JGASmits / AnanseSeurat

Single cell ANANSE Gene-regulatory-network analysis from Seurat objects

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NameError: name 'snakemake' is not defined

sylestiel opened this issue · comments

Dear all @JGASmits @Arts-of-coding @Rebecza,

There is a recurring error that reads as follows:
Traceback (most recent call last):
File "", line 1, in
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f_/lib/python3.10/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = main(fd, parent_sentinel)
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/multiprocessing/spawn.py", line 125, in main
prepare(preparation_data)
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/multiprocessing/spawn.py", line 236, in prepare
fixup_main_from_path(data['init_main_from_path'])
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/multiprocessing/spawn.py", line 287, in fixup_main_from_path
main_content = runpy.run_path(main_path,
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/runpy.py", line 289, in run_path
return run_module_code(code, init_globals, run_name,
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/runpy.py", line 96, in _run_module_code
run_code(code, mod_globals, init_globals,
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/runpy.py", line 86, in run_code
exec(code, run_globals)
File "/Users/pediatrics/mambaforge/envs/anansnake/lib/python3.8/site-packages/anansnake/scripts/maelstrom.py", line 13, in
log = snakemake.log
NameError: name 'snakemake' is not defined
Traceback (most recent call last):
File "", line 1, in
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = main(fd, parent_sentinel)
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/multiprocessing/spawn.py", line 125, in main
prepare(preparation_data)
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/multiprocessing/spawn.py", line 236, in prepare
fixup_main_from_path(data['init_main_from_path'])
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/multiprocessing/spawn.py", line 287, in fixup_main_from_path
main_content = runpy.run_path(main_path,
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/runpy.py", line 289, in run_path
return run_module_code(code, init_globals, run_name,
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/runpy.py", line 96, in _run_module_code
run_code(code, mod_globals, init_globals,
File "/Users/pediatrics/anansnake/.snakemake/conda/3f88efe941f72bcdb4d5867b0d6db92f
/lib/python3.10/runpy.py", line 86, in _run_code
exec(code, run_globals)
File "/Users/pediatrics/mambaforge/envs/anansnake/lib/python3.8/site-packages/anansnake/scripts/maelstrom.py", line 13, in
log = snakemake.log
NameError: name 'snakemake' is not defined

I believe this is happening during the mm10_maelstrom step of following command
anansnake --configfile /Users/pediatrics/Desktop/R_projects/scANANSE/analysis/config.yaml --resources mem_mb=48_000 --cores 12

Suggestions on how to troubleshoot this problem would be much appreciated.
Thank you in advance!!