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dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system
https://dib-lab.github.io/elvers/
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confusing lack of an error error when gene_trans_map is missing? #98

Closed ctb closed 5 years ago

ctb commented 5 years ago

ref #90.

With current master and following https://hackmd.io/yc3TNcmLQniKY2qv8kHY1w (but not putting in gene_trans_map), I get:

    benchmark: /home/diblions/eelpond/lab7_out_quant_DE/logs/deseq2/lab7_input.d
eseq2.init.benchmark
    wildcards: assembly=lab7_input

Rscript --vanilla /home/diblions/eelpond/.snakemake/scripts/tmpkqmw6fwj.deseq2-i
nit-tx2gene.R
Activating conda environment: /home/diblions/eelpond/.snakemake/conda/d1178ee8
[Mon Mar  4 09:36:47 2019]
Error in rule deseq2_init_tx2gene:
    jobid: 4
    output: /home/diblions/eelpond/lab7_out_quant_DE/diffexp/lab7_input.deseq2.r
ds  
    log: /home/diblions/eelpond/lab7_out_quant_DE/logs/deseq2/lab7_input.deseq2.
init.log
    conda-env: /home/diblions/eelpond/.snakemake/conda/d1178ee8

RuleException:
CalledProcessError in line 49 of /home/diblions/eelpond/rules/deseq2/deseq2.rule
:
Command 'source activate '/home/diblions/eelpond/.snakemake/conda/d1178ee8'; set
 -euo pipefail;  Rscript --vanilla /home/diblions/eelpond/.snakemake/scripts/tmp
kqmw6fwj.deseq2-init-tx2gene.R' returned non-zero exit status 1.
  File "/home/diblions/eelpond/rules/deseq2/deseq2.rule", line 49, in __rule_des
eq2_init_tx2gene
  File "/opt/miniconda/envs/eelpond-sw/lib/python3.6/concurrent/futures/thread.p
y", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

Apparently the fix is to set gene_trans_map to false, which is fine, but we should have a better error message ;)