BUG: cfg.py UserWarning

[bbidonb]

Hello everyone,

I am trying to run the rna-seq pipeline of seq2science but it seems that some pacakges required to run the pipeline are deprecated or are going to be.

/Users/.../miniforge3/envs/seq2science/lib/python3.10/site-packages/norns/cfg.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.

Am I the only one to have this problem? Is there a solution for it?

I search this issue but can't find applicable solution to my system. I am running under Linux 4.18.0-553.5.1.el8_10.x86_64 through PBS hpc.

I hope someone can help find out the reason beyond that issue.
Thank you,
Baptiste

config.yaml
samples.tsv

seq2science.e198840.txt

[Maarten-vd-Sande]

Hi @bbidonb

Thanks for your issue, and sorry for the late response. Seq2science doesn't get any real maintenance or support at the moment.

In your error log there is this error:

Error in rule dupRadar:
    jobid: 57
    input: /scratch/hpc/gst25-23/covid/rnaseq/infection/final_bam/ASM985889v3-MockA-APLI.samtools-coordinate.bam, /scratch/hpc/gst25-23/covid/rnaseq/infection/genomes/ASM985889v3/ASM985889v3.annotation.gtf, /scratch/hpc/gst25-23/covid/rnaseq/infection/qc/strandedness/ASM985889v3-MockA-APLI.strandedness.txt
    output: /scratch/hpc/gst25-23/covid/rnaseq/infection/qc/dupRadar/ASM985889v3-MockA-APLI.png
    log: /scratch/hpc/gst25-23/covid/rnaseq/infection/log/dupRadar/ASM985889v3-MockA-APLI.log (check log file(s) for error details)
    conda-env: /home/guest/gst25-23/.conda/envs/seq2science/lib/python3.10/site-packages/seq2science/.snakemake/b46be358b8a11bd91ae569afbccbc68b_

The pipeline fails because of this. Not the depcrecationwarning. You should inspect the log file for hints

/scratch/hpc/gst25-23/covid/rnaseq/infection/log/dupRadar/ASM985889v3-MockA-APLI.log