Mercurial > repos > nml > sistr_cmd

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
author nml
date Fri, 20 Dec 2024 18:34:03 +0000
parents
children
line wrap: on
line source

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
-:-:-		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