[Errno 1] Operation not permitted

GTDB-Tk
1

Hello developers,

I am getting the following error , when i run the : gtdbtk classify_wf

================================================================================
EXCEPTION: PermissionError
MESSAGE: [Errno 1] Operation not permitted: ‘classify/gtdbtk.bac120.summary.tsv’ → ‘gtdb_classify/gtdbtk.bac120.summary.tsv’

Traceback (most recent call last):
File “/home/bio5995/anaconda3/envs/gtdbtk-2.3.0/lib/python3.8/site-packages/gtdbtk/main.py”, line 102, in main
gt_parser.parse_options(args)
File “/home/bio5995/anaconda3/envs/gtdbtk-2.3.0/lib/python3.8/site-packages/gtdbtk/main.py”, line 1186, in parse_options
self.classify(options,all_classified_ani= all_classified_ani)
File “/home/bio5995/anaconda3/envs/gtdbtk-2.3.0/lib/python3.8/site-packages/gtdbtk/main.py”, line 587, in classify
reports = classify.run(genomes=genomes,
File “/home/bio5995/anaconda3/envs/gtdbtk-2.3.0/lib/python3.8/site-packages/gtdbtk/classify.py”, line 659, in run
symlink_f(PATH_BAC120_SUMMARY_OUT.format(prefix=prefix),
File “/home/bio5995/anaconda3/envs/gtdbtk-2.3.0/lib/python3.8/site-packages/gtdbtk/tools.py”, line 269, in symlink_f
os.symlink(src, dst)
PermissionError: [Errno 1] Operation not permitted: ‘classify/gtdbtk.bac120.summary.tsv’ → ‘gtdb_classify/gtdbtk.bac120.summary.tsv’

please help

2

Hello,
Do you still have this error when running the same gtdbtk command with another output directory ( gtdb_classify_2 instead of gtdb_classify ) ?

3

yes, the error is same, here is the actual error copied from the terminal

================================================================================
EXCEPTION: PermissionError
MESSAGE: [Errno 1] Operation not permitted: ‘classify/gtdbtk.bac120.summary.tsv’ → ‘gtdb_classify_2/gtdbtk.bac120.summary.tsv’

hope to hear from you soon

4

what is the current structure of gtdb_classify_2 ( ls -l information)? do you have full permission to write in this directory?

5

yes, I do have the permission. I had the same doubt hence tested it too.

drwxr-xr-x 3 bio5995 bio5995 2097152 May 31 21:22 gtdb_classify_2/
drwxr-xr-x 3 bio5995 bio5995 2097152 May 31 21:26 gtdb_result_1/