Model training with AED=0.7 made all contigs FAILED
Apologies this message was sent earlier today from an incorrect email address so it was flagged for verification.
I would just like some insight into a recent round of MAKER
annotation I performed and returned back 0 Finished contigs.
The genome is a white fly, which I successfully ran MAKE initially 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
24,613 genes with 49,547 transcripts containing
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.
I checked the run today and all ~8,000 contigs/scaffolds returned
as FAILED with all having tried to be retried once each. (Note I retried to run this time reverting the AED to 1, yet the same outcome happened again).
The following error appears throughout the log file:
MAKER WARNING: The file MAKER.contigs_datastore/BF/41/tig00000234//theVoid.tig00000234/0/tig00000234.0.all.rb.out
did not finish on the last run and must be erased
My initial feeling was, I feared I have just lost my initial set
of 24,613 gene models. I now 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 ? Are they retrievable ?
I had capturd all 1st round MAKER output files (GFF, Fasta files
etc) before attempting this 2nd round (i.e. 1st round of model
training) of MAKER .
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" /
As it stands, maker2zff and fasta_merge / gff3_merge all return nothing or empty output files. So clearly my gene models have been altered somehow.
Any advice on this would be much appreciated.
========================================== > Dr. Lahcen Campbell <