Question: GeneMark-ES exits with "error, file not found: info/training.fna"
gravatar for gauravdube007
9 months ago by
gauravdube0070 wrote:

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

error, file not found: info/training.fna

To run the program, I am using the following command:

./ --ES --fungus --sequence CBS_contigs.fasta.masked

The log file 'gmes.log' contains the following: : [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 : [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 : [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 : [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 : [Mon Jul 17 14:19:06 2017] /home/gaurav/2_GeneMark_results/gmes_petap/ --in data/dna.fna --out info/dna.gc.csv --w 1000,8000 : [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.

ADD COMMENTlink written 9 months ago by gauravdube0070

Do you have info/training.fna in the directory from where you are running the prog?

ADD REPLYlink written 9 months ago by Santosh Anand3.4k

Hi Santosh, I don't have training.fna in the 'info' directory. The following files are present in the info/ directory: training.trace, dna.trace, dna.multi_fasta, dna.general, dna.gc.csv, dna.gap_distr.

Please find my update below.

ADD REPLYlink modified 9 months ago • written 9 months ago by gauravdube0070

Update: After posting, I have used the same command on another assembly which has better genome statistics than the previous one and it worked !!! It seems the problem is with 'probuild', as it requires atleast 10Mb of good data for training (ref: []), which could not be retrieved from the poor assemblies. So now the question is what tool should I use to get the best out of even the poor assemblies. Thanks all.

ADD REPLYlink written 9 months ago by gauravdube0070

You might want to open a new question, and reference this one.

ADD REPLYlink written 9 months ago by

Agree with Open a new thread or change the subject line according to the new knowledge

ADD REPLYlink written 9 months ago by Santosh Anand3.4k
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