kundajelab/chipseq_pipeline

"-q [SLURM_ACCOUNT_NAME]" interpreted as file

jchap14 opened this issue · 1 comments

jchap14 commented

Hey Jin,

I can't figure out how to correctly specify the --account for SLURM job submission on SCG.

Your example: "python chipseq.py -system slurm -q_for_slurm_account -q [SLURM_ACCOUNT_NAME]"

I used:
python /srv/gsfs0/projects/snyder/chappell/TF_chipseq_pipeline/chipseq.py -type histone --screen GFP.H3K4me1 -system slurm -q_for_slurm_account -q mpsnyder -pe -species hg19 -nth 12 -fastq1_1 GFP.H3K4me1.repA.trim.R1.fq.gz -fastq1_2 GFP.H3K4me1.repA.trim.R2.fq.gz -fastq2_1 GFP.H3K4me1.repB.trim.R1.fq.gz -fastq2_2 GFP.H3K4me1.repB.trim.R2.fq.gz -ctl_fastq1_1 GFP.Input.repAB.trim.R1.fq.gz -ctl_fastq1_2 GFP.Input.repAB.trim.R2.fq.gz -out_dir GFP.H3K4me1 -mem_dedup 15G

Get the following error in .log output:
"sbatch: error: Unable to open file mpsnyder"