Pharmacogenetecist
commented
9 months ago This was a me issue, I was trying to write the files to a server directory I did not have write access to.
Closed Pharmacogenetecist closed 9 months ago
Pharmacogenetecist
commented
9 months ago This was a me issue, I was trying to write the files to a server directory I did not have write access to.
This looks like more a me issue, but I was hoping you could help to diagnose.
I just ran the pypgx create-input-vcf and it worked fine, but I am getting similar errors when trying to compute control statistics and depth-of-coverage.
pypgx compute-control-statistics chr12:47841537-47943048 CES_CS.zip --assembly GRCh38 "bam_ces.txt" --bed "/hg38.bed"
File "/home/ec2-user/anaconda3/envs/pypgx/bin/pypgx", line 10, in
sys.exit(main())
File "/home/ec2-user/anaconda3/envs/pypgx/lib/python3.7/site-packages/pypgx/main.py", line 33, in main
commands[args.command].main(args)
File "/home/ec2-user/anaconda3/envs/pypgx/lib/python3.7/site-packages/pypgx/cli/compute_control_statistics.py", line 84, in main
result.to_file(args.control_statistics)
File "/home/ec2-user/anaconda3/envs/pypgx/lib/python3.7/site-packages/pypgx/sdk/utils.py", line 93, in to_file
os.path.join(t, '..')))
File "/home/ec2-user/anaconda3/envs/pypgx/lib/python3.7/zipfile.py", line 1764, in write
shutil.copyfileobj(src, dest, 1024*8)
File "/home/ec2-user/anaconda3/envs/pypgx/lib/python3.7/zipfile.py", line 1172, in close
self._fileobj.seek(self._zipfile.start_dir)
OSError: [Errno 95] Operation not supported
Exception ignored in: <function ZipFile.del at 0x7f5bd95ad7a0>
Traceback (most recent call last):
File "/home/ec2-user/anaconda3/envs/pypgx/lib/python3.7/zipfile.py", line 1809, in del
self.close()
File "/home/ec2-user/anaconda3/envs/pypgx/lib/python3.7/zipfile.py", line 1831, in close
self._fpclose(fp)
File "/home/ec2-user/anaconda3/envs/pypgx/lib/python3.7/zipfile.py", line 1939, in _fpclose
fp.close()
OSError: [Errno 95] Operation not supported