sanger-pathogens/ariba

ARIBA error in Galaxy

ajkarloss opened this issue · 0 comments

WARNING: I tried to get the version of spades with: "/extra_storage1/miniconda3/envs/__ariba@2.14.6/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9.]+)"
Exception ignored in: <_io.TextIOWrapper name='' mode='w' encoding='UTF-8'>
BrokenPipeError: [Errno 32] Broken pipe
WARNING. 700 sequence(s) excluded. Please see the 01.filter.check_genes.log and 01.filter.check_noncoding.log for details. This will show them:
grep REMOVE megares/01.filter.check_genes.log
cat megares/01.filter.check_noncoding.log
WARNING. Problem with at least one variant. Problem variants are removed. Please see the file megares/01.filter.check_metadata.log for details.
Traceback (most recent call last):
File "/extra_storage1/galaxy_19.05/database/shed_tools/testtoolshed.g2.bx.psu.edu/repos/thanhlv/data_manager_build_ariba_database/218301fbbb99/data_manager_build_ariba_database/data_manager/ariba_database_builder.py", line 236, in
main()
File "/extra_storage1/galaxy_19.05/database/shed_tools/testtoolshed.g2.bx.psu.edu/repos/thanhlv/data_manager_build_ariba_database/218301fbbb99/data_manager_build_ariba_database/data_manager/ariba_database_builder.py", line 233, in main
open(args.params, 'wb').write(json.dumps(data_manager_dict))
TypeError: a bytes-like object is required, not 'str'