Error while running mmseqs2

Hi,

When running the following command (either with the test data our with our own data), we obtain this error, which seems to be related to mmseqs2.

Note: the numbers of --threads and/or --splits do not seem to be related as we obtain the same error independently of these parameters. Apart from the following command, we also tried with --threads in {0, 16, 32} and --splits in {0, 16, 32}.

We also checked the conformity of the md5sum of the files downloaded via the plasx setup command.

plasx search_de_novo_families \
    -g $PREFIX-gene-calls.txt \
    -o $PREFIX-de-novo-families.txt \
    --threads $THREADS \
    --splits 32 \
    --overwrite

The error:

Database /lustre04/scratch/luhuizho/MYENV/lib/python3.7/site-packages/plasx/data/PlasX_mmseqs_profiles/clu90.profile needs header information
poll: 1
Deleting temporary directory: /localscratch/luhuizho.37393814.0/tmpyp01fb16
Traceback (most recent call last):
  File "/lustre04/scratch/luhuizho/MYENV/lib/python3.7/site-packages/plasx/mmseqs.py", line 1674, in mmseqs_search
    utils.run_cmd(cmd, verbose=True)
  File "/lustre04/scratch/luhuizho/MYENV/lib/python3.7/site-packages/plasx/utils.py", line 220, in run_cmd
    assert poll==0, 'Did not successfully run command: {}'.format(cmd)
AssertionError: Did not successfully run command: mmseqs convertalis /localscratch/luhuizho.37393814.0/tmpyp01fb16/mmseqs/source_db /lustre04/scratch/luhuizho/MYENV/lib/python3.7/site-packages/plasx/data/PlasX_mmseqs_profiles/clu90.profile /localscratch/luhuizho.37393814.0/tmpyp01fb16/mmseqs/clu90.search /localscratch/luhuizho.37393814.0/tmpyp01fb16/mmseqs/clu90.m8 --format-output query,target,pident,alnlen,mismatch,gapopen,qstart,qend,qlen,tstart,tend,tlen,evalue,bits

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/lustre04/scratch/luhuizho/MYENV/bin/plasx", line 8, in <module>
    sys.exit(run())
  File "/lustre04/scratch/luhuizho/MYENV/lib/python3.7/site-packages/plasx/plasx_script.py", line 140, in run
    args.func(args)
  File "/lustre04/scratch/luhuizho/MYENV/lib/python3.7/site-packages/plasx/plasx_script.py", line 46, in search
    clean_tmp=not args.save_tmp)
  File "/lustre04/scratch/luhuizho/MYENV/lib/python3.7/site-packages/plasx/mmseqs.py", line 1944, in annotate_de_novo_families
    mmseqs_merge_search(mmseqs_source_db, target_db_dir, mmseqs_dir, ident_list, threads=threads, splits=splits, clean_tmp=clean_tmp)
  File "/lustre04/scratch/luhuizho/MYENV/lib/python3.7/site-packages/plasx/mmseqs.py", line 1719, in mmseqs_merge_search
    clean_tmp=clean_tmp)
  File "/lustre04/scratch/luhuizho/MYENV/lib/python3.7/site-packages/plasx/mmseqs.py", line 1678, in mmseqs_search
    raise FileNotFoundError(f"The file {output}.m8 was supposed to be created, but it doesn't exist. This might be because the search using mmseqs2 ran out of system RAM. Consider setting the -S flag to reduce the maximum RAM usage. E.g., if you only have ~8Gb RAM, we recommend setting -S to 32 or higher.")
FileNotFoundError: The file /localscratch/luhuizho.37393814.0/tmpyp01fb16/mmseqs/clu90.m8 was supposed to be created, but it doesn't exist. This might be because the search using mmseqs2 ran out of system RAM. Consider setting the -S flag to reduce the maximum RAM usage. E.g., if you only have ~8Gb RAM, we recommend setting -S to 32 or higher.

We are using a HPC running Linux. We are not allowed to use conda on the HPC. All dependencies (except mmseqs2) were installed via the pip command inside a virtual environnement. mmseqs2 is already installed on the HPC. We are using the same version of the tutorial: mmseqs2/10-6d92c.

Thank you for your help!

michaelkyu / PlasX

Error while running mmseqs2 #7