Closed ksavhughes closed 7 months ago
Hi, thanks for reporting. To avoid this issue, delete the build
folder inside of bacteria3_files
and try again. There are some temporary files created from previous attempts generating this error. This is a bug and will be fixed soon.
Thank you!
Fixed in v2.0.1 #281
Hi ganon team,
I'm not really sure what is going on here. Can you help me?
error message: Parse finished - skipping Building index (raptor) Traceback (most recent call last): File "/home/karsav1511/.conda/envs/ganon/bin/ganon", line 33, in
sys.exit(load_entry_point('ganon==2.0.0', 'console_scripts', 'ganon')())
File "/home/karsav1511/.conda/envs/ganon/lib/python3.10/site-packages/ganon/ganon.py", line 53, in main_cli
sys.exit(0 if main() else 1)
File "/home/karsav1511/.conda/envs/ganon/lib/python3.10/site-packages/ganon/ganon.py", line 36, in main
ret = build_custom(cfg)
File "/home/karsav1511/.conda/envs/ganon/lib/python3.10/site-packages/ganon/build_update.py", line 365, in build_custom
Path(build_output_folder + new_target + exts).symlink_to(first_file)
File "/home/karsav1511/.conda/envs/ganon/lib/python3.10/pathlib.py", line 1255, in symlink_to
self._accessor.symlink(target, self, target_is_directory)
FileExistsError: [Errno 17] File exists: '/ourdisk/hpc/hofmanlmamr/karsav1511/auto_archive_notyet/tape_2copies/RefSeq/ganonRefSeqLim3/refs/bacteria3/GCF_006777585.1_ASM677758v1_genomic.fna.gz' -> 'bacteria3_files/build/2078.fna.gz'