ERROR ~ Error executing process > 'VIROPROFILER:SETUP:DB_VREFSEQ'

[craftlord15]

Description of the bug

I think the link https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2022-08-01.zip has been change can you correct this one thanks.

Command used and terminal output

nextflow run deng-lab/viroprofiler -r main -profile podman --mode "setup" --max_cpus 12 --max_memory 16.GB --max_time 100.h

RROR ~ Error executing process > 'VIROPROFILER:SETUP:DB_VREFSEQ'                                                                                                                                           
                                                                                                                                                                                                            
Caused by:                                                                                                                                                                                                  
  Process `VIROPROFILER:SETUP:DB_VREFSEQ` terminated with an error exit status (4)                                                                                                                          
                                                                                                                                                                                                            
Command executed:                                                                                                                                                                                           
                                                                                                                                                                                                            
  # Download NCBI taxonomy                                                                                                                                                                                  
  if [ ! -d /root/viroprofiler/taxonomy/taxdump ]; then                                                                                                                                                     
      mkdir dl_taxdump                                                                                                                                                                                      
      cd dl_taxdump
      wget -O taxdump.zip https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2022-08-01.zip
      unzip taxdump.zip                                                                                
      # wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
      #tar -zxvf taxdump.tar.gz                     
      mkdir -p /root/viroprofiler/taxonomy/taxdump
      mv names.dmp nodes.dmp delnodes.dmp merged.dmp /root/viroprofiler/taxonomy/taxdump
      cd ..                                                                                            
      rm -rf dl_taxonkit                            
  else
      echo "NCBI taxonomy already exists"
  fi
                                                                                                       
  if [ ! -d /root/viroprofiler/taxonomy/mmseqs_vrefseq ]; then
      wget -O /root/viroprofiler/taxonomy/mmseqs_vrefseq.tar.gz "https://zenodo.org/record/7044674/files/mmseqs_vrefseq.tar.gz"
      tar -zxvf /root/viroprofiler/taxonomy/mmseqs_vrefseq.tar.gz -C /root/viroprofiler/taxonomy
      rm /root/viroprofiler/taxonomy/mmseqs_vrefseq.tar.gz
      cd /root/viroprofiler/taxonomy/mmseqs_vrefseq
      mmseqs createdb refseq_viral.faa refseq_viral
      mmseqs createtaxdb refseq_viral tmp --ncbi-tax-dump ../taxdump --tax-mapping-file virus.accession2taxid --threads 1
      mmseqs createindex refseq_viral tmp --threads 1
      rm -rf tmp                                                                                       
  else                                              
      echo "vRefSeq database already exists"        
  fi
Command exit status:
  4

Command output:
  (empty)

Command error:
  --2024-03-27 00:20:21--  https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2022-08-01.zip
  Resolving ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)... failed: Temporary failure in name resolution.
  wget: unable to resolve host address ‘ftp.ncbi.nih.gov’

Work dir:
  /root/work/1b/256f7ece6f13b689a9a52a29dfc957

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

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

Relevant files

No response

System information

No response