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 ;)
ref #90.
With current master and following https://hackmd.io/yc3TNcmLQniKY2qv8kHY1w (but not putting in gene_trans_map), I get:
Apparently the fix is to set gene_trans_map to false, which is fine, but we should have a better error message ;)