deseq2-init.R returned non-zero exit status 1.

[Mon Oct 15 15:42:46 2018]
rule deseq2_init:
    input: counts/all.tsv
    output: deseq2/all.rds
    log: logs/deseq2/init.log
    jobid: 3

Activating conda environment: /media/leochong/backup4/rna-seq-star-deseq2/.snakemake/conda/28f98caa
[Mon Oct 15 15:43:01 2018]
Error in rule deseq2_init:
    jobid: 3
    output: deseq2/all.rds
    log: logs/deseq2/init.log
    conda-env: /media/leochong/backup4/rna-seq-star-deseq2/.snakemake/conda/28f98caa

RuleException:
CalledProcessError in line 33 of /media/leochong/backup4/rna-seq-star-deseq2/rules/diffexp.smk:
Command 'source activate /media/leochong/backup4/rna-seq-star-deseq2/.snakemake/conda/28f98caa; set -euo pipefail;  Rscript /media/leochong/backup4/rna-seq-star-deseq2/.snakemake/scripts/tmpju9bqzqy.deseq2-init.R ' returned non-zero exit status 1.
  File "/media/leochong/backup4/rna-seq-star-deseq2/rules/diffexp.smk", line 33, in __rule_deseq2_init
  File "/home/leochong/miniconda3/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

Any input on why the pipeline is failing?

[sateeshperi]

@johanneskoester Yes ! …that fixes it 👍

[qins]

In case someone get error:

Error in .validate_names(colnames, ans_colnames, “assay colnames()”, “colData rownames()”) : assay colnames() must be NULL or identical to colData rownames() Calls: DESeqDataSetFromMatrix … SummarizedExperiment -> SummarizedExperiment -> .local -> .validate_names Execution halted

Solution: colnames(countDataDF) <- NULL

countDataDF is the input dataframe of countData parameter.