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cvn001 / transflow

A snakemake workflow for WGS-based tuberculosis transmission analysis
GNU General Public License v3.0
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Error running example #5

Closed Czirion closed 1 year ago

Czirion commented 1 year ago

Hello,

I installed Transflow using Mamba and cannot run the example. It only produced the FastQC outputs for S5 and S8

I ran the next code from the transflow/ directory: bash transflow.sh --configfile config/configfile.yaml --cores 4 --verbose

The first warning message that I get is: miniconda3/envs/transflow/lib/python3.10/site-packages/google/protobuf/internal/api_implementation.py:110: UserWarning: Selected implementation cpp is not available. warnings.warn(

I attach the complete log file transflow_example.log

Note: I am running it in a SLURM-based cluster and I have the conda environment in one user but I cloned the repository and ran the workflow from another user.

Please let me know if you need any more information.

Thank you,

Claudia

cvn001 commented 1 year ago

Hi Claudia,

Thanks for your interest in our pipeline.

Unfortunately we did not test TransFlow on a Slurm-based cluster.

According to the Snakemake manual, Snakemake provides a specific support for Slurm. Please re-run transflow.sh and add execution parameters related to Slurm.

Best,

Xiangchen Li

Czirion commented 1 year ago

Dear Xiangchen Li,

Thank you for quick your response.

I was not able to run it using the Slurm parameters --slum--jobs 1`.

But I persevered in making the installation with Conda instead of Mamba, and now it works fine, so it was an issue with the Mamba installation and not related to Slurm.

Thank you!

All the best,

Claudia