VOGDB issue--extra enclosing folder

[schmigle]

After repeatedly running into the following error when trying to extract the VOG databases:

The subcommand ['hmmpress', '-f', 'DRAM_data/vog_latest_hmms.txt'] experienced an error:
Error: File format problem in trying to open HMM file DRAM_data/vog_latest_hmms.txt.
File exists, but appears to be empty?

I finally tracked it down to the concatenation function at line 377 in the process_vogdb function in database_processing.py:

merge_files(glob(path.join(hmm_dir, 'VOG*.hmm')), vog_hmms)

Since decompressing the tarball vog.hmm.tar.gz produces a folder hmm inside whatever folder it gets assigned to, there's nothing to merge, and hmmpress comes up empty. To work properly, I slightly rewrote this function to add in the extra folder:

merge_files(glob(path.join(hmm_dir, 'hmm/VOG*.hmm')), vog_hmms)

I don't know what's causing this discrepancy, but I hope this problem and solution are helpful if anyone runs into a similar problem.

[anbadilla]

thanks @schmigle Can confirm it works!

[ghost]

Could you show me the path to this file? I installed DRAM throught conda.

[sahilrishav2]

your path should be like this : /home/your username/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_processing.py replace 'your username' with the actual username. If you are using miniconda then there would be miniconda3 otherwise anaconda3.

then you can use text editor like nano or gedit to edit the line number 376

[crane90]

worked perfectly for me !