Permission denied

[wardahjassiem]

When I try to run my pipeline on a cluster using slurm, I get the following command error:

Can't locate Config_heavy.pl: /usr/people/wjassiem/project/work/conda/chipseq-nf-c8e321ef0a6847733511c80b8ad8b081/lib/5.26.2/x86_64-linux-thread-multi/Config_heavy.pl: Permission denied at /usr/people/wjassiem/project/work/conda/chipseq-nf-c8e321ef0a6847733511c80b8ad8b081/lib/5.26.2/x86_64-linux-thread-multi/Config.pm line 105.

I'm using conda with nextflow, I'm not sure why i'm getting permission denied on the conda folder created by nextflow. Are there user configurations that should be done for my user name in the cluster?

[fmadani]

I faced similar issue. I am running this process which is part of my code:

process Presice_2 {
echo true

input:
	path R_file from Presice_ch_R
	path PCs_File from Presice_ch_PCs
	path cov_File from Presice_ch_cov
	
	path base_file from Presice_ch_base_file
	path target_file from Presice_ch_target_file
	path phenotype_file from Presice_ch_phenotype_file
	path covariate_file from Presice_ch_covariate_file
	
	
	
"""
Rscript $R_file  $PCs_File $cov_File  covariate_file  $params.Presice_columns_names

Rscript $baseDir/PRSice_linux/PRSice.R \
	--prsice $baseDir/PRSice_linux \           <------------- This line causes the error
	--base $baseDir/$base_file \
	--target $baseDir/$target_file \
	--binary-target F \
	--pheno $baseDir/$phenotype_file \
	--cov $baseDir/$covariate_file \
	--base-maf MAF:$params.MAF \
	--base-info INFO:$params.INFO \
	--stat $params.column_name_effect_size \ 
	--or \
	--out $params.out_filename_prefix
"""	

}

and I get this error

Command error:
sh: 1: /mnt/c/users/fmadani/Documents/healthlligence/Precision_Medicine/Polygenic_risk_score/nextflow/PRS_Calculation/PRSice/PRSice_linux/: Permission denied
Error:
Execution halted