search

Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
Other
363 stars 81 forks source link

Error, file not found: data/training.fna #704

Open SowmyaPulapet opened 12 months ago

SowmyaPulapet commented 12 months ago

Hi,

I have been using Braker2 for quite a while now. Right now I am working on a quite fragmented genome of size ~1 GB. I used Braker2 but couldn't run it past some issue related to GC content.

Now I installed Braker3 and am facing an issue while using it. The command I used is as follows:

perl /tools/BRAKER-3.06/scripts/braker.pl --genome=./scafSeq_masked.fasta --prot_seq=Metazoa.fa --AUGUSTUS_CONFIG_PATH=/tools/Augustus/config/ --AUGUSTUS_BIN_PATH=/tools/Augustus/bin/ --AUGUSTUS_SCRIPTS_PATH=/tools/Augustus/scripts/ --GENEMARK_PATH=/tools/gmes_linux_64_4/ --PROTHINT_PATH=/tools/ProtHint/bin/ --TSEBRA_PATH=/tools/TSEBRA/bin/ --threads=16 --gff3

I am getting the following error in GeneMark-ES.stderr:

error, file not found: data/training.fna

These are the last few lines from my braker.log: 

#**********************************************************************************
#                               PROCESSING HINTS                                   
#**********************************************************************************
#Thu Nov 16 11:11:22 2023: Running ProtHint to produce hints from protein sequence file (this may take a couple of hours)...
# Thu Nov 16 11:11:37 2023: Running Genemark-ES for ProtHint...
# Thu Nov 16 11:11:37 2023: Executing GeneMark-ES
# Thu Nov 16 11:11:37 2023: changing into GeneMark-ES directory /braker/GeneMark-ES
cd /braker/GeneMark-ES
# Thu Nov 16 11:11:37 2023: Executing gmes_petap.pl
perl /tools/gmes_linux_64_4/gmes_petap.pl --verbose --cores=16 --ES --gc_donor 0.001 --sequence=/braker/genome.fa  --soft_mask auto 1>/braker/GeneMark-ES.stdout 2>/braker/errors/GeneMark-ES.stderr

I am also attaching the complete log braker.log

My genome is already repeatmasked using RepeatMasker. Kindly help me to solve this issue.

Thank you.

SowmyaPulapet commented 11 months ago

Hi,

I still haven't solved this issue. Patiently waiting for your reply.

SaelinB commented 11 months ago

I was getting this same error because the largest contig in my assembly was <50kb and apparently GeneMark needs contigs > 50kb for training.