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CCBR / RENEE

A comprehensive quality-control and quantification RNA-seq pipeline
https://CCBR.github.io/RENEE/
MIT License
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RENEE GUI failing #175

Open samarth8392 opened 4 days ago

samarth8392 commented 4 days ago

module loaded ccbrpipeliner/7 and launched a job via renee gui. Terminal captured these errors (before dry run). Seems like some permissions issue under /data/CCBR_Pipeliner?

Traceback (most recent call last):
  File "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.6.2/main.py", line 16, in <module>
    sys.exit(main())
             ^^^^^^
  File "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.6.2/src/renee/__main__.py", line 1500, in main
    args.func(args)
  File "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.6.2/src/renee/gui.py", line 193, in launch_gui
    allout = exec_in_context(run, run_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311/lib/python3.11/site-packages/ccbr_tools/shell.py", line 18, in exec_in_context
    func(*args, **kwargs)
  File "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.6.2/src/renee/run.py", line 55, in run
    dryrun_output = dryrun(
                    ^^^^^^^
  File "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.6.2/src/renee/dryrun.py", line 55, in dryrun
    raise e
  File "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.6.2/src/renee/dryrun.py", line 20, in dryrun
    dryrun_output = subprocess.check_output(
                    ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311/lib/python3.11/subprocess.py", line 466, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311/lib/python3.11/subprocess.py", line 548, in run
    with Popen(*popenargs, **kwargs) as process:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311/lib/python3.11/subprocess.py", line 1024, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311/lib/python3.11/subprocess.py", line 1917, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: 'snakemake'
kopardev commented 4 days ago

@samarth8392 .. can you forcefully run an older version 2.5.x and see if gui works for that?