I installed the latest version of atlas and found this error when I run "atlas run qc"

[botellaflotante]

[Atlas] INFO: Atlas version: 2.9.1 Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem=300 Singularity containers: ignored Traceback (most recent call last): File "/home/jose/miniconda3/envs/atlasenv/lib/python3.8/site-packages/snakemake/init.py", line 722, in snakemake success = workflow.execute( File "/home/jose/miniconda3/envs/atlasenv/lib/python3.8/site-packages/snakemake/workflow.py", line 1092, in execute logger.run_info("\n".join(dag.stats())) File "/home/jose/miniconda3/envs/atlasenv/lib/python3.8/site-packages/snakemake/dag.py", line 2248, in stats yield tabulate(rows, headers="keys") File "/home/jose/miniconda3/envs/atlasenv/lib/python3.8/site-packages/tabulate/init.py", line 2048, in tabulate list_of_lists, headers = _normalize_tabular_data( File "/home/jose/miniconda3/envs/atlasenv/lib/python3.8/site-packages/tabulate/init.py", line 1471, in _normalize_tabular_data rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows)) File "/home/jose/miniconda3/envs/atlasenv/lib/python3.8/site-packages/tabulate/init.py", line 1471, in rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows)) File "/home/jose/miniconda3/envs/atlasenv/lib/python3.8/site-packages/tabulate/init.py", line 107, in _is_separating_line (len(row) >= 1 and row[0] == SEPARATING_LINE) File "/home/jose/miniconda3/envs/atlasenv/lib/python3.8/site-packages/snakemake/rules.py", line 1215, in eq return self.name == other.name and self.output == other.output AttributeError: 'str' object has no attribute 'name' [Atlas] CRITICAL: Command 'snakemake --snakefile /home/jose/miniconda3/envs/atlasenv/lib/python3.8/site-packages/atlas/workflow/Snakefile --directory /linuxhome/tmp/jose/endophytes --jobs 20 --rerun-incomplete --configfile '/linuxhome/tmp/jose/endophytes/config.yaml' --nolock --use-conda --conda-prefix /linuxhome/tmp/jose/endophytes/databases/conda_envs --resources mem=478 mem_mb=489818 java_mem=406 --scheduler greedy qc --resources mem=300 ' returned non-zero exit status 1.

Any clue?

[SilasK]

No clue. Can you check the snakemake version. You cal also try to update snakemake to the latest version.

[botellaflotante]

Thanks for the quick response, snakemake version from atlasenv is 7.3.8. Do you know how to update it?

Best

El mié, 2 nov 2022 a las 7:58, Silas Kieser @.***>) escribió:

No clue. Can you check the snakemake version. You cal also try to update snakemake to the latest version.

— Reply to this email directly, view it on GitHub https://github.com/metagenome-atlas/atlas/issues/574#issuecomment-1300051059, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMZB54PRM2LQCXDC6N2SULDWGJCNZANCNFSM6AAAAAARUS3ZTU . You are receiving this because you authored the thread.Message ID: @.***>

[SilasK]

mamba install snakemake=7.18.1

If you don't have mamaba installed:

conda install mamba

[SilasK]

ah and what is your python version? The update to python 3.11 could create such bugs.

[botellaflotante]

thanks, python is 3.8.13. when I try installing snakemake I get

" Looking for: ['snakemake=7.18.1']

ursky/linux-64 No change ursky/noarch No change r/linux-64 No change pkgs/r/noarch No change pkgs/r/linux-64 No change pkgs/main/noarch 817.7kB @ 1.5MB/s 0.2s r/noarch No change bioconda/linux-64 4.4MB @ 3.0MB/s 1.6s pkgs/main/linux-64 4.9MB @ 2.6MB/s 1.2s conda-forge/noarch @ 3.5MB/s 2.9s conda-forge/linux-64 @ 4.5MB/s 6.7s bioconda/noarch 3.8MB @ 289.5kB/s 13.3s

Pinned packages:

• python 3.8.*

Encountered problems while solving:

• package snakemake-7.18.1-hdfd78af_0 requires snakemake-minimal 7.18.1.*, but none of the providers can be installed"

best

El jue, 3 nov 2022 a las 6:54, Silas Kieser @.***>) escribió:

ah and what is your python version? The update to python 3.11 could create such bugs.

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[AroArz]

Your issue is related to https://github.com/snakemake/snakemake/issues/1899.

Solutions include upgrading to the latest snakemake version or running

mamba install 'tabulate=0.8.10'

[SilasK]

Should I adapt the conda package, to fix this?

[SilasK]

Thank you very much