<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">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" class="">kmkocot@ua.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt;" class="">Hi Carson and all,<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt;" class="">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?<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt;" class="">I’ve uploaded a<span style="" class=""><span class="Apple-converted-space"> </span>zipped sample output folder as well as my config files</span><span class="Apple-converted-space"> </span>and the datastore.log file here:<span class="Apple-converted-space"> </span><a href="http://genomes.ua.edu/Kocot/2021-09-10_Maker/" style="color: rgb(5, 99, 193); text-decoration: underline;" class="">http://genomes.ua.edu/Kocot/2021-09-10_Maker/</a><span style="" class=""></span><o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt;" class="">Any guidance on what might be the issue would be greatly appreciated.<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt;" class="">Thanks!<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt;" class="">Kevin</span><o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><p class="MsoNormal" style="margin: 7.5pt 0in 0in; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;"><b class=""><span style="font-size: 12pt; font-family: Helvetica, sans-serif; color: rgb(153, 0, 0);" class="">Kevin M. Kocot<br class=""></span></b><span style="font-size: 8pt; font-family: Helvetica, sans-serif;" class="">he/him/his</span><b class=""><span style="font-size: 12pt; font-family: Helvetica, sans-serif; color: rgb(153, 0, 0);" class=""><o:p class=""></o:p></span></b></p><p class="MsoNormal" style="margin: 0in 0in 7.5pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;"><span style="font-size: 11.5pt; font-family: Helvetica, sans-serif;" class="">Associate Professor & Curator of Invertebrates<br class="">Department of Biological Sciences & Alabama Museum of Natural History<br class=""></span><span style="font-size: 10.5pt; font-family: Helvetica, sans-serif;" class=""><a href="https://www.ua.edu/" style="color: rgb(5, 99, 193); text-decoration: underline;" class=""><span style="color: maroon; text-decoration: none;" class="">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" style="color: rgb(5, 99, 193); text-decoration: underline;" class=""><span style="" class="">205-348-4052</span></a><span class="Apple-converted-space"> </span></span><span style="font-size: 10.5pt; font-family: Helvetica, sans-serif; color: maroon;" class="">|</span><span style="font-size: 10.5pt; font-family: Helvetica, sans-serif;" class=""><span class="Apple-converted-space"> </span>fax 205-348-4039 <br class=""><a href="mailto:kmkocot@ua.edu" style="color: rgb(5, 99, 193); text-decoration: underline;" class=""><span style="" class="">kmkocot@ua.edu</span></a> </span><span style="font-size: 10.5pt; font-family: Helvetica, sans-serif; color: maroon;" class="">|</span><span style="font-size: 10.5pt; font-family: Helvetica, sans-serif;" class=""> <a href="http://www.kocotlab.com/" style="color: rgb(5, 99, 193); text-decoration: underline;" class=""><span style="" class="">www.kocotlab.com</span></a><br class=""></span><span style="font-family: Helvetica, sans-serif;" class=""><a href="https://uasystem.zoom.us/j/3755490727" style="color: rgb(5, 99, 193); text-decoration: underline;" class=""><span style="" class="">https://uasystem.zoom.us/j/3755490727</span></a></span><o:p class=""></o:p></p><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); 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