Exiting because a job execution failed.
Justan6 opened this issue · 3 comments
Hello,
I think something went wrong somewhere and it could not finish the job.
2022-08-12 15:10:26 (301 MB/s) - ‘/home/nwezejus/Peat_metagenome2022/ATLAS/databases/adapters.fa’ saved [13954/13954]
[Fri Aug 12 15:10:27 2022]
Finished job 8.
2 of 251 steps (1%) done
--2022-08-12 15:10:31-- https://zenodo.org/record/1134890/files/checkm_data_v1.0.9.tar.gz
Resolving zenodo.org (zenodo.org)... 137.138.76.77
Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 288590617 (275M) [application/octet-stream]
Saving to: ‘checkm_data_v1.0.9.tar.gz’
checkm_data_v1.0.9.tar.gz 100%[=========================================================================================================================================>] 275.22M 6.62MB/s in 48s
2022-08-12 15:11:20 (5.79 MB/s) - ‘checkm_data_v1.0.9.tar.gz’ saved [288590617/288590617]
[Fri Aug 12 15:12:10 2022]
Finished job 185.
3 of 251 steps (1%) done
Removing temporary output checkm_data_v1.0.9.tar.gz.
[Fri Aug 12 15:39:54 2022]
Finished job 22.
4 of 251 steps (2%) done
[Fri Aug 12 15:40:28 2022]
Finished job 34.
5 of 251 steps (2%) done
[Fri Aug 12 15:40:51 2022]
Finished job 46.
6 of 251 steps (2%) done
[Fri Aug 12 15:42:10 2022]
Finished job 7.
7 of 251 steps (3%) done
Touching output file /home/nwezejus/Peat_metagenome2022/ATLAS/databases/GTDB_V06/downloaded_success.
[Fri Aug 12 18:07:54 2022]
Finished job 218.
8 of 251 steps (3%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Note the path to the log file for debugging.
Documentation is available at: https://metagenome-atlas.readthedocs.io
Issues can be raised at: https://github.com/metagenome-atlas/atlas/issues
Complete log: .snakemake/log/2022-08-12T143045.422689.snakemake.log
[Atlas] CRITICAL: Command 'snakemake --snakefile /home/nwezejus/miniconda3/envs/atlasenv/lib/python3.8/site-packages/atlas/workflow/Snakefile --directory /home/nwezejus/Peat_metagenome2022/ATLAS --jobs 96 --rerun-incomplete --configfile '/home/nwezejus/Peat_metagenome2022/ATLAS/config.yaml' --nolock --use-conda --conda-prefix /home/nwezejus/Peat_metagenome2022/ATLAS/databases/conda_envs --resources mem=448 mem_mb=459457 java_mem=381 --scheduler greedy all ' returned non-zero exit status 1.
atlas run all 18626.63s user 3026.16s system 166% cpu 3:37:13.84 total
Hello Justan, I have the same issue. Anyone knows how to solve this problem? Many thanks!
Hey I just pushed the latest version on conda. Could you install the new version 2.12
If you ran again in the error please run grep Error -a7 on the snakemake log file
.snakemake/log/2022-08-12T143045.422689.snakemake.log
Here
There was no activity since some time. I hope your issue is solved in the mean time.
This issue will automatically close soon if no further activity occurs.
Thank you for your contributions.