Model training with AED=0.7 made all contigs FAILED

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Model training with AED=0.7 made all contigs FAILED

lahcen campbell

Apologies this message was sent earlier today from an incorrect email address so it was flagged for verification. 

Hi folks,

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 gene models

           24,613 genes with 49,547 transcripts containing 141130 cds.

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" / "model_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                                                  <
> Contact: [hidden email]                        <

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