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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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Fail in processing vogdb #341

Open ShangLiii opened 3 months ago

ShangLiii commented 3 months ago

I tried a lot of times to install dram (v.1.4.6) but failed at the step of vogdb. the error is "subprocess.SubprocessError(f"The subcommand {' '.join(command)} experienced an error" Does anyone know what is the problem and how to fix this? Here is what I have got:

2024-04-01 14:16:54,384 - Processing vogdb 2024-04-01 14:17:24,864 - The subcommand ['hmmpress', '-f', './DRAM_db/vog_latest_hmms.txt'] experienced an error: Error: File format problem in trying to open HMM file ./DRAM_db/vog_latest_hmms.txt. File exists, but appears to be empty?

Traceback (most recent call last): File "/data2/lishang/miniconda3/envs/DRAM/bin/DRAM-setup.py", line 184, in File "/data2/lishang/miniconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/database_processing.py", line 555, in prepare_databases File "/data2/lishang/miniconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/database_processing.py", line 317, in process_vogdb File "/data2/lishang/miniconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/utils.py", line 71, in run_process raise subprocess.SubprocessError(f"The subcommand {' '.join(command)} experienced an error, see the log for more info.") subprocess.SubprocessError: The subcommand hmmpress -f ./DRAM_db/vog_latest_hmms.txt experienced an error, see the log for more info.

yaojian1997 commented 2 months ago

I also meet this problem.

anbadilla commented 2 months ago

I'm facing the same problem when running DRAM through Atlas-Metagenome.

schmigle commented 2 months ago

See my solution here: https://github.com/WrightonLabCSU/DRAM/issues/340

Seems to be linked to a directory structure mismatch

sahilrishav2 commented 2 months ago

I also faced the same issue

SilasK commented 1 week ago

I think we found an solution to this issue. https://github.com/metagenome-atlas/atlas/issues/718

@WrightonLabAdmin would it be possible to release a v 1.4.7 with this small fix? It would solve some problems at metagenome atlas.

sahilrishav2 commented 1 week ago

Actually, i was also able to solve the problem