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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
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No alias or index file found for nucleotide database `ERROR` #129

Closed juliofdiaz closed 1 year ago

juliofdiaz commented 1 year ago

Hi devs,

I'm running mob v. 3.1.0 . When I run mob_recon, it seems to complete successfully with the following message.

2023-02-14 00:24:27,762 mob_suite.mob_recon INFO: MOB-recon completed and results written to /well/aanensen/projects/amr-landscape/mob-recon/klebsiella_pneumoniae/results/SRR6656623 [in /apps/eb/testing/skylake/software/MOB-suite/3.1.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/mob_suite/mob_recon.py:1445]

However, when I look at the log I see the following ERROR and WARNING messages:

2023-02-14 00:23:26,440 root ERROR: blastn on db /well/aanensen/projects/amr-landscape/mob-recon/klebsiella_pneumoniae/results/SRR6656623/__tmp/fixed.input.fasta and query /well/aanensen/shared/software/mob_database/2023-02-09/repetitive.dna.fas STDERR: b'BLAST Database error: No alias or index file found for nucleotide database [/well/aanensen/shared/software/mob_database/2023-02-09/repetitive.dna.fas] in search path [/gpfs3/well/aanensen/projects/amr-landscape/mob-recon/klebsiella_pneumoniae/scripts::]\n' [in /apps/eb/testing/skylake/software/MOB-suite/3.1.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/mob_suite/blast/__init__.py:160]
2023-02-14 00:23:26,441 root INFO: Filtering repetitive blast results /well/aanensen/projects/amr-landscape/mob-recon/klebsiella_pneumoniae/results/SRR6656623/__tmp/repetitive_blast_results.txt  [in /apps/eb/testing/skylake/software/MOB-suite/3.1.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/mob_suite/utils.py:1272]
2023-02-14 00:23:26,441 root WARNING: No BLASTN results to parse from file /well/aanensen/projects/amr-landscape/mob-recon/klebsiella_pneumoniae/results/SRR6656623/__tmp/repetitive_blast_results.txt [in /apps/eb/testing/skylake/software/MOB-suite/3.1.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/mob_suite/blast/__init__.py:181]

Could you help me understand this error, and whether it may have an effect on the results?

All the best

jrober84 commented 1 year ago

Hello, this issue is resolved in v. 3.1.4, please update to that and try again.

juliofdiaz commented 1 year ago

Thanks for the response @jrober84 . I'll try that. In the meantime, does this problem alter the results? Asking because it may take a me a bit to get the newer version installed.

jrober84 commented 1 year ago

The missing repetitive element "error" is pointing to an incorrectly setup database. It can affect the results since it would mask contigs that are just IS/TE etc from forming plasmids by themselves. So I would recommend first trying mob_init again and making sure that the blast database for /well/aanensen/shared/software/mob_database/2023-02-09/repetitive.dna.fas is constructed. Or you can call makeblastdb on the file directly makeblastdb -in /well/aanensen/shared/software/mob_database/2023-02-09/repetitive.dna.fas -dbtype nucl to make sure it is initialized.