Hello, I’m trying phylophlan tutorial.
However, in the Ethiopian cohort part (Example 03), I’ve got an error.
$ phylophlan_assign_sgbs -i input_metagenomic -o output_metagenomic --nproc 4 -n 1 -d ethoipia_tutorial --database_folder ethiopia_tutorial_db --verbose 2>&1 | tee
logs/phylophlan_metagenomic.log
phylophlan_assign_sgbs.py version 3.1.40 (6 March 2024)
Command line: /scratch/e1590a01/.conda/envs/mpa/bin/phylophlan_assign_sgbs -i input_metagenomic -o output_metagenomic --nproc 4 -n 1 -d ethoipia_tutorial --database_folder ethiopia_tutorial_db --verbose
Setting input extension to “.fna”
Folder “output_metagenomic_sketches” already present
Folder “output_metagenomic_sketches/inputs” already present
Folder “output_metagenomic_dists” already present
Folder “output_metagenomic_prefiltering” already present
Folder “output_metagenomic_prefiltering/pref_dbs” already present
Arguments: {‘input’: ‘input_metagenomic’, ‘output_prefix’: ‘output_metagenomic’, ‘database’: ‘ethoipia_tutorial’, ‘database_list’: False, ‘database_update’: False, ‘input_extension’: ‘.fna’, ‘how_many’: 1, ‘nproc’: 4, ‘database_folder’: ‘ethiopia_tutorial_db’, ‘only_input’: False, ‘add_ggb_fgb’: False, ‘overwrite’: False, ‘verbose’: True, ‘mapping’: ‘ethoipia_tutorial.txt.bz2’}
Checking “mash”
File “phylophlan_SGB_databases.txt” present
[e] invalid number of URLs for “ethoipia_tutorial” in the downloaded file
Retrying after clearing all output files and folders was resulted in the same error.
It wasn’t like this when I first tried, but after once I lose network connection while downloading tar files, I get this problem every time I try again.
I would appreciate it if you could tell me how to solve it.