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<p class="MsoNormal"><span style="font-size:11.0pt">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I am encountering some issues running MAKER on my Mac.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I’ve run MAKER in the past, and I was even able to run MAKER very quickly (I think less than 1 minute) for 1 of my 2 assemblies.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">For the successful run, I installed some headers from
</span><span style="font-size:11.5pt;font-family:"Arial",sans-serif;color:#242729;background:white">/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg</span><span style="font-size:11.0pt">, and MAKER worked (but the files were
not visible on my PC). Actually, on my Mac, I could see from my terminal, but not even through the Mac file browser (after a restart).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I’ve attached a copy of my configuration files, and I am running MAKER with the following command:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%">/opt/maker/bin/maker -nolock -fix_nucleotides<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I upgraded my OS within the past few months, but it seems like there is some issue with the permissions for the files being created.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I testing running MAKER from my Mac’s local hard drive (instead of the network folder). However, the run time is considerably longer than the assembly that ran to completion (but those .gff file is not visuable
through several interfaces, for some reason).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt">For example, MAKER has been stuck on this step since last Friday (for a 45,013 bp sequence), whereas annotation for a larger sequence completed within minutes:<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt"><o:p> </o:p></span></b></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">STATUS: Parsing control files...</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">WARNING: You have chosen to turn locking off which may create</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">race conditions if running in parallel.</span></span></span><span class="apple-converted-space"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">
</span></span></span><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">You have been warned.</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p2"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">STATUS: Processing and indexing input FASTA files...</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">STATUS: Setting up database for any GFF3 input...</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">A data structure will be created for you at:</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">/Users/cwarden/Documents/MAKER/AC270418_270441.maker.output/AC270418_270441_datastore</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p2"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">To access files for individual sequences use the datastore index:</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">/Users/cwarden/Documents/MAKER/AC270418_270441.maker.output/AC270418_270441_master_datastore_index.log</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p2"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">STATUS: Now running MAKER...</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">examining contents of the fasta file and run log</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p2"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="p2"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="p2"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">--Next Contig--</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p2"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">#---------------------------------------------------------------------</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">Now starting the contig!!</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">SeqID: AC270418_270441</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">Length: 45015</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="p1"><span class="s1"><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><span style="color:windowtext">#---------------------------------------------------------------------</span></span></span><span style="color:#A6A6A6;mso-style-textfill-fill-color:#A6A6A6;mso-style-textfill-fill-alpha:100.0%"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Can you please help me troubleshoot this issue?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank You,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Charles</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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