Duplicated Symlink
This problem is not reproducible, it happens randomly. When the corresponding files are deleted, than the error disappears.
Traceback (most recent call last):
File "/home/ubuntu/downloader.py", line 200, in <module>
asyncio.run(download_genomes(genomes, data_path, logger, config))
File "/home/ubuntu/miniconda3/lib/python3.9/asyncio/runners.py", line 44, in run
return loop.run_until_complete(main)
File "/home/ubuntu/miniconda3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
return future.result()
File "/home/ubuntu/downloader.py", line 178, in download_genomes
await asyncio.gather(*tasks)
File "/home/ubuntu/downloader.py", line 133, in download_file
file_path.symlink_to(link_file.absolute())
File "/home/ubuntu/miniconda3/lib/python3.9/pathlib.py", line 1403, in symlink_to
self._accessor.symlink(target, self, target_is_directory)
File "/home/ubuntu/miniconda3/lib/python3.9/pathlib.py", line 456, in symlink
return os.symlink(a, b)
FileExistsError: [Errno 17] File exists: '/home/ubuntu/data_path/test_genomes/klebsiella/aztreonam/573.13417.fa' -> 'data_path/test_genomes/klebsiella/amikacin/573.13417.fa'