jordanlab/stringmlst_datasets

stringMLST datasets

stringMLST datasets

This repository houses pre-built pubMLST databases for stringMLST. Please see the releases section for pre-built databases: https://github.com/jordanlab/stringMLST_datasets/releases

The datafiles are updated weekly on Saturday

We recommend building a new database any time stringMLST is run, or daily if under continual use, to ensure the most up to date definitions as possible

stringmlst_datasets's Issues

pip cache dir corrupted -> cron failure

pip's cache directory contains malformed HTTP cache objects

Fixes:

1. Remove existing cache
2. Add timeout to pip install command
3. If timeout exceeded, remove cache and retry

Broken build env on thebeast

The build environment for the datasets was broken during an upgrade to anaconda3

Leptospira spp dataset 1

Dear developers,
I am trying to characterize a strain of Leptospira with Leptospira spp dataset 1, but when I run the prediction I got the following error:
ERROR: gene names in config file do not match gene names in profile file

Checking config and profile files, I noticed that profile contains less columns than the number of genes included in the associated config, and moreover it seems to be identical to the profile file of Leptospira spp dataset 3.

Could you please check if there is any error in this profile file and eventually provide an updated version?

Thank you in advance!

Best Regards

Loris

Wrong name in stringMLST_datasets

Hi,

If you want to run stringMLST.py --getMLST -P datasets/ --species all
I get an error because of misspelling Stapylococcus_hominis.zip instead of Staphylococcus_hominis.zip in the datasets folder.

Thanks for fixing!

Marko

Automated database tests failed

A pubMLST process has gone awry and clobbered the Pasteurella multocida#1 database files and left them empty. Disable Pasteurella multocida#1 in stringMLST for now, rebuild databases