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jyyulab / SJARACNe

Scalable Tool for Gene Network Reverse Engineering
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problem when trying to runSJARACNe #25

Closed ERIGR closed 2 years ago

ERIGR commented 4 years ago

Hello,

thank you for you quick answer to my previous question.

Indeed, I was able to run the command sjaracne -h without any error message. However, when trying to run analysis on my own data and on the data presented as example : sjaracne local -e ~/data/AML/analysis_SJ_ARACNE/BRCA100.exp -g ~/data/AML/analysis_SJ_ARACNE/tf.txt -o ~/data/AML/analysis_SJ_ARACNE/SJARACNE_out.final . I get the following error message : ``` File "/home/esteve/anaconda2/envs/py36/lib/python3.6/subprocess.py", line 707, in init restore_signals, start_new_session) File "/home/esteve/anaconda2/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 WARNING [job ch_ending_exp] completed permanentFail WARNING [job ch_ending_probe] completed permanentFail WARNING [job validate_files] completed permanentFail ERROR [step ch_ending_exp] Output is missing expected field file:///home/esteve/anaconda2/envs/py36/lib/python3.6/site-packages/SJARACNe-0.2.0-py3.6.egg/SJARACNe/cwl/sjaracne_workflow.cwl#ch_ending_exp/out_file

ERIGR commented 4 years ago 

    restore_signals, start_new_session)
  File "/home/esteve/anaconda2/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
WARNING [job ch_ending_exp] completed permanentFail
WARNING [job ch_ending_probe] completed permanentFail
WARNING [job validate_files] completed permanentFail
ERROR [step ch_ending_exp] Output is missing expected field file:///home/esteve/anaconda2/envs/py36/lib/python3.6/site-packages/SJARACNe-0.2.0-py3.6.egg/SJARACNe/cwl/sjaracne_workflow.cwl#ch_ending_exp/out_file
```. Thanks.
adamdingliang commented 2 years ago

Please try to install the newest release SJARACNe 0.2.1. Also check issue #27 . Reopen this issue if the issue persists. Thanks.