Guillem Macip Sancho
12/03/2025, 11:49 AM(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.Junhong Jia
12/09/2025, 9:05 AMerror [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.