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PNNL-CompBio / coderdata

Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.
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Broad Sanger Omics Step Failing in Build_All.py #214

Closed jjacobson95 closed 1 month ago

jjacobson95 commented 1 month ago

There are a lot of errors in the broad_sanger omics generation step, but I'll keep track of them all here as they are all referring to the same build sequence.

broad_sanger omics step:

SyntaxWarning in Python script /app/04b-nci60-updated.py (Line 77):

SyntaxWarning: invalid escape sequence '\('
  'new_name':[re.split(' |\(|\/',a)[0] for a in nulls['CELL_NAME']],

Fatal Error in R (Likely 02-broadSangerOmics.R file):

Fatal error: cannot create 'R_TempDir'

OSError in Matplotlib (Python, Maybe fit_curve.py file):

OSError: Matplotlib requires access to a writable cache directory, but the default path (/tmp/matplotlib) is not a writable directory, and a temporary directory could not be created; set the MPLCONFIGDIR environment variable to a writable directory

ValueError in Python script /app/fit_curve.py, likely due to an upstream error.

ValueError: No objects to concatenate

Segmentation Fault in R in sanger_files generation. Likely due to the missing R_TempDir.

 *** caught segfault ***
address 0x7fdc5cf5805a, cause 'memory not mapped'

An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
jjacobson95 commented 1 month ago

This resulted from a device out of memory issue. It should be resolved but I will keep open until the whole build process has been confirmed to be working again.