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Error in rule haplotag #32

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sadhanagaddam3 opened this issue Apr 25, 2022 · 0 comments
Open

Error in rule haplotag #32

sadhanagaddam3 opened this issue Apr 25, 2022 · 0 comments

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@sadhanagaddam3
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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

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