version:
commit ccd826a5f8c8b8982b183c1efb819ba9d9328430
Author: Peter Audano peter.audano@jax.org
Date: Wed May 31 09:32:09 2023 -0400
In call.snakefile with pandas 2.0.1 you get this error:
RuleException:
AttributeError in file
/panfs/jay/groups/7/hsiehph/gordo893/pipelines/pav/rules/call.snakefile,
line 466:
'DataFrame' object has no attribute 'append'
File
"/panfs/jay/groups/7/hsiehph/gordo893/pipelines/pav/rules/call.snakefile",
line 466, in rule_call_integrate_sources
File
"/home/hsiehph/shared/conda_shared/envs/pav3/lib/python3.9/site-packages/pandas/core/generic.py",
line 5989, in getattr__
File
"/home/hsiehph/shared/conda_shared/envs/pav3/lib/python3.9/concurrent/futures/thread.py",
line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
So why wasn't this problem before now? Because pandas used to allow dataframe.append but doesn't any longer. But I think you intended to append to the python list insdel_drp_list which has no problem.
I also wonder if this caused some incorrect results in the past?
Hi, Pete,
version: commit ccd826a5f8c8b8982b183c1efb819ba9d9328430 Author: Peter Audano peter.audano@jax.org Date: Wed May 31 09:32:09 2023 -0400
In call.snakefile with pandas 2.0.1 you get this error: RuleException:
AttributeError in file
/panfs/jay/groups/7/hsiehph/gordo893/pipelines/pav/rules/call.snakefile,
line 466:
'DataFrame' object has no attribute 'append'
File
"/panfs/jay/groups/7/hsiehph/gordo893/pipelines/pav/rules/call.snakefile",
line 466, in rule_call_integrate_sources
File
"/home/hsiehph/shared/conda_shared/envs/pav3/lib/python3.9/site-packages/pandas/core/generic.py", line 5989, in getattr__
File
"/home/hsiehph/shared/conda_shared/envs/pav3/lib/python3.9/concurrent/futures/thread.py",
line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
The lines that have this problem are:
Or here are the lines in context:
I'm wondering if you really meant to write:
insdel_drp_list.append(df_insdel_drp)
snv_drp_list.append(df_snv_drp)
?
So why wasn't this problem before now? Because pandas used to allow dataframe.append but doesn't any longer. But I think you intended to append to the python list insdel_drp_list which has no problem.
I also wonder if this caused some incorrect results in the past?
Let me know.
Best wishes, David