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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
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No read out for 1 gene of the MLST scheme #103

Open mdiricks opened 3 years ago

mdiricks commented 3 years ago

Hi, I created a new scheme for Mabscessus with scheme definitions from Pasteur (instead of pubMLST). I followed the instructions on how to do that and the new database is visible with mlst --list | grep MabscessusPasteur. I am also able to run mlst on fasta files and st.out indicates that all alleles were found Found exact allele match MabscessusPasteur.argH-1 ... Found exact allele match MabscessusPasteur.purH-1 However, in the summary file, the allele for purH is not mentioned while the allele numbers for all other genes are... Example output for 1 strain: ERR1413175_Assembly_Shovill_spades.fasta MabscessusPasteur - argH(4) cya(4) glpK(5) gnd(7) murC(15) pta(8) purH This happens for all my samples (tried it in a sample set of 40 and another one of 1800) No idea what is going wrong. Using the database from pubMLST already included in mlst (mabscessus) runs without problems.