Error in rule
Closed this issue · 4 comments
Dear Silas,
I am running atlas assembly step, i can see I have assemblies for some of the samples and then some not. I get this error:
(atlasenv) atlas run assembly --ri
[Atlas] INFO: Atlas version: 2.9.1
Building DAG of jobs...
Traceback (most recent call last):
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/site-packages/snakemake/init.py", line 722, in snakemake
success = workflow.execute(
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/site-packages/snakemake/workflow.py", line 1051, in execute
dag.warn_about_changes(quiet)
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/site-packages/snakemake/dag.py", line 2289, in warn_about_changes
changed = self.get_outputs_with_changes(
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/site-packages/snakemake/dag.py", line 2279, in get_outputs_with_changes
changed = list(chain(*map(is_changed, self.jobs)))
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/site-packages/snakemake/persistence.py", line 477, in
return (f for f in job.expanded_output if func(job, file=f))
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/site-packages/snakemake/persistence.py", line 348, in _code_changed
recorded = self.code(file)
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/site-packages/snakemake/persistence.py", line 323, in code
return self.metadata(path).get("code")
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/site-packages/snakemake/persistence.py", line 302, in metadata
return self._read_record(self._metadata_path, path)
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/site-packages/snakemake/persistence.py", line 423, in _read_record_uncached
return json.load(f)
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/json/init.py", line 293, in load
return loads(fp.read(),
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/json/init.py", line 357, in loads
return _default_decoder.decode(s)
File "/gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/json/decoder.py", line 340, in decode
raise JSONDecodeError("Extra data", s, end)
json.decoder.JSONDecodeError: Extra data: line 1 column 1371 (char 1370)
[Atlas] CRITICAL: Command 'snakemake --snakefile /gxfs_home/cau/sunam162/.conda/envs/ATLAS/envs/atlasenv/lib/python3.8/site-packages/atlas/workflow/Snakefile --directory /gxfs_work1/fs2/work-sh1/sunam162/arch_MAGs_2 --jobs 64 --rerun-incomplete --configfile '/gxfs_work1/fs2/work-sh1/sunam162/arch_MAGs_2/config.yaml' --nolock --use-conda --conda-prefix /gxfs_work1/cau/sunam162/arch_MAGs_2/databases/conda_envs --resources mem=716 mem_mb=734087 java_mem=609 --scheduler greedy assembly --ri ' returned non-zero exit status 1.
I would appreciate your input.
best,
Cynthia
Sorry, I don't see what could be the problem here.
Can you tell me what snakemake version you have. maybe you can try to update it. with mamba install snakemake=7.18.2
does the same error happens when you run atlas run qc ?
can you try to delete the .snakmake directory in your working directory
You could also update atlas mamba install metagenome-atlas=2.12
Dear Silas, we did update to metagenome-atlas=2.12 and snakemake version is 7.15.2 and the problem is and snakemake-minimal.
The issue there is, that:
- package metagenome-atlas-2.12.0-pyhdfd78af_1 requires snakemake-minimal >=7.15.1,<7.16, but none of the providers can be installed