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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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Database preparation error 3 #195

Closed woodoo46 closed 1 year ago

woodoo46 commented 1 year ago

Hi there,

I am trying to run do database preparation as following:

DRAM-setup.py prepare_databases --output_dir ${outdir} --skip_uniref

But I had the following error:

subprocess.CalledProcessError: Command '['mmseqs', 'msa2profile', 'DRAM_data2/database_files/pfam.mmsmsa', 'DRAM_data2/database_files/pfam.mmspro', '--match-mode', '1', '--threads', '10']' returned non-zero exit status 3.

Thanks.

George

rmFlynn commented 1 year ago

Can you run mmseqs msa2profile DRAM_data2/database_files/pfam.mmsmsa DRAM_data2/database_files/pfam.mmspro --match-mode 1 --threads 10 I need more information and dram unfortunately obscures command line output. This will tell us if one of your files failed to download or if mmseqs is not installed.

woodoo46 commented 1 year ago

Thanks for your quick reply. I got it, it is because of lack of memory. Initially I ran as posted with 10 threads, it failed. I then tried with 2 threads, it used about 100g memory and still running.

George

rmFlynn commented 1 year ago

The memory problem is a big issue! Thanks!