Pierre Chaumeil

Results 24 comments of Pierre Chaumeil

[] are not present in the input list of genome to process

Hello, Seems like an issue with Tk Are you getting this error when you run --force on a new output_directory? or an existing one with data already in it?

Problem with empty files (such as produced by metabat)

Hello, Thanks for your feedback, We will add a test to disregard any empty genome files. This will be available in the next Tk release

pydantic.dev/2.6/v/missing

Hello, Please download the latest version of GTDB-Tk ( 2.3.2). This should fix this issue. Cheers, Pierre

Cannot open classify.tree file in Dendroscope

Hello, Apologies for the very late reply, Do you still have an issue with dendroscope?

Cannot open classify.tree file in Dendroscope

Ticket closed due to inactivity.

gtdbtk.exceptions.ProdigalException: An exception was caught while running Prodigal: Prodigal returned a non-zero exit code.

Hello, Did you manage to find what is happening during the Prodigal step?

gtdbtk.exceptions.ProdigalException: An exception was caught while running Prodigal: Prodigal returned a non-zero exit code.

Ticket closed due to inactivity.

Error running Prodigal on genome

Hello, Apologies for the very late reply. Do you still have an issue with Prodigal?

Error running Prodigal on genome

Could you please send few MAGS generating this error? Thanks, Pierre

How to get a tree containing all my MAGs

Hello, In order to have all the genomes placed in the reference tree ( split or not split ) you need to use the flag `--skip_ani_screen` . it will skip...