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Hi,
Thank you for developing this tool. I tried to run Scenic+ on my mutiome data and I got an error message that I don't quite understand.
Could you help me with this issue.
Thanks in advance
This is the error message 👍
Traceback (most recent call last):
File "/mnt/beegfs/userdata/conda/envs/scenicplus/bin/scenicplus", line 8, in<module>sys.exit(main())
^^^^^^
File "/mnt/beegfs/userdata/conda/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 1137, in main
args.func(args)
File "/mnt/beegfs/userdata/conda/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 388, in motif_enrichment_cistarget
run_motif_enrichment_cistarget(
File "/mnt/beegfs/userdata/conda/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/commands.py", line 242, in run_motif_enrichment_cistarget
cistarget_results: List[cisTarget] = joblib.Parallel(
^^^^^^^^^^^^^^^^
File "/mnt/beegfs/userdata/conda/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1952, in __call__
return output if self.return_generator else list(output)
^^^^^^^^^^^^
File "/mnt/beegfs/userdata/conda/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1595, in _get_outputs
yield from self._retrieve()
File "/mnt/beegfs/userdata/conda/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1699, in _retrieve
self._raise_error_fast()
File "/mnt/beegfs/userdata/conda/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1734, in _raise_error_fast
error_job.get_result(self.timeout)
File "/mnt/beegfs/userdata/conda/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 736, in get_result
returnself._return_or_raise()
^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/beegfs/userdata/conda/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 754, in _return_or_raise
raise self._result
joblib.externals.loky.process_executor.TerminatedWorkerError: A worker process managed by the executor was unexpectedly terminated. This could be caused by a segmentation fault while calling the functionor by an excessive memory usage causing the Operating System to kill the worker.
The exit codes of the workers are {SIGKILL(-9)}
[Tue Jul 23 15:45:06 2024]
Error in rule motif_enrichment_cistarget:
jobid: 12
output: ctx_results.hdf5, ctx_results.html
shell:
scenicplus grn_inference motif_enrichment_cistarget --region_set_folder /mnt/beegfs/scratch/multiome/integrated_objects/scenicplus_analysis/region_sets --cistarget_db_fname /mnt/beegfs/userdata/databases/motif_collections/hg38_screen_v10_clust.regions_vs_motifs.rankings.feather --output_fname_cistarget_result ctx_results.hdf5 --temp_dir /mnt/beegfs/scratch/multiome/integrated_objects/scenicplus_analysis/tmp --species homo_sapiens --fr_overlap_w_ctx_db 0.4 --auc_threshold 0.005 --nes_threshold 3.0 --rank_threshold 0.05 --path_to_motif_annotations /mnt/beegfs/userdata/databases/motif_collections/motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl --annotation_version v10nr_clust --motif_similarity_fdr 0.001 --orthologous_identity_threshold 0.0 --annotations_to_use Direct_annot Orthology_annot --write_html --output_fname_cistarget_html ctx_results.html --n_cpu 32
(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: /mnt/beegfs/scratch/multiome/integrated_objects/scenicplus_analysis/scplus_pipeline/Snakemake/.snakemake/log/2024-07-23T154118.004923.snakemake.log
slurmstepd: error: Detected 9 oom-kill event(s) in StepId=5783995.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.
The text was updated successfully, but these errors were encountered:
Hi,
Thank you for developing this tool. I tried to run Scenic+ on my mutiome data and I got an error message that I don't quite understand.
Could you help me with this issue.
Thanks in advance
This is the error message 👍
The text was updated successfully, but these errors were encountered: