Error running mageck vispr on a cluster
I'm trying to run the files I've configured through snakemake on a cluster server, and am using the command snakemake --cluster -j 11. The jobs get submitted but I keep getting this error Error in rule fastqc: jobid: 0 output: results/qc/T0_RepA_0 log: logs/fastqc/T0_RepA_0.log cluster_jobid: Submitted batch job 1458819 Repeated several times and then it closes the analysis.
The output file gives me this error: Error in rule fastqc: jobid: 0 output: results/qc/T0_RepA_0 log: logs/fastqc/T0_RepA_0.log
RuleException: CalledProcessError in line 40 of /igbgroup/a-m/liqunyu2/santa/Snakefile: Command 'set -euo pipefail; mkdir -p results/qc/T0_RepA_0; rm -rf results/qc/T0_RepA_0/*; fastqc -f fastq --extract -o result$ File "/igbgroup/a-m/liqunyu2/santa/Snakefile", line 40, in __rule_fastqc File "/home/apps/software/Python/3.6.1-IGB-gcc-4.9.4/lib/python3.6/concurrent/futures/thread.py", line 55, in run Removing output files of failed job fastqc since they might be corrupted: results/qc/T0_RepA_0
I don't really understand what I have to do now to get it to work.