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jyyulab / SJARACNe

Scalable Tool for Gene Network Reverse Engineering
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Permission Denied #27

Closed RavulaPitt closed 2 years ago

RavulaPitt commented 4 years ago

Hello,

I am testing SJARACNe on my university HPC in a conda env.

I created a conda env with python 3.6.1, installed dependencies, and installed from source as described on README.

When running SJARCNE I get the following errors as seen in excerpt of output file below.

  1. "PermissionError: [Errno 13] Permission denied"
  2. Output is missing expected field

I saw that there was a closed ticket that also referenced "permission denied" but what was mentioned in that thread was not helpful for me.

`/ihome/uchandran/raa144/.conda/envs/py36/bin/cwltool 1.0.20190618201008 Resolved '/ihome/uchandran/raa144/.conda/envs/py36/lib/python3.6/site-packages/SJARACNe-0.2.0-py3.6.egg/SJARACNe/cwl/sjaracne_workflow.cwl' to 'file:///ihome/uchandran/raa144/.conda/envs/py36/lib/python3.6/site-packages/SJARACNe-0.2.0-py3.6.egg/SJARACNe/cwl/sjaracne_workflow.cwl' [workflow ] start [workflow ] starting step create_seeds [step create_seeds] start [workflow ] starting step ch_ending_probe [step ch_ending_probe] start [job ch_ending_probe] /scratch/slurm-3928660/b9o4p57e$ ch_line_ending.py \ -i \ tf.txt [workflow ] starting step create_adjmat_names [step create_adjmat_names] start [workflow ] starting step ch_ending_exp [step ch_ending_exp] start

Exception while running job Traceback (most recent call last): File "/ihome/uchandran/raa144/.conda/envs/py36/lib/python3.6/site-packages/cwltool/job.py", line 319, in _execute monitor_function=monitor_function File "/ihome/uchandran/raa144/.conda/envs/py36/lib/python3.6/site-packages/cwltool/job.py", line 777, in _job_popen cwd=cwd) File "/ihome/uchandran/raa144/.conda/envs/py36/lib/python3.6/subprocess.py", line 707, in init restore_signals, start_new_session) File "/ihome/uchandran/raa144/.conda/envs/py36/lib/python3.6/subprocess.py", line 1326, in _execute_child raise child_exception_type(errno_num, err_msg) PermissionError: [Errno 13] Permission denied

[job ch_ending_probe] completed permanentFail [workflow ] starting step validate_files [step validate_files] start [job ch_ending_exp] /scratch/slurm-3928660/63isl_y2$ ch_line_ending.py \ -i \ input.exp [job validate_files] /scratch/slurm-3928660/ostrz224$ QC_input.py \ -e \ input.exp \ -g \ tf.txt [step ch_ending_probe] Output is missing expected field file:///ihome/uchandran/raa144/.conda/envs/py36/lib/python3.6/site-packages/SJARACNe-0.2.0-py3.6.egg/SJARACNe/cwl/sjaracne_workflow.cwl#ch_ending_probe/out_file [step ch_ending_probe] completed permanentFail`

RavulaPitt commented 4 years ago

Solution found:

https://github.com/jyyulab/SJARACNe/issues/19

As user points out, it is necessary to change the file permissions for all scripts in /usr/local/lib/python3.6/dist-packages/SJARACNe-0.2.0-py3.6.egg/SJARACNe/bin.

adamdingliang commented 4 years ago

It is kinda hard to replicate this error in my env. We are still trying to figure out the root cause.

zjgt commented 2 years ago

I encountered the same issue and solved by changing permission, although my mac site package location is different: Users/myname/opt/anaconda3/envs/py374/lib/python3.7/dist-packages/SJARACNe-0.2.0-py3.6.egg/SJARACNe/bin/. After entering into this directory in powershell, chmod 755 QC_input.py ch_line_ending.py then everything works fine.

adamdingliang commented 2 years ago

Don't see this problem in the new release SJARACNe 0.2.1. Please repen if the problem persists. Thanks.