Problem downloading databases

[Jokendo-collab]

I am getting the below error when I try to run this tool. Could you have a look and advise>

executor >  local (8)
[b0/8a92f7] process > download_pprmeta:pprmetaGet          [  0%] 0 of 1
[d0/df17a6] process > download_virsorter_db:virsorterGetDB [  0%] 0 of 1
[d2/c45151] process > download_virfinder_db:virfinderGetDB [  0%] 0 of 1
[30/bd3995] process > download_model_meta:metaGetDB        [  0%] 0 of 1
[50/094819] process > download_viphog_db:viphogGetDB       [  0%] 0 of 1
[b9/b1c453] process > download_ncbi_db:ncbiGetDB           [  0%] 0 of 1
executor >  local (8)
[-        ] process > download_pprmeta:pprmetaGet          -
[d0/df17a6] process > download_virsorter_db:virsorterGetDB [200%] 2 of 1, failed: 2 ✘
[d2/c45151] process > download_virfinder_db:virfinderGetDB [100%] 1 of 1, failed: 1 ✘
[30/bd3995] process > download_model_meta:metaGetDB        [200%] 2 of 1, failed: 2 ✘
[50/094819] process > download_viphog_db:viphogGetDB       [100%] 1 of 1, failed: 1 ✘
[b9/b1c453] process > download_ncbi_db:ncbiGetDB           [100%] 1 of 1, failed: 1 ✘
[-        ] process > download_checkv_db:checkvGetDB       -
[80/d3015d] process > preprocess:rename (1)                [100%] 1 of 1, failed: 1 ✘
[-        ] process > preprocess:length_filtering          -
[-        ] process > detect:virsorter                     -
[-        ] process > detect:virfinder                     -
[-        ] process > detect:pprmeta                       -
[-        ] process > detect:parse                         -
[-        ] process > postprocess:restore                  -
[-        ] process > annotate:prodigal                    -
[-        ] process > annotate:hmmscan_viphogs             -
[-        ] process > annotate:hmm_postprocessing          -
[-        ] process > annotate:ratio_evalue                -
[-        ] process > annotate:annotation                  -
[-        ] process > annotate:plot_contig_map             -
[-        ] process > annotate:assign                      -
[-        ] process > annotate:checkV                      -
[-        ] process > annotate:write_gff                   -
[-        ] process > plot:generate_krona_table            -
[-        ] process > plot:krona                           -
[-        ] process > plot:generate_sankey_table           -
[-        ] process > plot:sankey                          -
ERROR ~ Error executing process > 'download_ncbi_db:ncbiGetDB'

Caused by:
  Process `download_ncbi_db:ncbiGetDB` terminated with an error exit status (1)

Command executed:

  wget -nH ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/viral-pipeline/2022-11-01_ete3_ncbi_tax.sqlite.gz && gunzip -f 2022-11-01_ete3_ncbi_tax.sqlite.gz
  cp 2022-11-01_ete3_ncbi_tax.sqlite ete3_ncbi_tax.sqlite

Command exit status:
  1

Command output:
  (empty)

Command error:
  --2024-09-19 09:13:02--  ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/viral-pipeline/2022-11-01_ete3_ncbi_tax.sqlite.gz
             => ‘2022-11-01_ete3_ncbi_tax.sqlite.gz’
  Resolving ftp.ebi.ac.uk (ftp.ebi.ac.uk)... 193.62.193.165
  Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.193.165|:21... failed: Connection refused.
  cp: 2022-11-01_ete3_ncbi_tax.sqlite: No such file or directory
  cp: .command.out and .command.out are identical (not copied).
  cp: .command.err and .command.err are identical (not copied).

Work dir:
  /Users/Downloads/tmpFiles/b9/b1c453e0caba613d702489ec9b6072

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

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

[hoelzer]

Hey @Jokendo-collab does the download command work for you outside of the pipeline?

wget -nH ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/viral-pipeline/2022-11-01_ete3_ncbi_tax.sqlite.gz

[Jokendo-collab]

Hi @hoelzer ;

It's not working for me.

--2024-09-19 09:39:20--  ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/viral-pipeline/2022-11-01_ete3_ncbi_tax.sqlite.gz
           => ‘2022-11-01_ete3_ncbi_tax.sqlite.gz’
Resolving ftp.ebi.ac.uk (ftp.ebi.ac.uk)... 193.62.193.165
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.193.165|:21... failed: Connection refused.

[hoelzer]

I am afraid it's not a problem with the pipeline but your system/port/internet configuration. Are you working on a cluster machine with admins that you can ask? Some ports or URLs probably need to be included on an allowlist.

When you get that command working, you can try running the pipeline again.

[Jokendo-collab]

Hi;

I am using my PC and my institute seems to block the download. I will try this with another internet connection and let you know.

On Thu, Sep 19, 2024 at 10:26 AM Martin Hölzer @.***> wrote:

I am afraid it's not a problem with the pipeline but your system/port/internet configuration. Are you working on a cluster machine with admins that you can ask? Some ports or URLs probably need to be included on an allowlist.

When you get that command working, you can try running the pipeline again.

— Reply to this email directly, view it on GitHub https://github.com/EBI-Metagenomics/emg-viral-pipeline/issues/131#issuecomment-2361147683, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGJ34OYIDKQF5UZQWYJSYA3ZXLNHRAVCNFSM6AAAAABOP5DB5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRRGE2DONRYGM . You are receiving this because you were mentioned.Message ID: @.***>