Error in "binning.smk" and snakemake "returned non-zero exit status 1"

[akbyers]

Hi, I'm having trouble with the binning step, a couple of different error codes coming up. The first of several errors appear to be related to "No columns to parse from file" in the binning.smk workflow? The second critical error related to snakemake, with a non-zero exit status being returned.

Sorry I can't be anymore descriptive; i'm pretty new to all of this.

"Error in rule get_unique_cluster_attribution: jobid: 0 output: SL1-41/binning/metabat/cluster_attribution.tsv

RuleException: EmptyDataError in line 265 of /home/abyers/miniconda2/envs/atlasenv/lib/python3.8/site-packages/atlas/workflow/rules/binning.smk: No columns to parse from file File "/home/abyers/miniconda2/envs/atlasenv/lib/python3.8/site-packages/atlas/workflow/rules/binning.smk", line 265, in __rule_get_unique_cluster_attribution File "/home/abyers/miniconda2/envs/atlasenv/lib/python3.8/site-packages/pandas/util/_decorators.py", line 311, in wrapper File "/home/abyers/miniconda2/envs/atlasenv/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv File "/home/abyers/miniconda2/envs/atlasenv/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 575, in _read File "/home/abyers/miniconda2/envs/atlasenv/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 933, in init File "/home/abyers/miniconda2/envs/atlasenv/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1235, in _make_engine File "/home/abyers/miniconda2/envs/atlasenv/lib/python3.8/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 75, in init File "pandas/_libs/parsers.pyx", line 551, in pandas._libs.parsers.TextReader.cinit File "/home/abyers/miniconda2/envs/atlasenv/lib/python3.8/concurrent/futures/thread.py", line 57, in run Exiting because a job execution failed. Look above for error message Finished parsing hits for 10 of 19 (52.63%) bins.. Finished parsing hits for 19 of 19 (100.00%) bins. [2022-04-22 12:08:38] INFO: QA information written to: SL1-43/binning/DASTool/checkm/taxonomy.tsv [2022-04-22 12:08:38] INFO: { Current stage: 0:00:02.428 || Total: 0:00:02.428 } [Fri Apr 22 12:08:38 2022] Finished job 190. 44 of 61 steps (72%) done [2022-04-22 12:08:39] INFO: QA information written to: SL1-44/binning/DASTool/checkm/taxonomy.tsv [2022-04-22 12:08:39] INFO: { Current stage: 0:00:02.899 || Total: 0:00:02.899 } [Fri Apr 22 12:08:39 2022] Finished job 191. 45 of 61 steps (74%) 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 The code used to generate one or several output files has changed: To inspect which output files have changes, run 'snakemake --list-code-changes'. To trigger a re-run, use 'snakemake -R $(snakemake --list-code-changes)'. The input used to generate one or several output files has changed: To inspect which output files have changes, run 'snakemake --list-input-changes'. To trigger a re-run, use 'snakemake -R $(snakemake --list-input-changes)'. The params used to generate one or several output files has changed: To inspect which output files have changes, run 'snakemake --list-params-changes'. To trigger a re-run, use 'snakemake -R $(snakemake --list-params-changes)'. Complete log: .snakemake/log/2022-04-22T094143.983408.snakemake.log [Atlas] CRITICAL: Command 'snakemake --snakefile /home/abyers/miniconda2/envs/atlasenv/lib/python3.8/site-packages/atlas/workflow/Snakefile --directory /raid/projects/scratch/mbiome/atlas --jobs 60 --rerun-incomplete --configfile '/raid/projects/scratch/mbiome/atlas/config.yaml' --nolock --use-conda --conda-prefix /raid/projects/scratch/mbiome/databases/conda_envs --resources mem=5385 mem_mb=5515077 java_mem=4577 --scheduler greedy binning ' returned non-zero exit status 1.

Atlas version 2.9

All the best, Alexa

[SilasK]

The problem is that metabat didn't find any bins.

Could you confirm that the SL1-41/binning/metabat/cluster_attribution.tmp is empty. Check also if there is something in SL1-41/logs/binning/metabat.txt

Probably your samples are difficult to assemble or bin. What microbiome is it? There is not too much you can do.

• You can exclude this sample if it is not a problem for others.
• You can try vamb as final_binner in the config file.
• or only focus on the genes with atlas run genecatalog

I should make this error message much easier. Sorry.

[akbyers]

Thanks for your response! I can confirm it was an issue with that sample, I ran the data through a different binning pipeline and there were 0 bins found. It was soil microbiome data, thankfully just a small test dataset before we move onto the more important samples of interest.

Thanks again

[SilasK]

Good to know. Have you tried different Bonners?

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