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medema-group / bigslice

A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data
GNU Affero General Public License v3.0
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Running on a job queue / non-interactive environment #63

Open cmfield opened 1 year ago

cmfield commented 1 year ago

When you provide an output folder path that already exists, the program checks whether it's ok to use this folder, asking for input Y/N. This doesn't work in a non-interactive environment, such as in a job queue on a cluster.

For now, the simple solution is not to create the output folder in advance. Better if you could automatically refuse to write to an existing folder unless an argument flag is set?

Caiyulu-818 commented 1 year ago

I use the query mode with the script bigslice --query ~/data1/LUCY/done_antismash/mag_gbk/ /efs/lucy1 -t 8 --program_db_folder /home/ec2-user/miniconda3/bin/bigslice-models but with the error "Output folder didn't exists! BiG-SLiCE run failed."

And I have tried not to create the output folder in advance, and create the output folder. I always meet this error. Could you offer any tips about this problem?

Caiyulu-818 commented 1 year ago

I use the query mode with the script bigslice --query ~/data1/LUCY/done_antismash/mag_gbk/ /efs/lucy1 -t 8 --program_db_folder /home/ec2-user/miniconda3/bin/bigslice-models but with the error "Output folder didn't exists! BiG-SLiCE run failed."

And I have tried not to create the output folder in advance, and create the output folder. I always meet this error. Could you offer any tips about this problem?