sylvinite
commented
3 years ago Copied from IM:
microSALT analyse /home/proj/stage/microbial/queries/ACC5551.json --input /home/proj/stage/microbial/fastq/ACC5551
INFO - Profile table profile_streptococcus_agalactiae initialized
INFO - Profile table profile_paenibacillus_larvae initialized
INFO - Profile table profile_pasteurella_multocida initialized
INFO - Profile table profile_staphylococcus_epidermidis initialized
INFO - Profile table profile_acinetobacter_baumannii initialized
INFO - Profile table profile_clostridium_difficile initialized
INFO - Profile table profile_staphylococcus_haemolyticus initialized
INFO - Profile table profile_salmonella_spp. initialized
INFO - Profile table profile_streptococcus_uberis initialized
INFO - Profile table profile_citrobacter_freundii initialized
INFO - Profile table profile_streptococcus_zooepidemicus initialized
INFO - Profile table profile_brachyspira_pilosicoli initialized
INFO - Profile table profile_brachyspira_spp. initialized
INFO - Profile table profile_salmonella_enterica initialized
INFO - Profile table profile_glaesserella_parasuis initialized
INFO - Profile table profile_neisseria_spp. initialized
INFO - Profile table profile_klebsiella_aerogenes initialized
INFO - Profile table novel_streptococcus_agalactiae initialized
INFO - Profile table novel_paenibacillus_larvae initialized
INFO - Profile table novel_pasteurella_multocida initialized
INFO - Profile table novel_staphylococcus_epidermidis initialized
INFO - Profile table novel_acinetobacter_baumannii initialized
INFO - Profile table novel_clostridium_difficile initialized
INFO - Profile table novel_staphylococcus_haemolyticus initialized
INFO - Profile table novel_salmonella_spp. initialized
INFO - Profile table novel_streptococcus_uberis initialized
INFO - Profile table novel_citrobacter_freundii initialized
INFO - Profile table novel_streptococcus_zooepidemicus initialized
INFO - Profile table novel_brachyspira_pilosicoli initialized
INFO - Profile table novel_brachyspira_spp. initialized
INFO - Profile table novel_salmonella_enterica initialized
INFO - Profile table novel_glaesserella_parasuis initialized
INFO - Profile table novel_neisseria_spp. initialized
INFO - Profile table novel_klebsiella_aerogenes initialized
INFO - Checking versions of references..
INFO - pubMLST reference for Acinetobacter baumannii updated to 2021-02-17 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/acinetobacter_baumannii
INFO - pubMLST reference for Brachyspira spp. updated to 2012-01-18 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/brachyspira_spp.
INFO - pubMLST reference for Glaesserella parasuis updated to 2021-02-11 from 0
BLAST Database creation error: Multi-letters chain PDB id is not supported in v4 BLAST DB
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/glaesserella_parasuis
INFO - pubMLST reference for Klebsiella aerogenes updated to 2021-02-20 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/klebsiella_aerogenes
INFO - pubMLST reference for Neisseria spp. updated to 2021-03-01 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/neisseria_spp.
INFO - pubMLST reference for Paenibacillus larvae updated to 2020-12-10 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/paenibacillus_larvae
INFO - pubMLST reference for Pasteurella multocida updated to 2021-01-06 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/pasteurella_multocida
INFO - pubMLST reference for Salmonella spp. updated to 2021-03-01 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/salmonella_spp.
INFO - pubMLST reference for Staphylococcus aureus updated to 2021-02-28 from 2021-02-19
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/staphylococcus_aureus
INFO - pubMLST reference for Staphylococcus epidermidis updated to 2021-02-26 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/staphylococcus_epidermidis
INFO - pubMLST reference for Staphylococcus haemolyticus updated to 2021-02-04 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/staphylococcus_haemolyticus
INFO - pubMLST reference for Streptococcus agalactiae updated to 2020-12-22 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/streptococcus_agalactiae
INFO - pubMLST reference for Streptococcus uberis updated to 2021-02-23 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/streptococcus_uberis
INFO - pubMLST reference for Streptococcus zooepidemicus updated to 2021-02-14 from 0
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/streptococcus_zooepidemicus
INFO - Downloading new MLST profiles for Brachyspira pilosicoli
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/brachyspira_pilosicoli
INFO - Downloading new MLST profiles for Citrobacter freundii
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/citrobacter_freundii
INFO - Downloading new MLST profiles for Escherichia coli#1
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/escherichia_coli
INFO - Downloading new MLST profiles for Salmonella enterica
INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/salmonella_enterica
INFO - Cached resFinder database identical to remote.
INFO - Version check done. Creating sbatch jobs
Description
Issues with downloading some references hosted at pubMLST. The main issue is that references are labelled inconsistently by pubMLST. This PR updates the search for correct href links on pubMLST.
Primary function of PR
Test
Sign-offs