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snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

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Error in rule diffexp_datavzrd

aFienemann opened this issue · comments

commented

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!

commented
  1. 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:
               ...