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annotate test-data/sistr-results.tab @ 0:ebee10be4297 draft

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planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
author nml
date Wed, 01 Mar 2017 12:35:39 -0500
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ebee10be4297 planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
nml
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1 cgmlst_distance cgmlst_genome_match cgmlst_matching_alleles cgmlst_subspecies fasta_filepath genome h1 h2 mash_distance mash_genome mash_match mash_serovar o_antigen qc_messages qc_status serogroup serovar serovar_antigen serovar_cgmlst
ebee10be4297 planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
nml
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2 0.827272727273 73530 57 enterica /mnt/ssd240/work/repos/galaxy_tools/tools/sistr_cmd/test-data/AE014613-699860.fasta AE014613-699860 - - 0.0637124 60369 151 Typhi - 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. | 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