Question: Error in gene prediction using BRAKER
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gravatar for tt.tolassa
4 months ago by
tt.tolassa0
tt.tolassa0 wrote:

Hello, I am running braker with a portion of Egrandis genome using braker along with protein file from Arabidopsis to obtain gene prediction files.

I used: braker.pl --genome=genome.fa --prot_seq=proteins.fa --epmode --cores=15 --softmasking --workingdir=workdir --prg=gth --gff3

[Thu Jun 18 18:45:15 2020] 58787/58787 (100%) pairs aligned [Thu Jun 18 18:45:15 2020] Alignment of pairs finished [Thu Jun 18 18:45:15 2020] Translating coordinates from local pair level to contig level [Thu Jun 18 18:45:16 2020] Finished spliced alignment [Thu Jun 18 18:45:16 2020] Processing the output [Thu Jun 18 18:45:21 2020] Output processed [Thu Jun 18 18:45:21 2020] ProtHint finished.

Use of uninitialized value $evidence_hints in concatenation (.) or string at /home/tamene/anaconda3/envs/braker2/bin/braker.pl line 6174.

The following error has been produced at the end.

Thu Jun 18 19:12:43 2020: ERROR: in file /home/tamene/anaconda3/envs/braker2/bin/braker.pl at line 7099

Training gene file in genbank format /home/tamene/braker2/braker_geneprediction/braker/train.f.gb does not contain any training genes. Possible known cause: no training genes with sufficient extrinsic evidence support or of sufficient length were produced by GeneMark-ES/ET. If you think this is the cause for your problems, consider running BRAKER with different evidence or without any evidence (--esmode) for training.

I wonder if someone could forward suggestion of help in this regard, Thank you

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