ERROR: Uncontrolled exit resulting from an unexpected error.

[tarunaaggarwal]

Environment

• Installed via pip (include the output of pip list)
• Using a conda environment (include the output of conda list && conda list --revisions)
• Using a Docker container (include the IMAGE ID of the container)

Server information

• CPU: model name : Intel(R) Xeon(R) CPU X5670 @ 2.93GHz 12
• RAM: MemTotal: 98822068 kB
• OS:

NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

Debugging information

• gtdbtk.log has been included (drag and drop the file to upload).
• Genomes have been included (if possible, and there are few).

Additional comments

gtdbtk.log

[tarunaaggarwal]

Hi @pchaumeil - I'm confused about what the next steps are. Should I reinstall the latest version of gtdbtk?

[pchaumeil]

Hello,
Yes, I would recommend doing so.

[tarunaaggarwal]

Hi @pchaumeil - I did that but unfortunately, I'm getting the same errors.

[tarunaaggarwal]

Hi @pchaumeil - I downgraded to gsl 2.6 but I'm still getting the same errors. Thoughts on how I can resolve this issue?

[pchaumeil]

Hi,
Do you still get the same pydantic error?
If so I would recommend either deleting this conda environment and reinstalling it completely OR making sure the pydantic library within is downgraded in the already installed conda environment (using pip).

pip install 'pydantic>=1.9.2,<2' --force-reinstall

Hope this helps,
Pierre

[tarunaaggarwal]

Thank you very much @pchaumeil - the newer version is working now. I really appreciate you sending the specific command.

Taruna

[pchaumeil]

Glad it helps!
I am closing this ticket now :) .