<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">The error is coming from Augustus. There is a problem with the species file you selected. Or you put it in the wrong place.<div><br></div><div>This is the error —> </div><div><font face="Courier New">Could not find the config file /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/BUSCO_evans_trout_hap1/BUSCO_evans_trout_hap1_parameters.cfg</font><br><div><br></div><div>The species info must exist under this base directory by default (it’s where you let MAKER install Augustus) —> /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/</div><div><br></div><div>You can also place the species files somewhere else but you need to set the AUGUSTUS_CONFIG_PATH so Augustus knows where to look.</div><div><br></div><div>Example (in your ~/.bash_profile):</div><div><font face="Courier New">export AUGUSTUS_CONFIG_PATH=$HOME/muy_augustus_species</font></div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br><blockquote type="cite"><div>On Aug 11, 2023, at 7:20 AM, Hayley Mangelson <hayley@phasegenomics.com> wrote:</div><br class="Apple-interchange-newline"><div><div dir="ltr">Hi Carson,<div><br></div><div>Sure thing! Sorry for the delay, I was on vacation. I reran with just a single scaffold. Here is the STDERR.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jul 31, 2023 at 12:06 PM Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="auto">Can you send me the STDERR from the maker run? If you don’t have it, run maker again with the output from the screen redirected to a file. Example —> maker &> all_output.txt<div><br><div dir="ltr">--Carson<div><br></div><div>Sent from my iPhone</div></div><div dir="ltr"><br><blockquote type="cite">On Jul 31, 2023, at 10:04 AM, Hayley Mangelson <<a href="mailto:hayley@phasegenomics.com" target="_blank">hayley@phasegenomics.com</a>> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="ltr">Hi!<br><br>I am trying to get a fresh install of MAKER to work for me and am having a few issues. <br><br>1. I got MAKER installed (I thought) and now the log is saying all contigs failed. See attached log.<br>2. Having tried several versions and methods of installation, I cannot get multithreading to work.<br><br>Could you help me work through these issues?<br clear="all"><div>Thanks,<br><br>Hayley</div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><font color="#666666">Hayley Mangelson<br></font></div><div><font color="#666666">Senior Bioinformatics Lead</font></div><div><font color="#666666">Phase Genomics, Inc</font></div><div><a href="http://www.phasegenomics.com/" style="color:rgb(17,85,204)" target="_blank">www.phasegenomics.com</a><font color="#666666"><br></font></div><div><br></div></div></div></div></div></div></div>
<div><PGA_assembly_hap1_master_datastore_index.log></div><span>_______________________________________________</span><br><span>maker-devel mailing list</span><br><span><a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a></span><br><span><a href="http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a></span><br></div></blockquote></div></div></blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><font color="#666666">Hayley Mangelson<br></font></div><div><font color="#666666">Senior Bioinformatics Lead</font></div><div><font color="#666666">Phase Genomics, Inc</font></div><div><a href="http://www.phasegenomics.com/" style="color:rgb(17,85,204)" target="_blank">www.phasegenomics.com</a><font color="#666666"><br></font></div><div><br></div></div></div></div></div></div>
<span id="cid:f_ll6m87vq0"><all_output.txt></span></div></blockquote></div><br></div></body></html>