" style="word-wrap:break-word; line-break:after-white-space">What I really need is the captured STDERR from the failed run.
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<div class="">—Carson<br class="">
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<div class="">On Sep 10, 2021, at 9:19 AM, Kevin Kocot <<a href="mailto:kmkocot@ua.edu" target="_blank" rel="noopener noreferrer" data-auth="NotApplicable" class="">kmkocot@ua.edu</a>> wrote:</div>
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<span class="" style="font-size:12pt">Hi Carson and all,</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 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_Apple-converted-space"> </span>zipped sample output folder as well as my config files</span><span class="x_Apple-converted-space"> </span>and the datastore.log file
here:<span class="x_Apple-converted-space"> </span><a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/" target="_blank" rel="noopener noreferrer" data-auth="NotApplicable" 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">Thanks!</span></div>
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<span class="" style="font-size:12pt">Kevin</span></div>
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<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>
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<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" data-auth="NotApplicable" 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" data-auth="NotApplicable" class="" style="color:rgb(5,99,193); text-decoration:underline"><span class="" style="">205-348-4052</span></a><span class="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_Apple-converted-space"> </span>fax
205-348-4039 <br class="">
<a href="mailto:kmkocot@ua.edu" target="_blank" rel="noopener noreferrer" data-auth="NotApplicable" 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="http://www.kocotlab.com/" target="_blank" rel="noopener noreferrer" data-auth="NotApplicable" class="" style="color:rgb(5,99,193); text-decoration:underline"><span class="" style="">www.kocotlab.com</span></a><br class="">
</span><span class="" style="font-family:Helvetica,sans-serif"><a href="https://uasystem.zoom.us/j/3755490727" target="_blank" rel="noopener noreferrer" data-auth="NotApplicable" class="" style="color:rgb(5,99,193); text-decoration:underline"><span class="" style="">https://uasystem.zoom.us/j/3755490727</span></a></span></p>
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<a href="mailto:maker-devel@yandell-lab.org" target="_blank" rel="noopener noreferrer" data-auth="NotApplicable" class="" style="color:rgb(5,99,193); text-decoration:underline; font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">maker-devel@yandell-lab.org</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
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