Describe the bug
AMR genes reported in the _srst2.gamma output are missing from the _summaryline.tsv report, despite meeting all of the filtering requirements listed in the v1.1.0 update.
Below is the output of the _summaryline.tsv file:
<html xmlns:v="urn:schemas-microsoft-com:vml"
xmlns:o="urn:schemas-microsoft-com:office:office"
xmlns:x="urn:schemas-microsoft-com:office:excel"
xmlns="http://www.w3.org/TR/REC-html40">
Describe the bug AMR genes reported in the _srst2.gamma output are missing from the _summaryline.tsv report, despite meeting all of the filtering requirements listed in the v1.1.0 update.
Below is the output of the _summaryline.tsv file: <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">
ID | Auto_QC_Outcome | Warning_Count | Estimated_Coverage | Genome_Length | Assembly_Ratio_(STDev) | #_of_Scaffolds_>500bp | GC_% | Species | Taxa_Confidence | Taxa_Source | Kraken2_Trimd | Kraken2_Weighted | MLST_Scheme_1 | MLST_1 | MLST_Scheme_2 | MLST_2 | GAMMA_Beta_Lactam_Resistance_Genes | GAMMA_Other_AR_Genes | AMRFinder_Point_Mutations | Hypervirulence_Genes | Plasmid_Incompatibility_Replicons | Auto_QC_Failure_Reason -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- isolate1 | PASS | 2 | 49.3 | 2815991 | 0.9944 (.0847) | 13 | 32.73 | Staphylococcus aureus | 94.31 ANI_match | ANI_REFSEQ | Staphylococcus(94.31%) aureus(41.63%) | Staphylococcus(100.00%) aureus(100.00%) | saureus | ST5 | - | - | blaI_of_Z_NG_047499.1,blaZ_29_JDXN01000019 | apH-Stph_HE579073,dha1_BA000018,fexA_JQ041372,fosB-Saur_NG_065844.1,lmrS_CP000046.1,mepA_BA000018.3,norA_D90119,tet(38)_NG_048133.1,tet(M)_NG_048223.1 | repUS43_1_CDS12738(DOp1),rep20_7_repA(SAP074A)