error using cellex esmu files

[JonnyBaseball]

Hi -

Thank you for developing these packages. I have been successful running my data in CELLECT with the precomputed CELLEX datasets. The results look great. However, I have run into issues with using the .esmu files. For example, I've tried running the MOCA trajectory files and have run into errors. I have also tried the CELLEX example with the mousebrain vascular scRNA data and have also run into errors. Here is the error from trying the vascular mousebrain.esmu data:

Error in rule prioritize_annotations:
jobid: 2
output: GWAS.vascular.test/CELLECT-MAGMA/out/prioritization/mousebrain_vascular_cells.esmu__GWAS.magmause.cell_type_results.txt
log: GWAS.vascular.test/CELLECT-MAGMA/logs/log.prioritize_annotations_snake.mousebrain_vascular_cells.esmu.GWAS.magmause.txt (check log file(s) for error message)
conda-env: /Users/XX/Downloads/cellect/CELLECT/.snakemake/conda/c2fb0307e0730e9c68f49bed1826c2eb
RuleException:
CalledProcessError in line 276 of /Users/XX/Downloads/cellect/CELLECT/cellect-magma.snakefile:
Command 'source /Users/XX/anaconda-master/ENTER/bin/activate '/Users/XX/Downloads/cellect/CELLECT/.snakemake/conda/c2fb0307e0730e9c68f49bed1826c2eb'; python /Users/XX/Downloads/cellect/CELLECT/.snakemake/scripts/tmps14v46z1.prioritize_annotations_snake.py' returned non-zero exit status 1.
File "/Users/XX/Downloads/cellect/CELLECT/cellect-magma.snakefile", line 276, in __rule_prioritize_annotations
File "/Users/XX/anaconda-master/ENTER/envs/cellect/lib/python3.8/concurrent/futures/thread.py", line 57, in run

RuleException:
CalledProcessError in line 276 of /Users/XX/Downloads/cellect/CELLECT/cellect-magma.snakefile:
Command 'source /Users/XX/anaconda-master/ENTER/bin/activate '/Users/XX/Downloads/cellect/CELLECT/.snakemake/conda/c2fb0307e0730e9c68f49bed1826c2eb'; python /Users/XX/Downloads/cellect/CELLECT/.snakemake/scripts/tmpawe26t4t.prioritize_annotations_snake.py' returned non-zero exit status 1.
File "/Users/XX/Downloads/cellect/CELLECT/cellect-magma.snakefile", line 276, in __rule_prioritize_annotations
File "/Users/XX/anaconda-master/ENTER/envs/cellect/lib/python3.8/concurrent/futures/thread.py", line 57, in run

Is there a way to convert the .esmu files to .mu like the other precomputed datafiles? Or is there a step that I'm missing in preprocessing?

Thanks,
Jon

[pascaltimshel]

Hi Jon,
What do you mean by "convert the .esmu files to .mu"? Can you give more details to you problem?

[DC-Jade]

Hi -

Thank you for developing these packages. I have been successful running my data in CELLECT with the precomputed CELLEX datasets. The results look great. However, I have run into issues with using the .esmu files. For example, I've tried running the MOCA trajectory files and have run into errors. I have also tried the CELLEX example with the mousebrain vascular scRNA data and have also run into errors. Here is the error from trying the vascular mousebrain.esmu data:

Error in rule prioritize_annotations: jobid: 2 output: GWAS.vascular.test/CELLECT-MAGMA/out/prioritization/mousebrain_vascular_cells.esmu__GWAS.magmause.cell_type_results.txt log: GWAS.vascular.test/CELLECT-MAGMA/logs/log.prioritize_annotations_snake.mousebrain_vascular_cells.esmu.GWAS.magmause.txt (check log file(s) for error message) conda-env: /Users/XX/Downloads/cellect/CELLECT/.snakemake/conda/c2fb0307e0730e9c68f49bed1826c2eb RuleException: CalledProcessError in line 276 of /Users/XX/Downloads/cellect/CELLECT/cellect-magma.snakefile: Command 'source /Users/XX/anaconda-master/ENTER/bin/activate '/Users/XX/Downloads/cellect/CELLECT/.snakemake/conda/c2fb0307e0730e9c68f49bed1826c2eb'; python /Users/XX/Downloads/cellect/CELLECT/.snakemake/scripts/tmps14v46z1.prioritize_annotations_snake.py' returned non-zero exit status 1. File "/Users/XX/Downloads/cellect/CELLECT/cellect-magma.snakefile", line 276, in __rule_prioritize_annotations File "/Users/XX/anaconda-master/ENTER/envs/cellect/lib/python3.8/concurrent/futures/thread.py", line 57, in run

RuleException: CalledProcessError in line 276 of /Users/XX/Downloads/cellect/CELLECT/cellect-magma.snakefile: Command 'source /Users/XX/anaconda-master/ENTER/bin/activate '/Users/XX/Downloads/cellect/CELLECT/.snakemake/conda/c2fb0307e0730e9c68f49bed1826c2eb'; python /Users/XX/Downloads/cellect/CELLECT/.snakemake/scripts/tmpawe26t4t.prioritize_annotations_snake.py' returned non-zero exit status 1. File "/Users/XX/Downloads/cellect/CELLECT/cellect-magma.snakefile", line 276, in __rule_prioritize_annotations File "/Users/XX/anaconda-master/ENTER/envs/cellect/lib/python3.8/concurrent/futures/thread.py", line 57, in run

Is there a way to convert the .esmu files to .mu like the other precomputed datafiles? Or is there a step that I'm missing in preprocessing?

Thanks, Jon

I ran into the same problem
log:
'
Error in rule prioritize_annotations:
jobid: 2
input: /Volumes/backup/project/project_scz/result/20231007_magma_cell_type_specific/CELLECT-MAGMA/precomputation/pgc_scz/pgc_scz.resid_correct_all.gsa.genes.out, ~/.github/CELLECT/example/mousebrain.mu.32.csv
output: /Volumes/backup/project/project_scz/result/20231007_magma_cell_type_specific/CELLECT-MAGMA/out/prioritization/mousebrain32__pgc_scz.cell_type_results.txt
log: /Volumes/backup/project/project_scz/result/20231007_magma_cell_type_specific/CELLECT-MAGMA/logs/log.prioritize_annotations_snake.mousebrain32.pgc_scz.txt (check log file(s) for error details)
conda-env: ~/.github/CELLECT/.snakemake/conda/d4d153c95762c01c2da4ee28484ad4db_
'