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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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config-metawrap file not recognized after editing #553

Open tga2taa opened 2 weeks ago

tga2taa commented 2 weeks ago

I have Metawrap installed on a cluster by: conda install -y -c ursky metawrap-mg=1.3.2. Using which config-metawrap, I found the location of the file as: /work/myname/opt/metawrap-env/bin/config-metawrap

To start using the NCBI database option, I moved the file from the cluster to BBEdit on my local computer then edited the bottom two lines which read now, pointing to the database locations: BLASTDB=/work/myname/2metawrap/NCBI_nt TAXDUMP=/work/myname/2metawrap/NCBI_tax

Saved the file, then moved it back to its original location. I can see the file listed under /bin and typing cat config-metawrap shows the file contents exactly as it was edited.

However, config-metawrap is now not found by typing which config-metawrap. When trying to start Metawrap, there is an error message: cannot find config-metawrap file - something went wrong with the installation!

Previously Metawrap was working fine until CheckM in the pipeline. I don't know if this has anything to do with the issue, but when initially downloaded and opened, the config-metawrap file showed as an executable Unix file (as interpreted by my Mac) which required admin privileges for opening. It still showed as such after saving it with the same name after editing it (this is the file uploaded back). However, after re-downloading from the cluster my local computer is opening it without an admin warning and my Mac interprets it as a regular txt file. Did something inadvertently change in the file format? Nothing else in the file was edited besides the bottom two lines of text.

Advice is greatly appreciated!

tga2taa commented 5 days ago

In case anyone runs into this issue: it was resolved by making the file executable by: chmod +x config-metawrap