config.yaml not found or is it found?

[ycsong]

Hello,

I was able to have metaGEM installed in the internal server in our lab. I am going through the tutorials (https://github.com/franciscozorrilla/unseenbio_metaGEM using the set of data that I have in our internal server. I am particularly interested in binning the contigs using metabat.

bash metaGEM.sh -t metabat -j 1 -c 24 -m 80 -h 10

I noticed in the standard output messages that config.yaml wasn’t found (although I am sure I set it up before running the code.:

Proceeding with metabat job(s) ... 
 
Please verify parameters set in the config.yaml file: 
 
paste: config.yaml: No such file or directory
 
Please pay close attention to make sure that your paths are properly configured!
Do you wish to proceed with this config.yaml file? (y/n)y

I don’t understand the last line of the message, because it seems like it is using config.yaml from somewhere although it says previously that no such file or directory exists.

Also, if I were to submit this job to one of the clusters in our server (instead of running it on our log-in node), would this prevent the job from running in interactive mode (i.e. would this circumvent the y/n questions?)

If you could help me clarify these questions, it would be helpful.

Thank you,

Young

[franciscozorrilla]

Hey Young,

Based on your error message, it looks like your config.yaml file is not present in the same directory as your the metaGEM.sh wrapper script. To verify this, simply list the files in your directory ls -la or ll, as shown in this section of the tutorial you are referencing.

Thank you for bringing this bug my attention, as it is a small inconsistency that was generated after remodelling the metaGEM repository structure to be compliant with the Snakemake workflow catalogue rules.

I will fix this issue ASAP and make a note of it in the tutorial, but for now please modify the following line in your metaGEM.sh script:

metaGEM/workflow/metaGEM.sh

Line 270 in 978ae33

paste config.yaml

to:

paste ../config/config.yaml

This should work for you assuming that your files are in the same structure as the repository files.

Thanks again for opening a discussion on this topic!
Best,
Francisco

[franciscozorrilla]

fixed in #151 , thanks again for pointing out this bug :)