unicycler error : [Errno 13] Permission denied:
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Entering edit mode
3 months ago
jiyoung ▴ 20

I was running unicycler and encountered an error in permisson, what steps should I take to resolve this issue?

[Errno 13] Permission denied: 


Command line: /home/default1/miniconda3/envs/unicycler/bin/spades.py    -o  /mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly -k  27  --threads   9   --isolate   -1  /mnt/d/raw/2023nudi/01.RawData/De-unicycler/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.1qc.fq  -2  /mnt/d/raw/2023nudi/01.RawData/De-unicycler/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.2qc.fq  -m  1024    

System information:
  SPAdes version: 3.15.5
  Python version: 3.10.8
  OS: Linux-4.4.0-19041-Microsoft-x86_64-with-glibc2.31

Output dir: /mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
  Isolate mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/mnt/d/raw/2023nudi/01.RawData/De-unicycler/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.1qc.fq']
      right reads: ['/mnt/d/raw/2023nudi/01.RawData/De-unicycler/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.2qc.fq']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: [27]
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
Other parameters:
  Dir for temp files: /mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly/tmp
  Threads: 9
  Memory limit (in Gb): 1024


======= SPAdes pipeline started. Log can be found here: /mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly/spades.log

/mnt/d/raw/2023nudi/01.RawData/De-unicycler/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.1qc.fq: max reads length: 150
/mnt/d/raw/2023nudi/01.RawData/De-unicycler/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.2qc.fq: max reads length: 150

Reads length: 150

[('/mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly/configs/debruijn', '/mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly/K27/configs', "[Errno 13] Permission denied: '/mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly/K27/configs'")]
Traceback (most recent call last):
  File "/home/default1/miniconda3/envs/unicycler/bin/spades.py", line 626, in main
    pipeline.generate_configs(cfg, spades_home, tmp_configs_dir)
  File "/home/default1/miniconda3/envs/unicycler/share/spades/spades_pipeline/stages/pipeline.py", line 43, in generate_configs
    stage.generate_config(cfg)
  File "/home/default1/miniconda3/envs/unicycler/share/spades/spades_pipeline/stages/spades_stage.py", line 368, in generate_config
    stage.generate_config(self.cfg)
  File "/home/default1/miniconda3/envs/unicycler/share/spades/spades_pipeline/stages/spades_iteration_stage.py", line 142, in generate_config
    support.copy_tree(os.path.join(self.tmp_configs_dir, "debruijn"), dst_configs, preserve_times=False)
  File "/home/default1/miniconda3/envs/unicycler/share/spades/spades_pipeline/support.py", line 963, in copy_tree
    shutil.copytree(src, dst, copy_function = copy_fn)
  File "/home/default1/miniconda3/envs/unicycler/lib/python3.10/shutil.py", line 558, in copytree
    return _copytree(entries=entries, src=src, dst=dst, symlinks=symlinks,
  File "/home/default1/miniconda3/envs/unicycler/lib/python3.10/shutil.py", line 512, in _copytree
    raise Error(errors)
shutil.Error: [('/mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly/configs/debruijn', '/mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly/K27/configs', "[Errno 13] Permission denied: '/mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly/K27/configs'")]


== Error ==  exception caught: <class 'shutil.Error'>

In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.

SPAdes log can be found here: /mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly/spades.log

Thank you for using SPAdes!
unicycler • 265 views
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2
Entering edit mode

This is not really a bioinformatics question.

Either you're not the owner or in the group of the directory or the directory don't have write permission.

Checkout this post: https://www.baeldung.com/linux/chown-chmod-permissions

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