Kat Holt comments

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                                            Kat Holt

Gubbins tree scale?

I wanted to know the answer to this question too! As there was no answer here, I did some digging and found that if you take the Gubbins output file...

Error at first stage of pipeline

I just got this too, with the latest version cloned from the repo. Must be something that was introduced in the last fix David?

Error at first stage of pipeline

I was using V1beta.7 (BlackCat)

Error at first stage of pipeline

Actually I'm not sure if it's the same error. With me it is: Starting pipeline... 19 jobs to be executed in total stage = makeDir Error: command failed: python makeDir.py...

VFDB Parse the cluster output and tabulate the results using the specific Virulence gene DB compatible script:

This looks like a python3 issue - note srst2 is written for python2.

Colistin resistance due to truncation or loss of MgrB or PmrB

The reference sequences are in the /data directory: https://github.com/katholt/Kleborate/blob/master/kleborate/data/MgrB_and_PmrB.fasta

Difference in log files for negatives when using gene_db

OK so if the sams/bams are empty but bowtie2 didn’t error out, it means no reads mapped to your database and it's a true negative. We will add a check...

Port to Python 3 and other changes

Thanks Peter. Converting to py3 is something we know needs to be done, but have been putting off doing ourselves as it was not needed for our own workflows and...

Fos resistance

As you note, fosA is a core gene carried by ~all K. pneumoniae, however at wildtype expresssion levels, this chromosomal gene results in a fosfomycin MIC of only 16-32 mg/L,...

Please port to Python3

Thanks Andreas. I really appreciate this - we simply haven't had time to try porting, but we will do some testing of this patch and hopefully can update srst2 release...