Open twinklevhatkar opened 1 month ago
Hi @twinklevhatkar
Could you run
scenicplus prepare_data prepare_GEX_ACC \
--cisTopic_obj_fname /home/scenicplus/outs/cistopic_obj_final.pkl \
--GEX_anndata_fname /home/scenicplus/outs/integrated_fibro_harmony_final.h5ad \
--out_file /home/scenicplus/outs/ACC_GEX.h5mu \
--bc_transform_func \
--is_not_multiome \
--key_to_group_by GEX:annotation \
--nr_cells_per_metacells 10
This might reveal the underlying error.
Best,
Seppe
Hi! I am fairly new to the Scenic plus tool. I have been able to successfully install and get the snakemake workflow running. I have been working with non multiome data. My workflow runs just fine until it reaches "prepare_GEX_ACC_non_multiome:" module. Because it is non multiomics data, I know the cell barcodes will not match. I have the "GEX:annotation" metadata present for both my assays which helps integrating the two assays.
Here's the log file with my error:
Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 2 Rules claiming more threads will be scaled down. Job stats: job count
AUCell_direct 1 AUCell_extended 1 all 1 eGRN_direct 1 eGRN_extended 1 get_search_space 1 prepare_GEX_ACC_non_multiome 1 prepare_menr 1 region_to_gene 1 scplus_mudata 1 tf_to_gene 1 total 11
Select jobs to execute... Execute 1 jobs...
[Mon Jul 15 00:20:13 2024] localrule prepare_GEX_ACC_non_multiome: input: /home/scenicplus/outs/cistopic_obj_final.pkl, /home/scenicplus/outs/integrated_fibro_harmony_final.h5ad output: /home/scenicplus/outs/ACC_GEX.h5mu jobid: 2 reason: Missing output files: /home/scenicplus/outs/ACC_GEX.h5mu resources: tmpdir=/tmp
[Mon Jul 15 00:20:14 2024] Error in rule prepare_GEX_ACC_non_multiome: jobid: 2 input: /home/scenicplus/outs/cistopic_obj_final.pkl, /home/scenicplus/outs/integrated_fibro_harmony_final.h5ad output: /home/scenicplus/outs/ACC_GEX.h5mu shell:
Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-07-15T002013.095171.snakemake.log WorkflowError: At least one job did not complete successfully.
######## My log file doesn't indicate where the issue is. Any help would be appreciated. I am not sure what I'm missing here?!
Thanks!
2024-07-15T002013.095171.snakemake.log