<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="">If you disabled evidence for round 3 (i.e. protein= and est=) then you will get no annotations and EVM will not run. You can look at the GFF3 in a browser, and if you see that there are no protein/est alignments, then that is likely why.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 15, 2019, at 2:48 PM, Brandon Pickett <<a href="mailto:pickettbd@gmail.com" class="">pickettbd@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Good afternoon!</div><div class=""><br class=""></div><div class="">I just finished my third round of maker. I trained snap, augustus, etc. between the rounds. I used fasta_merge and gff3_merge to extract files after each round of maker. gff3_merge performed as expected each time, but fasta_merge surprised me. I will show you which files fasta_merge generated after each round. Please note that, as many people do, I renamed my output files from the default. Accordingly, I will list all the files with a generalized prefix of "maker" and show the rest of the file name as it was generated for me. Also note that I've changed .fasta to .fa for brevity.</div><div class=""><br class=""></div><div class="">After round #1:</div><div class="">transcripts.fa</div><div class="">proteins.fa</div><div class=""><br class=""></div><div class="">After round #2:</div><div class="">non_overlapping_ab_initio.proteins.fa<br class="">non_overlapping_ab_initio.transcripts.fa<br class="">transcripts.fa<br class="">augustus_masked.proteins.fa<br class="">augustus_masked.transcripts.fa<br class="">evm.proteins.fa<br class="">evm.transcripts.fa<br class="">genemark.proteins.fa<br class="">genemark.transcripts.fa<br class="">snap_masked.proteins.fa<br class="">snap_masked.transcripts.fa<br class="">proteins.fa</div><div class=""><br class=""></div><div class="">After round #3:</div><div class="">non_overlapping_ab_initio.proteins.fa<br class="">non_overlapping_ab_initio.transcripts.fa<br class="">augustus_masked.proteins.fa<br class="">augustus_masked.transcripts.fa<br class="">genemark.proteins.fa<br class="">genemark.transcripts.fa<br class="">snap_masked.proteins.fa<br class="">snap_masked.transcripts.fa</div><div class=""><br class=""></div><div class="">I am unsurprised that I didn't get all these files after round #1 because I used round #1 to generate gene models from transcript evidence. I didn't expect so many files after round #2 (having only seen the output from round #1 up to that point), but it makes sense that I would get output from augustus, evidence modeler (evm), genemark, and snap since I provided them as input to this round (#2) of maker. Between rounds #2 and #3, I re-trained snap and augustus. Genemark was trained between rounds #1 and #2 without gene models from maker and thus did not require re-training. The only difference in my maker control files between rounds #2 and #3 were the paths to the snap and augustus files. In both #2 and #3, the control files had run_evm=1. I can provide my control files for each round, if needed. <b class="">My question is why transcripts.fa, proteins.fa, evm.proteins.fa, and evm.transcripts.fa were not generated after round #3? </b>I recognize that this is probably not an error, rather a lack of my understanding of when each file is and is not generated.</div><div class=""><br class=""></div><div class="">Thank you,</div><div class="">Brandon Pickett<br class=""></div><br class=""></div>
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