TCDB.dmnd not included in Globus-distributed dbcan database

[cduvallet]

Description of the bug

Running DRAM2 with --anno_dbs including dbcan fails during dbCAN's internal CGCFinder step with FileNotFoundError: Database file not found: dbcan/TCDB.dmnd. This file isn't present anywhere in the dbcan/ database directory as distributed via Globus. Related to #515 (same db, different file).

Workaround: manually downloading the file directly from dbCAN fixes it:

wget -O databases/dbcan/TCDB.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/TCDB.dmnd"

Edit: it seems that other files were missing as well, workaround:

cd databases/dbcan
wget -O TCDB.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/TCDB.dmnd"
wget -O TF.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/TF.dmnd"
wget -O TF.hmm "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/TF.hmm"
wget -O STP.hmm "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/STP.hmm"
wget -O PUL.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/PUL.dmnd"
wget -O sulfatlas_db.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/sulfatlas_db.dmnd"
wget -O peptidase_db.dmnd "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/peptidase_db.dmnd"
wget -O dbCAN-PUL.xlsx "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/dbCAN-PUL.xlsx"
wget -O dbCAN-PUL.tar.gz "https://pro.unl.edu/dbCAN2/download_file.php?file=run_dbCAN_database_total/db_current/dbCAN-PUL.tar.gz"

System information

• OS: Ubuntu 26.04 LTS, x86_64 (AWS EC2, r6i.8xlarge)
• Nextflow: 26.04.6
• DRAM: 2.0.0-beta28, dev branch, revision e7fa28b
• Execution profile: docker (Docker Engine 29.1.3)
• Databases sourced via Globus

Command used and terminal output

nextflow run WrightonLabCSU/DRAM -r dev --input_fasta input_fasta --outdir results_full --rename --call --annotate --anno_dbs dram_db,kofam,camper,canthyd,dbcan,fegenie,merops,methyl,sulfur,metals,antismash,card,tcdb,vog,viral --tiny_gb_mem_limit 4 -profile docker -resume

Terminal output:
FileNotFoundError: Database file not found: dbcan/TCDB.dmnd

Container:
  quay.io/biocontainers/dbcan:5.2.6--pyhdfd78af_0

Relevant files

No response