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statgen / pheweb

A tool to build a website to browse hundreds or thousands of GWAS.
MIT License
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"AssertionError" in `pheweb sites -f && pheweb add-rsids && pheweb add-genes` #140

Closed Shicheng-Guo closed 3 years ago

Shicheng-Guo commented 3 years ago

Hi Peter,

Do you have any idea bout AssertionError in pheweb sites -f && pheweb add-rsids && pheweb add-genes

(base) [sguo2@comet-ln2 pheweb]$ pheweb sites -f && pheweb add-rsids && pheweb add-genes

An exception occurred
(Details in /projects/ps/dsci-csb/user/sguo2/pheweb/generated-by-pheweb/tmp/exception-2020-07-27T23-41-47.823037)

(base) [sguo2@comet-ln2 pheweb]$ less /projects/dsci-csb/user/sguo2/pheweb/generated-by-pheweb/tmp/exception-2020-07-27T23-41-47.823037
======= Exception ====
======= Traceback ====
Traceback (most recent call last):
  File "/home/sguo2/bin/miniconda3/lib/python3.7/site-packages/pheweb/command_line.py", line 148, in main
    run(sys.argv[1:])
  File "/home/sguo2/bin/miniconda3/lib/python3.7/site-packages/pheweb/command_line.py", line 142, in run
    handlers[subcommand](argv[1:])
  File "/home/sguo2/bin/miniconda3/lib/python3.7/site-packages/pheweb/command_line.py", line 63, in f
    module.run(argv)
  File "/home/sguo2/bin/miniconda3/lib/python3.7/site-packages/pheweb/load/sites.py", line 36, in run
    manna = MergeManager()
  File "/home/sguo2/bin/miniconda3/lib/python3.7/site-packages/pheweb/load/sites.py", line 83, in __init__
    assert os.path.exists(filepath)
AssertionError
pjvandehaar commented 3 years ago

It sounds like somehow a file in generated-by-pheweb/pheno/ went missing, and now pheweb will tell you which if it ever happens again.