2021-06-09 14:18:11,612 mob_suite.utils ERROR: Downloading databases failed, please check your internet connection and retry [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:226]
2021-06-09 14:18:11,612 mob_suite.utils ERROR: Process failed with error [Errno 2] No such file or directory: 'mash': 'mash'. Removing lock file [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:227]
Some solutions to try at:
https://githubmemory.com/repo/phac-nml/mob-suite/issues/86
Mine specifically looks like mash is not installed so msh file is not generated causing the error.
$ conda install -c bioconda mash
$ mob_init
2021-06-09 14:51:02,838 mob_suite.utils INFO: Database directory folder already exists at /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/databases [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:133]
2021-06-09 14:51:02,838 mob_suite.utils INFO: Placed lock file at /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/databases/.lock [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:144]
2021-06-09 14:51:02,838 mob_suite.utils INFO: Initializing databases...this will take some time [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:167]
2021-06-09 14:51:02,838 mob_suite.utils INFO: Downloading databases...this will take some time [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:180]
2021-06-09 14:51:02,838 mob_suite.utils INFO: Trying mirror https://share.corefacility.ca/index.php/s/oeufkw5HyKz0X5I/download [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:184]
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 214M 100 214M 0 0 3638k 0 0:01:00 0:01:00 --:--:-- 3942k
2021-06-09 14:52:04,226 mob_suite.utils INFO: Download data.zip sha256 checksum is 92a9008caa2bbc273bdb9cb76c5df001f25d71be819fa85a19f7e6d13e56073c [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:68]
2021-06-09 14:52:04,227 mob_suite.utils INFO: Download data.zip size in bytes is 225377917 [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:69]
2021-06-09 14:52:04,241 mob_suite.utils INFO: Downloading databases successful, now building databases [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:198]
2021-06-09 14:52:04,241 mob_suite.utils INFO: Decompressing /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/databases/data.zip [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:106]
2021-06-09 14:52:04,932 mob_suite.utils INFO: Decompressing /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/databases/ncbi_plasmid_full_seqs.fas.gz [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:106]
2021-06-09 14:52:12,348 mob_suite.utils INFO: Decompressing /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/databases/orit.fas.gz [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:106]
2021-06-09 14:52:12,350 mob_suite.utils INFO: Decompressing /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/databases/rep.dna.fas.gz [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:106]
2021-06-09 14:52:12,372 mob_suite.utils INFO: Decompressing /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/databases/mob.proteins.faa.gz [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:106]
2021-06-09 14:52:12,381 mob_suite.utils INFO: Decompressing /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/databases/repetitive.dna.fas.gz [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:106]
2021-06-09 14:52:12,460 mob_suite.utils INFO: Decompressing /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/databases/mpf.proteins.faa.gz [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:106]
2021-06-09 14:52:12,477 mob_suite.utils INFO: Building repetitive mask database [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:212]
2021-06-09 14:52:12,696 mob_suite.utils INFO: Building complete plasmid database [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:216]
2021-06-09 14:52:17,531 mob_suite.utils INFO: Sketching complete plasmid database [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:220]
2021-06-09 14:52:23,037 mob_suite.utils INFO: Init ete3 library ... [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:232]
NCBI database not present yet (first time used?)
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...
Loading node names...
2334637 names loaded.
247459 synonyms loaded.
Loading nodes...
2334637 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /home/prakki/.etetoolkit/taxa.sqlite ...
2334000 generating entries...
Uploading to /home/prakki/.etetoolkit/taxa.sqlite
Inserting synonyms: 50000 2021-06-09 14:53:57,919 mob_suite.utils ERROR: Init of ete3 library failed with error UNIQUE constraint failed: synonym.spname, synonym.taxid. Removing lock file [in /home/prakki/sw/pyenv/versions/3.6.4/lib/python3.6/site-packages/mob_suite/mob_init.py:238]
