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iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
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Wrong covg in JSON for specific sample #60

Closed iqbal-lab closed 9 years ago

iqbal-lab commented 9 years ago

Mykrobe.predictor.tb --file /Net/wombat/dipro/mmm/gorm/v3/dat/Mtub/stampy/00020000/C00020636_R00000039.bam --install_dir ~/dev/git/Mykrobe-predictor { "expected_depth": "5", <<<<<<<<<< ???? Sample is 200x "mean_read_length": "150", "phylogenetics": { "phylo_group": { "MTBC": "207" }, "species": { "M. bovis": "70" }, "lineage": { "Unknown Lineage": "-1" } }, "susceptibility" :{ "Isoniazid": "S", "Rifampicin": "S", "Ethambutol": "S", "Pyrazinamide": "R", "Quinolones": "S", "Streptomycin": "S", "Amikacin": "S", "Capreomycin": "S", "Kanamycin": "S" }, "called_variants" :{ "pncA_H57D" :{ "R_per_cov": "100", "S_per_cov": "0", "R_median_cov": "194", "S_median_cov": "0", "conf": "1079", "induced_resistance": "Pyrazinamide" } }, "called_genes" :{ }, "virulence_toxins" :{ } }

iqbal-lab commented 9 years ago

Not a bug - I ran the ONT branch on illumina sequence