Installation/Mantis: errors during installation
Current version of Mantis
(mantis_pfa=1.4.5=py39h38f01e4_0
) fails when running the installation step.
The error has been reported by a user (see here) and was replicated on iris
:
Error message:
Traceback (most recent call last):
File "/mnt/lscratch/users/vgalata/tmp/imp3_install/.snakemake/conda/f03de4bf2925e98d26bee375be6819ef/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/mnt/lscratch/users/vgalata/tmp/imp3_install/.snakemake/conda/f03de4bf2925e98d26bee375be6819ef/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/mnt/lscratch/users/vgalata/tmp/imp3_install/.snakemake/conda/f03de4bf2925e98d26bee375be6819ef/lib/python3.9/site-packages/mantis/Database_generator.py", line 195, in worker_setup_databases
self.download_database(database, taxon_id, stdout_path)
File "/mnt/lscratch/users/vgalata/tmp/imp3_install/.snakemake/conda/f03de4bf2925e98d26bee375be6819ef/lib/python3.9/site-packages/mantis/Database_generator.py", line 230, in download_database
if database == 'taxonomy': self.download_taxonomy_resources(stdout_file=stdout_file)
File "/mnt/lscratch/users/vgalata/tmp/imp3_install/.snakemake/conda/f03de4bf2925e98d26bee375be6819ef/lib/python3.9/site-packages/mantis/Database_generator.py", line 266, in download_taxonomy_resources
self.create_taxonomy_db()
File "/mnt/lscratch/users/vgalata/tmp/imp3_install/.snakemake/conda/f03de4bf2925e98d26bee375be6819ef/lib/python3.9/site-packages/mantis/Taxonomy_SQLITE_Connector.py", line 119, in create_taxonomy_db
self.download_data()
File "/mnt/lscratch/users/vgalata/tmp/imp3_install/.snakemake/conda/f03de4bf2925e98d26bee375be6819ef/lib/python3.9/site-packages/mantis/Taxonomy_SQLITE_Connector.py", line 108, in download_data
self.ar_file = [i for i in os.listdir(self.temp_folder) if i.startswith('ar122') and i.endswith('.tsv')][0]
IndexError: list index out of range
Used configuration for installation:
mantis:
# default HMMs
default:
nog_ref_folder: null
pfam_ref_folder: null
kofam_ref_folder: "/mnt/isilon/projects/ecosystem_biology/data/mantis_references/kofam/"
ncbi_ref_folder: null
tcdb_ref_folder: null
# custom HMMs (list)
custom: []
# weights: <name>_hmm_folder --> <name>_weight
weights:
ncbi_weight: 0.9
nog_weight: 0.8
pfam_weight: 0.9
uniprot_ec_weight: 0.9
Check if updating the tool would resolve the issue.