Skip to content

Issue with DRAM-setup.py in uniref database #4

@beadelcor

Description

@beadelcor

Hi!

First, thanks for developing this program, seems really cool. My problem: I've been trying to install the databases for DRAM with this command:

DRAM-setup.py prepare_databases --output_dir DRAM_data

I have not used the conda option for installing DRAM, as it wasn't working for me, but the git option has seemed to work. Once I run the command above I get this error:

2020-04-13 17:23:14.769752: Database preparation started Traceback (most recent call last): File "/srv/home/s4566521/.conda/envs/DRAM/bin/DRAM-setup.py", line 7, in <module> exec(compile(f.read(), __file__, 'exec')) File "/srv/home/s4566521/software/DRAM/scripts/DRAM-setup.py", line 136, in <module> args.func(**args_dict) File "/srv/home/s4566521/software/DRAM/mag_annotator/database_processing.py", line 437, in prepare_databases output_dbs['uniref_db_loc'] = download_and_process_uniref(uniref_loc, temporary, uniref_version=uniref_version, File "/srv/home/s4566521/software/DRAM/mag_annotator/database_processing.py", line 110, in download_and_process_uniref download_file(uniref_url, uniref_fasta_zipped, verbose=verbose) File "/srv/home/s4566521/software/DRAM/mag_annotator/utils.py", line 28, in download_file run_process(['wget', '-O', output_file, url], verbose=verbose) File "/srv/home/s4566521/software/DRAM/mag_annotator/utils.py", line 39, in run_process return subprocess.run(command, check=check, shell=shell, stdout=subprocess.PIPE, File "/srv/home/s4566521/.conda/envs/DRAM/lib/python3.8/subprocess.py", line 512, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['wget', '-O', 'DRAM_data/database_files/uniref90.fasta.gz', 'ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz']' returned non-zero exit status 4.

Do you know what I'm doing wrong? Everything seemed pretty straightforward but I can't get past this step.

Thanks very much

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions