Mercurial > repos > nml > sistr_cmd

diff test-data/sistr-results.tabular @ 4:17fcac7ddf54 draft

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"planemo upload commit 5d0cc76371b061089f1399d21aea86540cbcab4f"
author nml
date Thu, 06 Aug 2020 11:48:49 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sistr-results.tabular	Thu Aug 06 11:48:49 2020 -0400
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+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	/galaxy/database/files/000/dataset_695.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