Process `pre_processing (test_vcf_files.tsv)` terminated with an error exit status (255)

[Jokendo-collab]

I am using neoflow and I am getting the following error with the example data that the pipeline comes with. What could be the problem? I am running this work on HPC nextflow run neoflow_db.nf bin/ --ref_dir /scratch/oknjav001/transcriptomics/proteogenomics/annovar/annovar/humandb --vcf_file test_vcf_files.tsv --annovar_dir /scratch/oknjav001/transcriptomics/proteogenomics/annovar/annovar --ref_ver hg19 --out_dir . N E X T F L O W ~ version 19.04.1 Launching neoflow_db.nf [condescending_bell] - revision: 96dbe17e38 Format input mapping file: /scratch/oknjav001/transcriptomics/proteogenomics/neoflow/test_vcf_files.tsv! New mapping file: ./test_vcf_files.tsv! [warm up] executor > local WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /scratch/oknjav001/transcriptomics/proteogenomics/neoflow/work/singularity Pulling Singularity image docker://proteomics/pga:latest [cache /scratch/oknjav001/transcriptomics/proteogenomics/neoflow/work/singularity/proteomics-pga-latest.img] executor > local (1) [a6/9d551d] process > pre_processing [100%] 1 of 1, failed: 1 ✘ ERROR ~ Error executing process > 'pre_processing (test_vcf_files.tsv)'

Caused by: Process pre_processing (test_vcf_files.tsv) terminated with an error exit status (255)

Command executed:

#!/usr/bin/env /usr/local/bin/Rscript

library(dplyr) library(readr)

a = read.delim("/scratch/oknjav001/transcriptomics/proteogenomics/neoflow/test_vcf_files.tsv") experiment_names = unique(a[,"experiment"]) for(f in experiment_names){ dat = a %>% filter(experiment == f) out_file = paste(f,"-mapping_file.tsv",sep="") write_tsv(dat,out_file) }

Command exit status: 255

Command output: (empty)

Command error: FATAL: could not open image 1821:1821: failed to retrieve path for 1821:1821: lstat 1821:1821: no such file or directory

Work dir: /scratch/oknjav001/transcriptomics/proteogenomics/neoflow/work/a6/9d551d5f30602f53e2d23a1da77c1d

Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option -resume

-- Check '.nextflow.log' file for details