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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
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AttributeError #197

Open OsmanthusZhang opened 3 weeks ago

OsmanthusZhang commented 3 weeks ago

Hi, when i running snpArcher, the run result shows error:

AttributeError in file /data_32T/yaozc/snpArcher_1/workflow/rules/fastq.smk, line 6: 'Workflow' object has no attribute 'default_remote_prefix' File "/data_32T/yaozc/snpArcher_1/workflow/rules/fastq.smk", line 6, in

here is my command: nohup snakemake --use-conda --core 16 > logs/PNG_sequencing_20240523_1.log 2>&1 & tail -f logs/PNG_sequencing_20240523_1.log

I checked the file fastq.smk and there are no syntax errors. Then i reset the file about snpArcher, it also have some problem:

subprocess.CalledProcessError: Command 'conda info --json' returned non-zero exit status 127.

here is my command:

snakemake -d .test/ecoli --core 12 --use-conda

Thanks

cademirch commented 3 weeks ago

Please check your snakemake version and that you have pulled the latest commits from the snparcher repo.

OsmanthusZhang commented 3 weeks ago

Thanks for your adivce. Which snakemake version do you suggest I download?

tsackton commented 3 weeks ago

The most recent version of snpArcher works with the most recent version of snakemake (8.x).