Error in rule diffexp_datavzrd

[aFienemann]

Hello,

the workflow ran almost through to the end. But the following Error occurred:

Error in rule diffexp_datavzrd:
jobid: 41
input: results/datavzrd/diffexp/model_X.yaml, results/tables/logcount-matrix/model_X.logcount-matrix.tsv, results/tables/diffexp/model_X.transcripts.diffexp.tsv, results/tables/diffexp/model_X.genes-aggregated.diffexp.tsv, results/tables/diffexp/model_X.genes-representative.diffexp.tsv, results/plots/interactive/volcano/model_X.vl.json
output: results/datavzrd-reports/diffexp-model_X
log: logs/datavzrd-report/diffexp.model_X/diffexp.model_X.log (check log file(s) for error details)
conda-env: /home/afienemann/kallisto/.snakemake/conda/e31e6658fb06c01d5e441b8bd51e5051_

RuleException:
CalledProcessError in file https://raw.githubusercontent.com/snakemake-workflows/rna-seq-kallisto-sleuth/v2.5.1/workflow/rules/datavzrd.smk, line 95:
Command 'source /home/afienemann/miniconda3/bin/activate '/home/afienemann/kallisto/.snakemake/conda/e31e6658fb06c01d5e441b8bd51e5051_'; set -euo pipefail; /home/afienemann/miniconda3/envs/snakemake/bin/python3.11 /home/afienemann/kallisto/.snakemake/scripts/tmpy4hs05xj.wrapper.py' returned non-zero exit status 1.
File "https://raw.githubusercontent.com/snakemake-workflows/rna-seq-kallisto-sleuth/v2.5.1/workflow/rules/datavzrd.smk", line 95, in __rule_diffexp_datavzrd
File "/home/afienemann/miniconda3/envs/snakemake/lib/python3.11/concurrent/futures/thread.py", line 58, in run
Exiting because a job execution failed. Look above for error message

The mentioned log:

"Error: Column "B6_mtb_d14_N1-1" under path "results/tables/diffexp/model_X.transcripts.diffexp.tsv" seems to have multiple definitions. Please check your config file."

1. Does the log refer to this config file? => /results/datavzrd/diffexp/model_X.yaml

2. What does "multiple definitions" mean in this context?

Thanks!

[fxwiegand]

2. What does "multiple definitions" mean in this context?

This means that your datavzrd config file contains more than one definition for the column named B6_mtb_d14_N1-1 so datavzrd does not know which one it should use. It probably looks like this:

render-table:
      columns:
          B6_mtb_d14_N1-1:
               ...
          B6_mtb_d14_N1-1:
               ...