Pore-C-Snakemake
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Error in rule haplotag
When running the pipeline using the test data, I encountered the below error. Could you please help me figure out how to solve this issue? (Until step 5 pipeline ran successfully.) I have seen someone posted same issue previously but I haven't found any solution for the Issue.
Activating conda environment: Pore-C-Snakemake/.snakemake/conda/837059b3 [Mon Apr 25 10:57:32 2022] Finished job 37. 6 of 44 steps (14%) done
[Mon Apr 25 10:57:32 2022] rule haplotag: input: results.test/mapping/NlaIII_run02_batch1_draft1.coord_sort.bam, results.test/mapping/NlaIII_run02_batch1_draft1.coord_sort.bam.bai, results.test/refgenome/draft1.rg.fa output: results.test/mapping/NlaIII_run02_batch1_draft1_unphased.haplotagged.txt log: results.test/logs/results.test/mapping/NlaIII_run02_batch1_draft1_unphased.haplotagged.txt.log jobid: 38 benchmark: results.test/benchmarks/results.test/mapping/NlaIII_run02_batch1_draft1_unphased.haplotagged.txt.bench.txt wildcards: enzyme=NlaIII, run_id=run02, batch_id=batch1, refgenome_id=draft1, phase_set_id=unphased
Activating conda environment: Pore-C-Snakemake/.snakemake/conda/28e79ddf [Mon Apr 25 10:57:35 2022] Error in rule haplotag: jobid: 38 output: results.test/mapping/NlaIII_run02_batch1_draft1_unphased.haplotagged.txt log: results.test/logs/results.test/mapping/NlaIII_run02_batch1_draft1_unphased.haplotagged.txt.log (check log file(s) for error message) conda-env: Pore-C-Snakemake/.snakemake/conda/28e79ddf
RuleException: NoSuchProcess in line 54 of Pore-C-Snakemake/rules/mapping.smk: process PID not found (pid=22217) File "miniconda3/envs/pore-c-snakemake/lib/python3.8/site-packages/snakemake/executors/init.py", line 2114, in run_wrapper File "Pore-C-Snakemake/rules/mapping.smk", line 54, in __rule_haplotag File "miniconda3/envs/pore-c-snakemake/lib/python3.8/contextlib.py", line 113, in enter File "miniconda3/envs/pore-c-snakemake/lib/python3.8/site-packages/psutil/init.py", line 332, in init File "miniconda3/envs/pore-c-snakemake/lib/python3.8/site-packages/psutil/init.py", line 373, in _init File "miniconda3/envs/pore-c-snakemake/lib/python3.8/site-packages/snakemake/executors/init.py", line 529, in _callback File "miniconda3/envs/pore-c-snakemake/lib/python3.8/concurrent/futures/thread.py", line 57, in run File miniconda3/envs/pore-c-snakemake/lib/python3.8/site-packages/snakemake/executors/init.py", line 515, in cached_or_run File "miniconda3/envs/pore-c-snakemake/lib/python3.8/site-packages/snakemake/executors/init.py", line 2199, in run_wrapper Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: Pore-C-Snakemake/.snakemake/log/2022-04-25T102602.105254.snakemake.log