search

sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly
http://sanger-pathogens.github.io/ariba/
Other
167 stars 52 forks source link

Unable to download Escherichia coli#1 and Escherichia coli#2 #308

Open RotimiDada opened 3 years ago

RotimiDada commented 3 years ago

Traceback (most recent call last): File "/usr/local/bin/ariba", line 4, in import('pkg_resources').run_script('ariba==2.14.4', 'ariba') File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 658, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 1438, in run_script exec(code, namespace, namespace) File "/usr/local/lib/python3.6/dist-packages/ariba-2.14.4-py3.6-linux-x86_64.egg/EGG-INFO/scripts/ariba", line 312, in args.func(args) File "/usr/local/lib/python3.6/dist-packages/ariba-2.14.4-py3.6-linux-x86_64.egg/ariba/tasks/pubmlstget.py", line 11, in run preparer.run() File "/usr/local/lib/python3.6/dist-packages/ariba-2.14.4-py3.6-linux-x86_64.egg/ariba/pubmlst_ref_preparer.py", line 85, in run self._load_fasta_files_and_write_clusters_file(self.mlst_download_dir) File "/usr/local/lib/python3.6/dist-packages/ariba-2.14.4-py3.6-linux-x86_64.egg/ariba/pubmlst_ref_preparer.py", line 49, in _load_fasta_files_and_write_clusters_file raise Error('Cannot find file "' + infile + '" for gene ' + gene_name) ariba.pubmlst_ref_preparer.Error: Cannot find file "get_mlst/pubmlst_download/arcC.tfa" for gene arcC

fino0000 commented 1 year ago

Hi. Did you solve this issue? I am having the same problem

RotimiDada commented 1 year ago

@fino0000, I got it fixed by installing the latest version of Ariba - 2.14.6 (I am not sure if there is a more recent version now. I experienced the bug about 2 years ago). One of our IT guys suggested that I could get it fixed this way. By the way, are you using Ariba version 2.14.4? That's the version that produced the bug then. Cheers!