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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.
MIT License
64 stars 43 forks source link

Added title to heatmap and mention in report annotation that the heat… #7

Closed HenningTimm closed 4 years ago

HenningTimm commented 4 years ago

…map shows tpm values.

HenningTimm commented 4 years ago

I am not sure, why this failed. 

[Wed Oct 30 12:40:52 2019]
Error in rule biomart_ens_gene_to_go:
    jobid: 33
    output: resources/ontology/ens_gene_to_go.tsv
    log: logs/resources/biomart.ens_gene_to_go.download.log (check log file(s) for error message)
    conda-env: /github/workspace/.test/.snakemake/conda/653f1da1

RuleException:
CalledProcessError in line 95 of /github/workspace/workflow/rules/enrichment.smk:
Command 'source /opt/conda/bin/activate '/github/workspace/.test/.snakemake/conda/653f1da1'; set -euo pipefail;  Rscript --vanilla /github/workspace/.test/.snakemake/scripts/tmpazku3f7d.biomart-ens_gene_to_go.R' returned non-zero exit status 1.
  File "/github/workspace/workflow/rules/enrichment.smk", line 95, in __rule_biomart_ens_gene_to_go
  File "/opt/conda/lib/python3.7/concurrent/futures/thread.py", line 57, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

This might be a temporary problem on the biomart side of things. I would try to trigger a rerun, but I don't seem to have permissions to do so.

dlaehnemann commented 4 years ago

So much for merging, I don't have write access... Will let @johanneskoester know...

johanneskoester commented 4 years ago

@HenningTimm can you update to latest master?

HenningTimm commented 4 years ago

@johanneskoester Done. I had a merge conflict with the ngs-testdata submodule, which is strange, since I did not do any work there.

HenningTimm commented 4 years ago

@johanneskoester This was a problem with my local version of the workflow and can be considered resolved. @dlaehnemann and I did review this and it should be good to merge.