<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">There is probably an issue with the GFF3 file being passed in (I’m guessing the Augustus one). I would avoid passing in Augustus results as GFF3, it removes the ability of MAKER to dynamically provide Augustus with hints as it runs. You are essentially handicapping the pipeline.<div class=""><br class=""></div><div class="">If your first genes were est2genome or protein2genome based, I would not pass them back in. Those models are suitable for training but will really reduce the accuracy of downstream final annotations (that is why we tell people to turn off est2genome/protein2genome after training a gene predictor in the MAKER documentation). Also if your inputs to the first round were GFF3 files it will have to be reread regardless. Any protein or transcript data that was aligned by MAEKR will still have the BLAST results archived, so you don’t need to worry about that unless you alter repeat masking options (which would cause it to rerun). Also if you are changing GFF3 file input between runs but using the same directory, you might want to delete any “.db” files in the output folder. those hold an SQLite database of the GFF3 input that may be corrupted if it failed while attempting to update the database content with the Augustus gff3 file.</div><div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 9, 2017, at 4:13 AM, Lahcen Campbell <<a href="mailto:lcampbell@ebi.ac.uk" class="">lcampbell@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="content-type" content="text/html; charset=utf-8" class="">
<div text="#000000" bgcolor="#FFFFFF" class=""><p class="">Hi folks,</p><p class="">I would just like some insight into a recent round of MAKER
annotation I performed and returned back 0 Finished contigs. <br class="">
</p><p class="">The genome is a white fly, which I successfully ran MAKER on
initally with the first round of "Evidence in", so passing in EST
evidence as aligned transcript gffs, protein homology evidence
etc. The run was successful and produced a lot of good quality
gene models</p><div class="">
<br class="webkit-block-placeholder"></div>
<div style="-en-clipboard:true;" class="">Statistics:
</div>
<div class=""> 24,613 genes with 49,547 transcripts containing
141130 cds.<br class="">
<br class="">
Now, I know this count is very high for our species, so in the 2nd
round (completed running over 1 night due to all contigs failing)
I attempted to increase the threshold for support, by reducing AED
to 0.7 from an initial 1. Prior to starting the second round I had
trained SNAP on the first round results and also ran Augustus
separately and passed this via the snaphmm, pred_gff option.
Finally I set min protein to be no less than 100Aa and set
est2genome and prot2genome off to allow for gene model refinement.
<br class="">
<br class="">
I checked the run today and all ~8,000 contigs/scaffolds returned
as FAILED with all having tried to be retried once each. <br class="">
<br class="">
My initial feeling was, I feared I have just lost my initial set
of 24,613 gene models. I know believe that this won't be the case
but Im not sure... Can anyone explain what might have happened
here and what consequences will follow given they all returned as
failed ? Have they been deleted from the MAKER data store ? <br class="">
<br class="">
I had capturdD all 1st round MAKER output files (GFF, Fasta files
etc) before attempting this 2nd round (i.e. 1st round of model
training) of MAKER . <br class="">
<br class="">
If I have irrevocably changed the datastore for MAKER and lost
those genes, might I be able to restore to an earlier point (say
back to the first round of evidence in gene models) by passing the
first MAKER gff in as "maker_gff=" / "pred_pass=1" /
"model_pass=1" ? <br class="">
<br class="">
Any advice on this would be much appreciated<br class="">
Lahcen<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
</div>
</div>
_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></div></body></html>