I'm having some trouble when tyring to download th...
# bacass
g
I'm having some trouble when tyring to download the latest version of the KmerFinder database
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(base) ruben@FCP10492:~/Nextflow/nfcore_bacass/database$ KmerFinder_DB=$(pwd)
(base) ruben@FCP10492:~/Nextflow/nfcore_bacass/database$ cd kmerfinder_db/
(base) ruben@FCP10492:~/Nextflow/nfcore_bacass/database/kmerfinder_db$ bash INSTALL.sh $KmerFinder_DB bacteria latest

Downloading database(s) for bacteria
curl: /home/ruben/miniconda3/lib/libcurl.so.4: no version information available (required by curl)
Input date tag is not valid. There is no database available for this date. Please check the ftp site <ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/> for valid updates tags of the databases.
--2025-12-03 12:43:20--  <ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/latest/bacteria*>
           => '/home/ruben/Nextflow/nfcore_bacass/database/.listing'
Resolving ftp.cbs.dtu.dk (ftp.cbs.dtu.dk)... 130.225.74.194
Connecting to ftp.cbs.dtu.dk (ftp.cbs.dtu.dk)|130.225.74.194|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /public/CGE/databases/KmerFinder/version/latest ... 
No such directory 'public/CGE/databases/KmerFinder/version/latest'.

--2025-12-03 12:43:21--  <ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/latest/config>
           => '/home/ruben/Nextflow/nfcore_bacass/database/config'
Resolving ftp.cbs.dtu.dk (ftp.cbs.dtu.dk)... 130.225.74.194
Connecting to ftp.cbs.dtu.dk (ftp.cbs.dtu.dk)|130.225.74.194|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /public/CGE/databases/KmerFinder/version/latest ... 
No such directory 'public/CGE/databases/KmerFinder/version/latest'.

tar (child): /home/ruben/Nextflow/nfcore_bacass/database/bacteria.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
rm: cannot remove '/home/ruben/Nextflow/nfcore_bacass/database/*.tar.gz': No such file or directory
It seems there is no file called latest and when i try to check which one is the latest version (by number) i cannot connect to their ftp sever because it requires me to have password For now i'm using the version from Zenodo, but i would like to get the latest posible. So if anyone could provide me with the actual latest number I woudl appreciate it.
j
I am having the same issue and I used the 2019 database. However, the pipeline couldn't proceed through KMERFINDER_DOWNLOAD_REFERENCE for me.
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error [nextflow.exception.ProcessFailedException]: Process `NFCORE_BACASS:BACASS:KMERFINDER_SUMMARY_DOWNLOAD:KMERFINDER_DOWNLOAD_REFERENCE (NFCORE_BACASS:BACASS:KMERFINDER_SUMMARY_DOWNLOAD:KMERFINDER_DOWNLOAD_REFERENCE)` terminated with an error exit status (1)
Dec-07 00:34:21.092 [TaskFinalizer-2] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_BACASS:BACASS:KMERFINDER_SUMMARY_DOWNLOAD:KMERFINDER_DOWNLOAD_REFERENCE (NFCORE_BACASS:BACASS:KMERFINDER_SUMMARY_DOWNLOAD:KMERFINDER_DOWNLOAD_REFERENCE)'

Caused by:
  Process `NFCORE_BACASS:BACASS:KMERFINDER_SUMMARY_DOWNLOAD:KMERFINDER_DOWNLOAD_REFERENCE (NFCORE_BACASS:BACASS:KMERFINDER_SUMMARY_DOWNLOAD:KMERFINDER_DOWNLOAD_REFERENCE)` terminated with an error exit status (1)


Command executed:

  ## Find the common reference genome
  find_common_reference.py \
      -d reports/ \
      -o references_found.tsv

  ## Download the winner reference genome from the ncbi database
  download_reference.py \
      -f references_found.tsv \
      -o .

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_BACASS:BACASS:KMERFINDER_SUMMARY_DOWNLOAD:KMERFINDER_DOWNLOAD_REFERENCE":
      python: $(python --version | awk '{print $2}')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)
I was able to find
references_found.tsv
in the work directory, but it seems that
download_reference.py
couldn't function, or it was missing.