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Clinical-Genomics / microSALT

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
GNU General Public License v3.0
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Blast db creation bug #138

Closed talnor closed 2 years ago

talnor commented 3 years ago

Describe the bug A clear and concise description of what the bug is.

Running microSALT manually, the following error message appears during the reference updates: BLAST Database creation error: Multi-letters chain PDB id is not supported in v4 BLAST DB

To Reproduce Steps to reproduce the behavior:

  1. Start any case with microSALT manually

Expected behavior Update should finish without the error message.

Screenshots

microSALT analyse /home/proj/production/microbial/queries/ACC8133A95.json --input /home/proj/production/microbial/fastq/usablegoblin/ACC8133A95/
INFO - Checking versions of references.. WARNING - Unable to find requested organism 'SARS-CoV-2' in pubMLST database INFO - pubMLST reference for Enterobacter cloacae updated to 2021-06-30 from 2021-06-23 INFO - Re-indexed contents of /home/proj/production/microbial/references/ST_loci/enterobacter_cloacae INFO - pubMLST reference for Enterococcus faecium updated to 2021-06-29 from 2021-06-23 INFO - Re-indexed contents of /home/proj/production/microbial/references/ST_loci/enterococcus_faecium INFO - pubMLST reference for Glaesserella parasuis updated to 2021-06-29 from 2021-03-25 BLAST Database creation error: Multi-letters chain PDB id is not supported in v4 BLAST DB INFO - Re-indexed contents of /home/proj/production/microbial/references/ST_loci/glaesserella_parasuis INFO - pubMLST reference for Pseudomonas aeruginosa updated to 2021-07-01 from 2021-06-23 INFO - Re-indexed contents of /home/proj/production/microbial/references/ST_loci/pseudomonas_aeruginosa INFO - pubMLST reference for Salmonella spp. updated to 2021-07-01 from 2021-06-25 INFO - Re-indexed contents of /home/proj/production/microbial/references/ST_loci/salmonella_spp. INFO - pubMLST reference for Staphylococcus aureus updated to 2021-06-29 from 2021-06-25 INFO - Re-indexed contents of /home/proj/production/microbial/references/ST_loci/staphylococcus_aureus INFO - pubMLST reference for Staphylococcus epidermidis updated to 2021-06-28 from 2021-06-26 INFO - Re-indexed contents of /home/proj/production/microbial/references/ST_loci/staphylococcus_epidermidis INFO - pubMLST reference for Streptococcus pneumoniae updated to 2021-06-29 from 2021-06-09 INFO - Re-indexed contents of /home/proj/production/microbial/references/ST_loci/streptococcus_pneumoniae INFO - Downloading new MLST profiles for Escherichia coli#1 INFO - Re-indexed contents of /home/proj/production/microbial/references/ST_loci/escherichia_coli WARNING - Unable to update pubMLST external data: HTTP Error 503: Service Unavailable INFO - Cached resFinder database identical to remote. INFO - Version check done. Creating sbatch jobs INFO - Created runfile for sample ACC8133A95 in folder /home/proj/production/microbial/results//ACC8133A95_2021.7.2_15.4.9 INFO - Saved Trailblazer slurm report file to /home/proj/production/microbial/results/reports/trailblazer/ACC8133A95_slurm_ids.yaml and /home/proj/production/microbial/results/ACC8133A95_2021.7.2_15.4.9/ACC8133A95_slurm_ids.yaml INFO - Execution finished!

Software version (please complete the following information):

Additional context Error appear to be species specific. Might be affecting Glaesserella parasuis analayses.

talnor commented 3 years ago

Reference update successful on 2021-08-19:

INFO - Checking versions of references..
WARNING - Unable to find requested organism 'SARS-CoV-2' in pubMLST database
INFO - pubMLST reference for Enterococcus faecium updated to 2021-08-18 from 2021-08-16
INFO - Re-indexed contents of /home/proj/production/microbial/references/ST_loci/enterococcus_faecium
INFO - Cached resFinder database identical to remote.
INFO - Version check done. Creating sbatch jobs
talnor commented 2 years ago

Seems to be working well.