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tzhu-bio / cisDynet_snakemake

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Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message #5

Open wangzhaohui-001 opened 4 months ago

wangzhaohui-001 commented 4 months ago

when use snakemake -s cisDynet_snakemake.py -j 20. i get this error Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message. fllow is my log file and config.yaml

wangzhaohui-001 commented 4 months ago

2024-02-29T174317.275290.snakemake.log config.yam.txt.txt

tzhu-bio commented 4 months ago

Specific error messages are not available in the log file, please try to run it again and then show the specific error messages.

wangzhaohui-001 commented 4 months ago

image

wangzhaohui-001 commented 4 months ago

i have run it again and again, each time show same error.

tzhu-bio commented 4 months ago

Snakemake does not stop immediately when an error is reported during a run, it will finish running the unfinished task. Please go up and find out exactly where the error was reported.

wangzhaohui-001 commented 4 months ago

Error in rule Organell_mapping_rate: jobid: 0 output: temp_file/T14-8-01_organell_mapping_rate.csv

RuleException: CalledProcessError in line 196 of /home/ug1561/workspace/wangzhaohui/cisDynet_snakemake/cisDynet_snakemake-main/atacqc/cisDynet_snakemake.py: Command 'set -euo pipefail; python /home/ug1561/workspace/wangzhaohui/cisDynet_snakemake/cisDynet_snakemake-main/atacqc/cal_organelle_reads_num.py temp_file/T14-8-01_idxstats.txt temp_file/T14-8-01_organell_mapping_rate.csv --chromosome None' returned non-zero exit status 1. File "/home/ug1561/miniconda3/envs/cisDynet_pipeline/lib/python3.8/site-packages/snakemake/executors/init.py", line 2326, in run_wrapper File "/home/ug1561/workspace/wangzhaohui/cisDynet_snakemake/cisDynet_snakemake-main/atacqc/cisDynet_snakemake.py", line 196, in rule_Organell_mapping_rate File "/home/ug1561/miniconda3/envs/cisDynet_pipeline/lib/python3.8/site-packages/snakemake/executors/init.py", line 568, in _callback File "/home/ug1561/miniconda3/envs/cisDynet_pipeline/lib/python3.8/concurrent/futures/thread.py", line 57, in run File "/home/ug1561/miniconda3/envs/cisDynet_pipeline/lib/python3.8/site-packages/snakemake/executors/init.py", line 554, in cached_or_run File "/home/ug1561/miniconda3/envs/cisDynet_pipeline/lib/python3.8/site-packages/snakemake/executors/init__.py", line 2357, in run_wrapper Exiting because a job execution failed. Look above for error message

i think maybe Organell name paramter is error in config.yaml. My sample is plant , so the Organell name paramte should [organell_chr: mitochondria , chloroplasts ] ?

tzhu-bio commented 4 months ago

Yes, you are right, like the "ChrMt, ChrPt".

wangzhaohui-001 commented 4 months ago

thank you for you reply, but it still no work . i set the organell_chr: ChrMt, ChrPt . 微信图片_20240304090433

tzhu-bio commented 4 months ago

Make sure the chromosome ID for your organelle sequence is correct.

wangzhaohui-001 commented 4 months ago

in my sequence no have organelle sequence , i try set NA or blank ,but still error . so the Organell name paramte should ?

tzhu-bio commented 4 months ago

Sorry, but this step is a must run, so you need to set the sequence of organelles or you will get an error.