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nigyta / dfast_core

DDBJ Fast Annotation and Submission Tool
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Prodigal version could not be determined #48

Open mariafpv opened 3 months ago

mariafpv commented 3 months ago

Hello, I am trying to use metaphor with my data. I installed it in a cluster (NAME="CentOS Linux", VERSION="8", PLATFORM_ID="platform:el8") using conda. I used DFAST with the default configuration, and it worked very well. However, when I specified Prodigal for metagenomes, 

dfast -g $fasta_file --use_prodigal --metagenome -o $mag_output_dir

I encountered the following error:

Checking Prodigal version... Prodigal version could not be determined. Aborted...

I understand that an additional installation of Prodigal should not be necessary. Do you know how I could solve this issue? Thanks!

nigyta commented 3 months ago

Thank you for using DFAST. If you have installed DFAST with conda, prodigal can be found in your PATH. Please type prodigal to confirm if it is installed properly. If prodigal installed with conda does not work, you can manually install and put it in your PATH. Alternatively, you can put the prodigal binary under DFAST_INSTA_DIR/bin/Linux, which will be automatically added to PATH when running DFAST.

mariafpv commented 3 months ago

Thanks for your answer. I just installed Prodigal in my DFAST environment and is working.

Thanks!