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nanoporetech / DTR-phage-pipeline

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job execution failed #8

Closed snayfach closed 3 years ago

snayfach commented 3 years ago

Hello and thanks for the promising tool. I've install the pipeline and am trying to run the example using: snakemake --use-conda --conda-frontend mamba -p -r -j 10

Here's the error I'm getting (with the full log attached):

Traceback (most recent call last): File "/global/homes/s/snayfach/.conda/envs/iontorrent/lib/python3.6/site-packages/snakemake/init.py", line 778, in snakemake executesubworkflows=execute_subworkflows, File "/global/homes/s/snayfach/.conda/envs/iontorrent/lib/python3.6/site-packages/snakemake/workflow.py", line 701, in execute dag.update_checkpoint_dependencies() File "/global/homes/s/snayfach/.conda/envs/iontorrent/lib/python3.6/site-packages/snakemake/dag.py", line 1296, in update_checkpoint_dependencies logger.info("Updating job {} ({}).".format(self.jobid(j), j)) File "/global/homes/s/snayfach/.conda/envs/iontorrent/lib/python3.6/site-packages/snakemake/dag.py", line 702, in jobid return self._jobid[job] KeyError: align_dtr_seqs_to_polished_refs [Tue Dec 22 13:13:19 2020] Finished job 23. 137 of 147 steps (93%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /global/projectb/scratch/snayfach/projects/checkv-db/4_sra/ion_torrent/DTR-phage-pipeline/.snakemake/log/2020-12-22T130253.555676.snakemake.log

log.txt

jmeppley commented 3 years ago

Hi, Stephen,

That is a snakemake bug that I'm hoping will be fixed soon. In the test case at least, simply running snakemake again finishes the workflow.

-John

On Tue, Dec 22, 2020 at 1:27 PM Stephen Nayfach notifications@github.com wrote:

Hello and thanks for the promising tool. I've install the pipeline and am trying to run the example using: snakemake --use-conda --conda-frontend mamba -p -r -j 10

Here's the error I'm getting (with the full log attached):

Traceback (most recent call last): File "/global/homes/s/snayfach/.conda/envs/iontorrent/lib/python3.6/site-packages/snakemake/ init.py", line 778, in snakemake executesubworkflows=execute_subworkflows, File "/global/homes/s/snayfach/.conda/envs/iontorrent/lib/python3.6/site-packages/snakemake/workflow.py", line 701, in execute dag.update_checkpoint_dependencies() File "/global/homes/s/snayfach/.conda/envs/iontorrent/lib/python3.6/site-packages/snakemake/dag.py", line 1296, in update_checkpoint_dependencies logger.info("Updating job {} ({}).".format(self.jobid(j), j)) File "/global/homes/s/snayfach/.conda/envs/iontorrent/lib/python3.6/site-packages/snakemake/dag.py", line 702, in jobid return self._jobid[job] KeyError: align_dtr_seqs_to_polished_refs [Tue Dec 22 13:13:19 2020] Finished job 23. 137 of 147 steps (93%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /global/projectb/scratch/snayfach/projects/checkv-db/4_sra/ion_torrent/DTR-phage-pipeline/.snakemake/log/2020-12-22T130253.555676.snakemake.log

log.txt https://github.com/nanoporetech/DTR-phage-pipeline/files/5732068/log.txt

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snayfach commented 3 years ago

Hi John. Thanks for the quick reply and solution to my problem! Feel free to leave open or close as you prefer.

jmeppley commented 3 years ago

So, it worked for you to run it again?

On Tue, Dec 22, 2020, 2:41 PM Stephen Nayfach notifications@github.com wrote:

Hi John. Thanks for the quick reply and solution to my problem! Feel free to leave open or close as you prefer.

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