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annotate test-data/sistr-results-AE014613-699860.tabular @ 6:cf767360ede1 draft default tip

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planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
author nml
date Fri, 20 Dec 2024 18:34:03 +0000
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cf767360ede1 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
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1 antigenic_formula cgmlst_ST cgmlst_distance cgmlst_found_loci cgmlst_genome_match cgmlst_matching_alleles cgmlst_subspecies fasta_filepath genome h1 h2 mash_distance mash_genome mash_match mash_serovar mash_subspecies o_antigen qc_messages qc_status serogroup serovar serovar_antigen serovar_cgmlst
cf767360ede1 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
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2 -:-:- 0.8272727272727273 58 2014-LET-0419 57 enterica /tmp/tmp656s4p6h/files/9/9/2/dataset_99219622-876a-4d86-831f-68e03402a64e.dat AE014613-699860 - - 1.0 0 - FAIL: Large number of cgMLST330 loci missing (n=272 > 30) | FAIL: Wzx/Wzy genes missing. Cannot determine O-antigen group/serogroup. Cannot accurately predict serovar from antigen genes. | INFO: Number of cgMLST330 loci found (n=58) | WARNING: H1 antigen gene (fliC) missing. Cannot determine H1 antigen. Cannot accurately predict serovar from antigen genes. | WARNING: Input genome size (699860 bp) not within expected range of 4000000-6000000 (bp) for Salmonella | WARNING: Only matched 57 cgMLST330 loci. Min threshold for confident serovar prediction from cgMLST is 297.0 FAIL - -:-:- -:-:- Typhi