Lock file is created in /usr/local/ though the database is in a different directory

[vbrover]

$ /usr/local/mob-suite/3.0.3/bin/mob_recon --infile skesa/SRR7653407  --outdir SRR7653407.mob_recon  -n 16 --database_directory /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/home/brovervv/PD-plasmid/mob.data 
2021-10-07 10:29:29,427 mob_suite.mob_recon INFO: MOB-recon version 3.0.2  [in /usr/local/mob-suite/3.0.3/lib/python3.9/site-packages/mob_suite/mob_recon.py:983]
2021-10-07 10:29:29,457 mob_suite.mob_recon INFO: SUCCESS: Found program blastn at /usr/bin/blastn [in /usr/local/mob-suite/3.0.3/lib/python3.9/site-packages/mob_suite/utils.py:571]
2021-10-07 10:29:29,457 mob_suite.mob_recon INFO: SUCCESS: Found program makeblastdb at /usr/bin/makeblastdb [in /usr/local/mob-suite/3.0.3/lib/python3.9/site-packages/mob_suite/utils.py:571]
2021-10-07 10:29:29,458 mob_suite.mob_recon INFO: SUCCESS: Found program tblastn at /usr/bin/tblastn [in /usr/local/mob-suite/3.0.3/lib/python3.9/site-packages/mob_suite/utils.py:571]
2021-10-07 10:29:29,459 mob_suite.mob_recon INFO: Processing fasta file skesa/SRR7653407 [in /usr/local/mob-suite/3.0.3/lib/python3.9/site-packages/mob_suite/mob_recon.py:1004]
2021-10-07 10:29:29,459 mob_suite.mob_recon INFO: Analysis directory SRR7653407.mob_recon [in /usr/local/mob-suite/3.0.3/lib/python3.9/site-packages/mob_suite/mob_recon.py:1005]
2021-10-07 10:29:29,470 root INFO: Creating Lock file /usr/local/mob-suite/3.0.3/lib/python3.9/site-packages/mob_suite/databases/ETE3_DB.lock [in /usr/local/mob-suite/3.0.3/lib/python3.9/site-packages/mob_suite/utils.py:438]
Traceback (most recent call last):
  File "/usr/local/mob-suite/3.0.3/bin/mob_recon", line 8, in <module>
    sys.exit(main())
  File "/usr/local/mob-suite/3.0.3/lib/python3.9/site-packages/mob_suite/mob_recon.py", line 1096, in main
    dbstatus = ETE3_db_status_check(1, ETE3_LOCK_FILE, ETE3DBTAXAFILE, logging)
  File "/usr/local/mob-suite/3.0.3/lib/python3.9/site-packages/mob_suite/utils.py", line 439, in ETE3_db_status_check
    open(file=lockfilepath, mode="w").close()
OSError: [Errno 30] Read-only file system: '/usr/local/mob-suite/3.0.3/lib/python3.9/site-packages/mob_suite/databases/ETE3_DB.lock'

[kbessonov1984]

Thank you for reaching to us. Yes, the tool tries the default location to place the .lock file. Nevertheless your instance should still run even on read-only file system. Is that the case? My understanding that you have database files in other than default directory and you are just concerned about this error message? The .lock mechanism was more designed for HPC system when several tool instances could trigger ETE3 library update and crush the server. Let us know more specifics please and will try to fix this minor issue in the next release

[vbrover]

Nevertheless your instance should still run even on read-only file system. Is that the case?

Yes, and the creatiion of the lock ETE3_DB.lock breaks.
Ideally, I would suppress creating this lock file because we are not updating the ETE3 library while running mob_recon.

[jrober84]

The issue is that ETE3 will trigger its own update if it detects there has been a change in the NCBI database. I have removed the locking mechanism from the new pending release but there is a risk to cascade multiple attempts to update the ncbi taxonomy database