Bonjour,
I tried the Snakemake tutorial interactively (srun) and it worked after some tinkering. But when trying the same Snakefile, env.yaml, and config.yaml with slurm-drmaa, the Fastqc rule is throwing up an error. I solved this error earlier in the srun by updating Fastqc. So, not sure why this same problem is happening with slurm. Maybe because the conda needs to be up-to-date?
I'll greatly appreciate any pointers/help.
[Wed Oct 4 11:09:29 2023]
rule fastqc:
input: result/CRN-107_11_R1.fastq, result/CRN-107_11_R2.fastq
output: result/CRN-107_11-R1.html, result/CRN-107_11-R2.html, result/CRN-107_11_R1_fastqc.zip, result/CRN-107_11_R2_fastqc.zip
jobid: 0
reason: Missing output files: result/CRN-107_11-R1.html, result/CRN-107_11-R2.html
wildcards: sample=CRN-107_11
resources: tmpdir=/tmp
Submitted DRMAA job 0 with external jobid 35412539.
[Wed Oct 4 11:09:59 2023]
Error in rule fastqc:
jobid: 0
input: result/CRN-107_11_R1.fastq, result/CRN-107_11_R2.fastq
output: result/CRN-107_11-R1.html, result/CRN-107_11-R2.html, result/CRN-107_11_R1_fastqc.zip, result/CRN-107_11_R2_fastqc.zip
conda-env: /shared/ifbstor1/projects/sarscov2mex/00_test/snakemake_tutorial/.snakemake/conda/86e28c1a593c1e0dae62c46bef024c9a_
shell:
fastqc --nogroup result/CRN-107_11_R1.fastq
fastqc --nogroup result/CRN-107_11_R2.fastq
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Error executing rule fastqc on cluster (jobid: 0, external: 35412539, jobscript: /shared/ifbstor1/projects/sarscov2mex/00_test/snakemake_tutorial/.snakemake/tmp.pzjmwo15/snakejob.fastqc.0.sh). For error details see the cluster log and the log files of the involved rule(s).
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-10-04T110916.652317.snakemake.log
path to the project: /shared/projects/sarscov2mex/00_test/snakemake_tutorial
tutorial: Perform a quality check on raw sequencing data with Snakemake and Conda
slurm command: snakemake --drmaa --jobs=10 result/CRN-107_11-R1.html result/CRN-107_11-R2.html
P.S.: I also checked disc space, which doesn't seem to be a problem.
(base) [dchakraborty@core-login1 snakemake_tutorial]$ lfs quota -h -p 163032 /shared/home/dchakraborty
Disk quotas for prj 163032 (pid 163032):
Filesystem used quota limit grace files quota limit grace
/shared/home/dchakraborty
5.416G 100G 150G - 92337 100000 150000 -
Merci d'avance.
Bonne journée,
Débo