Unable to create the group "/sketches/": (Links) Object already exists

[danielarothschild]

Versions Using PopPUNK version 2.6.5 and pp-sketchlib v2.1.2

Command used and output returned Just trying to run the standard poppunk_assign using one of the downloaded databases from poppunk to cluster the genomes: poppunk_assign --db database --query qfile.txt --output poppunk_clusters --threads 8

but this error comes up:

in constructDatabase
    pp_sketchlib.constructDatabase(db_name=dbname,
pp_sketchlib.HDF5Exception: Unable to create the group "/sketches/": (Links) Object already exists

I also tried to add the --overwrite option but nothing changed. I then tried re-installing poppunk and the database in a new conda environment (same error). So I tried to create my own database in case this was the issue using: poppunk --create-db --output database --r-files rlist.txt --threads 8

but the same error came up.

I was able to run this before a few months ago with no issues. Sorry if it's basic, not an advanced programer here, any help is appreciated!

[johnlees]

Thanks for the clear description and versions

This is odd, and I think must be something with the installation. Is this installed with conda? What does conda list give?

Can you try with a different --output prefix too (with --create-db)?

Can you try with sketchlib directly? (see https://poppunk.bacpop.org/sketching.html#using-pp-sketchlib-directly)

[danielarothschild]

Thanks for the reply.

Sorry I was having issues again, but finally found the cause of the error (path to sequences on the rlist.txt file was shortcutted and not complete...silly error) just fixed that and now it works smoothly. Thanks again!!