GenoTools: Advanced Genotype Data Analysis A robust suite for processing genotype data, offering genotype calling (.idat to PLINK), comprehensive sample/variant QC, and ancestry estimation. Ideal for computational biology and genetics research.
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containerized predictions fail due to permissions in the container #141
Describe the bug
when attempting to run containerized predictions, a user with an unknown OS encountered the following error:
Getting Common SNPs
/usr/local/lib/python3.10/dist-packages/genotools/utils.py:404: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
bim1 = pd.read_csv(f'{geno_path1}.bim', sep='\t', header=None)
Traceback (most recent call last):
File "/usr/local/bin/genotools", line 8, in <module>
sys.exit(handle_main())
File "/usr/local/lib/python3.10/dist-packages/genotools/__main__.py", line 152, in handle_main
out_dict = execute_pipeline(run_steps_list, ordered_steps, args_dict['geno_path'], args_dict['out'], samp_qc=samp_qc, var_qc=var_qc, ancestry=ancestry, assoc=assoc, args=args_dict, tmp_dir=tmp_dir)
File "/usr/local/lib/python3.10/dist-packages/genotools/pipeline.py", line 128, in execute_pipeline
out_dict[step] = steps_dict[step]()
File "/usr/local/lib/python3.10/dist-packages/genotools/ancestry.py", line 1103, in run_ancestry
trained_clf, pred = self.get_containerized_predictions(
File "/usr/local/lib/python3.10/dist-packages/genotools/ancestry.py", line 681, in get_containerized_predictions
X_test.to_csv(f'{container_dir}/X_test.txt', sep='\t', index=False)
File "/usr/local/lib/python3.10/dist-packages/pandas/core/generic.py", line 3772, in to_csv
return DataFrameRenderer(formatter).to_csv(
File "/usr/local/lib/python3.10/dist-packages/pandas/io/formats/format.py", line 1186, in to_csv
csv_formatter.save()
File "/usr/local/lib/python3.10/dist-packages/pandas/io/formats/csvs.py", line 240, in save
with get_handle(
File "/usr/local/lib/python3.10/dist-packages/pandas/io/common.py", line 859, in get_handle
handle = open(
PermissionError: [Errno 13] Permission denied: '/usr/local/lib/python3.10/dist-packages/genotools/container/X_test.txt'
To Reproduce
Steps to reproduce the behavior (NA if not applicable). Can include commands that were run:
user attempted to run:
Expected behavior
predictions should be assigned via a model that is copied over to the container
Desktop (please complete the following information):
OS:
Version 1.0.0
Python version: 3.10
Additional context
This is expected to be a result of processes being run in an hpc system that does not have docker available. the --singularity option should solve this if singularity is available on the system, otherwise user will have to train a new model locally using the base command:
Describe the bug when attempting to run containerized predictions, a user with an unknown OS encountered the following error:
To Reproduce Steps to reproduce the behavior (NA if not applicable). Can include commands that were run: user attempted to run:
Expected behavior predictions should be assigned via a model that is copied over to the container
Desktop (please complete the following information):
Additional context This is expected to be a result of processes being run in an hpc system that does not have docker available. the --singularity option should solve this if singularity is available on the system, otherwise user will have to train a new model locally using the base command: