FATAL: could not open image 10158:10011: failed to retrieve path for 10158:10011: lstat

[Jokendo-collab]

N E X T F L O W ~ version 19.10.0 Launching neoflow_db.nf [kickass_mcnulty] - revision: 96dbe17e38 Format input mapping file: /cbio/users/javanokendo/proteogenomics/example_data/test_vcf_files.tsv! New mapping file: ./test_vcf_files.tsv! executor > local (1) [6e/622d9c] process > pre_processing (test_vcf_files.tsv) [100%] 1 of 1, failed: 1 ✘ [- ] process > variant_annotation - [- ] process > database_construction - [- ] process > format_db - [- ] process > generate_decoy_db - 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("/cbio/users/javanokendo/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 10158:10011: failed to retrieve path for 10158:10011: lstat 10158:10011: no such file or directory Work dir: /cbio/users/javanokendo/proteogenomics/neoflow/work/6e/622d9c1d14877e59caa996bfe306b2

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