First time running the pipeline, somewhile during a zcat command (I think) I'm getting an error about the rule of header_Crick_R2. I'm not sure why this happens, as for other files, this process seemed to have run already fine. I am running the epiGBS2.3 version on linux, with all default settings.
I'm pasting the part from the log file concerning the error below.
Best wishes,
Isolde
##########
Error in rule header_Crick_R2:
jobid: 357
output: /tmp/demultiplex/samplesHeader/EU42.1-Crick.2.fq.gz
conda-env: /beegfs/work/tu_bbmiv01/epiGBS2v3/.snakemake/conda/735d77df036c5fde9a425156af8e5e9f
shell:
zcat /beegfs/work/tu_bbmiv01/run1_epiGBS/output/output_demultiplex/clone-stacks/EU42.1-Crick.2.fq.gz | cut -f1 -d ' ' | sed -e '/^@/ s/$/ RG:Z:novaseq_1_EU42.1 ST:Z:Crick/' | gzip -c > /tmp/demultiplex/samplesHeader/EU42.1-Crick.2.fq.gz
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Hi Maarten et al.,
First time running the pipeline, somewhile during a zcat command (I think) I'm getting an error about the rule of header_Crick_R2. I'm not sure why this happens, as for other files, this process seemed to have run already fine. I am running the epiGBS2.3 version on linux, with all default settings. I'm pasting the part from the log file concerning the error below.
Best wishes,
Isolde ########## Error in rule header_Crick_R2: jobid: 357 output: /tmp/demultiplex/samplesHeader/EU42.1-Crick.2.fq.gz conda-env: /beegfs/work/tu_bbmiv01/epiGBS2v3/.snakemake/conda/735d77df036c5fde9a425156af8e5e9f shell: zcat /beegfs/work/tu_bbmiv01/run1_epiGBS/output/output_demultiplex/clone-stacks/EU42.1-Crick.2.fq.gz | cut -f1 -d ' ' | sed -e '/^@/ s/$/ RG:Z:novaseq_1_EU42.1 ST:Z:Crick/' | gzip -c > /tmp/demultiplex/samplesHeader/EU42.1-Crick.2.fq.gz (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)