mob_recon - conda installation - sqlite/ete3-related issue

[omegatro]

Hello!

While running mob_recon, there was a problem that seems to be related to this unmerged PR in ete3.

• Log:

Not 93_d42b257742c09745af06b059c354537d_circular=false_3834 to cluster AA002 assigned as already present in cluster AA170
Traceback (most recent call last):
  File "/opt/conda/envs/mob_suite_3.1.9/bin/mob_recon", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/conda/envs/mob_suite_3.1.9/lib/python3.11/site-packages/mob_suite/mob_recon.py", line 1400, in main
    build_mobtyper_report(contig_memberships['plasmid'], out_dir, mobtyper_report,contig_seqs, ncbi, lit, ETE3DBTAXAFILE, database_dir)
  File "/opt/conda/envs/mob_suite_3.1.9/lib/python3.11/site-packages/mob_suite/utils.py", line 1080, in build_mobtyper_report
    host_range = hostrange(rep_types, relaxase_types, mob_cluster_id, ncbi, lit, ETE3DBTAXAFILE, database_directory)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/mob_suite_3.1.9/lib/python3.11/site-packages/mob_suite/utils.py", line 254, in hostrange
    'observed_host_range_ncbi_name'] = getTaxonConvergence(ncbi_unique_taxids, ETE3DBTAXAFILE, database_directory)
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/mob_suite_3.1.9/lib/python3.11/site-packages/mob_suite/utils.py", line 167, in getTaxonConvergence
    ranks = ncbi.get_rank(lineage)
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/mob_suite_3.1.9/lib/python3.11/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 201, in get_rank
    result = self.db.execute(cmd)
             ^^^^^^^^^^^^^^^^^^^^
sqlite3.OperationalError: no such column: "1" - should this be a string literal in single-quotes?

• Setup: mob_suite 3.1.9, conda-based installation.

• Temporary work-around: Creating environment definition file, adding - sqlite <= 3.41.2 (did not test other versions) and building from it.

[ricmedveterinario]

If you're experiencing issues running MOB-suite, the solution may be to reinstall the software while ensuring compatibility with its dependencies. Run the following command in your terminal:

mamba install -c bioconda -c conda-forge mob_suite sqlite=3.42.0 pandas=1.5.3 ete3=3.1.3 --yes

This installation ensures that the correct versions of sqlite, pandas, and ete3 are present in your environment, preventing errors related to incompatible dependencies. After reinstalling, try running mob_typer again. 🚀