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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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subprocess.CalledProcessError #101

Closed ghost closed 1 year ago

ghost commented 3 years ago

Hello, We are facing error: "Failed to mmap memory dataSize=80676316565 File=DRAM_data/database_files/pfam.mmsmsa. Error 12." while preparing for database.

It is halting with "subprocess.CalledProcessError: Command '['mmseqs', 'msa2profile', 'DRAM_data/database_files/pfam.mmsmsa', 'DRAM_data/database_files/pfam.mmspro', '--match-mode', '1', '--threads', '10']' returned non-zero exit status 1."

Any suggestions to resolve it?

shafferm commented 3 years ago

Hi!

How much RAM is available on your system? It looks like there might not be enough RAM assigned to run this step.

Mike

ghost commented 3 years ago

Hello!

Currently, we are using a system with 16GB. What is the minimum RAM requirement while skipping uniref90 and commercial KEGG?

Parth

rmFlynn commented 3 years ago

Unfortunately, even with skipping those databases, you may still need ~64GB for this step. You still have 2 options.

  1. You can try using dram through kbase.
  2. @shafferm has uploaded a minimum database set to zenodo, you can download the files and use DRAM-setup.py set_database_locations to skip this memory intensive step. However, there are problems with this approach, as detailed in this issue thread.

Good luck.

ghost commented 3 years ago

@rmFlynn Thank you. The second option worked for us. We are using DRAMv with the output of virsorter2, but it is giving an error given below:

ValueError: No virsorter calls found in for-dramv/viral-affi-contigs-for-dramv.tab for scaffold V11(paired)_contig_51-cat_1 from input fasta.

If the viral-affi-contigs-for-dramv.tab file is skipped during annotation then it gives an auxiliary score error for the distill module. Is there any way to solve this issue?

rmFlynn commented 3 years ago

In this case the problem could be the "(", ")" characters. If you have not already, run DRAM-v.py remove_bad_characters -v tabfile.tab and clean_tabfile.tab and DRAM-v.py remove_bad_characters -i input_fasta.fa clean_input_fasta.fa this may not remove the parens, so you may need to run your own command replacing "(" and ")" with "_". If running with the cleaned output does not work, then search for any matches in the viral-affi-contigs-for-dramv.tab that have the parens replaced, for example grep "V1_1_.*paired.*_contig_51-cat_1" viral-affi-contigs-for-dramv.tab. If there are no matches, then we need to figure out where that name went.

rmFlynn commented 1 year ago

Looks like this is solved