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Old 07-17-2017, 02:05 AM   #1
gauravdube
Junior Member
 
Location: India

Join Date: Feb 2014
Posts: 7
Default GeneMark-ES exits with "error, file not found: info/training.fna"

Dear All,
I am trying to use GeneMark-ES Suite 4.32 to predict genes from a fungal genome. But GeneMark exits with:

Quote:
error, file not found: info/training.fna
To run the program, I am using the following command:

PHP Code:
./gmes_petap.pl --ES --fungus --sequence CBS_contigs.fasta.masked 
The log file 'gmes.log' contains the following:

Quote:
gmes_petap.pl : [Mon Jul 17 14:19:04 2017] /home/gaurav/2_GeneMark_results/gmes_petap/probuild --reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/dna.trace --in /home/gaurav/1_Masking_Genome/CBS/CBS_contigs.fasta.masked

gmes_petap.pl : [Mon Jul 17 14:19:04 2017] /home/gaurav/2_GeneMark_results/gmes_petap/probuild --seq data/dna.fna --allow_x --stat info/dna.general

gmes_petap.pl : [Mon Jul 17 14:19:05 2017] /home/gaurav/2_GeneMark_results/gmes_petap/probuild --seq data/dna.fna --allow_x --stat_fasta info/dna.multi_fasta

gmes_petap.pl : [Mon Jul 17 14:19:05 2017] /home/gaurav/2_GeneMark_results/gmes_petap/probuild --seq data/dna.fna --allow_x --substring_n_distr info/dna.gap_distr

gmes_petap.pl : [Mon Jul 17 14:19:06 2017] /home/gaurav/2_GeneMark_results/gmes_petap/gc_distr.pl --in data/dna.fna --out info/dna.gc.csv --w 1000,8000

gmes_petap.pl : [Mon Jul 17 14:19:06 2017] /home/gaurav/2_GeneMark_results/gmes_petap/probuild --seq /home/gaurav/2_GeneMark_results/gmes_petap/data/dna.fna --split dna.fa --max_contig 5000000 --min_contig 50000 --letters_per_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n --trace ../../info/training.trace
I have tried troubleshooting this error, but it did not resolved. Please help me resolve this error. Let me know if you need any further information. (I have even configured GeneMark-ET with the Braker pipeline, it works fantastic there. But I don't know what's the problem with GeneMark-ES over here.) Any help is appreciated. Thanks in advance.
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