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perslab / CELLECT

CELLECT (CELL-type Expression-specific integration for Complex Traits)
GNU General Public License v3.0
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python3: can't open file 'scripts/parse_results_cmdline.py': [Errno 2] No such file or directory #28

Closed JonThom closed 5 years ago

JonThom commented 5 years ago

[...] /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/out/prioritization/romanov2017SYSTOLICadjMED_UKBB_Loh2018.cell_type_results.txt, /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/out/prioritization/romanov2017T1D_Bradfield2011.cell_type_results.txt, /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/out/prioritization/romanov2017T2D_DIAMANTE_Mahajan2018.cell_type_results.txt, /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/out/prioritization/romanov2017T2D_UKBB_Loh2018.cell_type_results.txt, /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/out/prioritization/romanov2017UC_Jostins2012.cell_type_results.txt, /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/out/prioritization/romanov2017__WHR_Pulit2019.cell_type_results.txt, /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/out/prioritization/romanov2017WHRadjBMI_Pulit2019.cell_type_results.txt, /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/out/prioritization/romanov2017WHRadjBMI_UKBB_Loh2018.cell_type_results.txt, /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/out/prioritization/romanov2017WORRY_Nagel2018.cell_type_results.txt output: /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/results/prioritization.csv output: /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/results/prioritization.csv jobid: 1 wildcards: BASE_OUTPUT_DIR=/scratch/rkm916/BMIcelltypes/CELLECT-LDSC

python3: can't open file 'scripts/parse_results_cmdline.py': [Errno 2] No such file or directory [Fri Oct 11 04:53:44 2019] Error in rule parse_results: jobid: 1 output: /scratch/rkm916/BMIcelltypes/CELLECT-LDSC/results/prioritization.csv shell: python3 scripts/parse_results_cmdline.py --base_output_dir /scratch/rkm916/BMIcelltypes/CELLECT-LDSC (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /nfsdata/projects/jonatan/tools/sc-genetics/CELLECT/.snakemake/log/2019-10-10T122854.199803.snakemake.log

Tobi1kenobi commented 5 years ago

Pushed a hotfix and tested on command line, develop branch should work fine now. But need your approval to push to master @pascaltimshel

pascaltimshel commented 5 years ago

Problem resolved: https://github.com/perslab/CELLECT/commit/2e1ae2262be496f00eebc387ba692f16c865cab3 (Sorry for this stupid error)