Mark Renton

install by conda with spades-3.13, same error as above. downgrade to 3.11, everything is fine now.

right now I use this revised mlst-download_pub_mlst nasty script to grab pubmlst data. ```bash #!/bin/bash set -e OUTDIR=pubmlst mkdir -p "$OUTDIR" wget --no-clobber -P "$OUTDIR" http://pubmlst.org/data/dbases.xml for URL in $(grep...

> To make sure 'mlst-make_blast_db' functions correctly, one suggestion I would make here is to alter: > > ``` > echo "(cd '$PROFILEDIR' && echo "$URL" && wget -q '$URL'...

It's look like differ version of samtools or other type thing. I dont recommend REALPHY as a SNP calling pipeline with no long-term software stability. Sometimes if the tools is...

I have a closed issue when running on shell, the locus alignment file return nothing so that AlleleCallEvaluator returned wrong "Core-genome Neighbor-Joining Tree". By checking the codes I found out...

first of all, I recommend you install 1.17 version of samtools and bcftools. And I got the similar problem in my new installation. Check the result if you run: ```...