Error on database

[portillanath]

We are having an error on database, the prgramme is not reading correctly the kmer_size.txt file, but this is fine. Where is the error? Thanks

[Oliver-Lorenz-dev]

Hello,

We are now maintaining a new version of SeroBA which has an updated database and output file structure: https://github.com/sanger-bentley-group/seroba

The docker image is stored here - https://hub.docker.com/r/sangerbentleygroup/seroba

The database is prebuilt in the image (/seroba/database)

Could you try running this version of SeroBA?

You will need to mount the directory where your reads are stored when you run the docker image as well, otherwise you will get no such file errors as you have here.

E.g.

docker run --rm -it -v /path/to/reads:/data sangerbentleygroup/seroba seroba runSerotyping /seroba/database /data/read_1.fastq.gz /data/read_2.fastq.gz /data/output_folder

Hope this helps.

Oli