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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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Error in rule compute_d4 #119

Closed weirdo-onlooker closed 10 months ago

weirdo-onlooker commented 10 months ago

I have just installed and executed snakemake -d .test/ecoli --cores 1 --use-conda according to the documentation. Now, I am encountering an error. [Sat Aug 12 10:16:32 2023] Error in rule compute_d4: jobid: 16 input: results/GCA_000008865.2/bams/SAMN12676327_final.bam, results/GCA_000008865.2/bams/SAMN12676327_final.bam.bai output: results/GCA_000008865.2/callable_sites/SAMN12676327.mosdepth.global.dist.txt, results/GCA_000008865.2/callable_sites/SAMN12676327.per-base.d4, results/GCA_000008865.2/callable_sites/SAMN12676327.mosdepth.summary.txt log: logs/GCA_000008865.2/computed4/SAMN12676327.txt (check log file(s) for error details) conda-env: /ifs1/User/lengliang/yaozc/biosoft/snpArcher/.test/ecoli/.snakemake/conda/5cf955825d414ab876796f0a36009909 shell: mosdepth --d4 -t 1 results/GCA_000008865.2/callable_sites/SAMN12676327 results/GCA_000008865.2/bams/SAMN12676327_final.bam &> logs/GCA_000008865.2/compute_d4/SAMN12676327.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2023-08-12T101149.778379.snakemake.log

shell: snakemake -d .test/ecoli --cores 1 --use-conda

What should I do to address this issue?

cademirch commented 10 months ago

Hi @weirdo-onlooker, can you pull the latest version of snpArcher? There was an issue with the latest version of mosdepth that is likely causing your issue.

weirdo-onlooker commented 10 months ago

Hi @cademirch, I downloaded snpArcher again by using "git clone https://github.com/harvardinformatics/snpArcher.git," but I still encountered the same issue. Could you please provide specific instructions on how to resolve this?

cademirch commented 10 months ago

@weirdo-onlooker Sorry that didn't work. Could you paste the contents of the log file: .test/ecoli/logs/GCA_000008865.2/compute_d4/SAMN12676327.txt? Could you also run the command snakemake --version and paste the output of that.

weirdo-onlooker commented 10 months ago

@cademirch The "compute_d4" file has not been generated in the folder GCA_000008865.2. And the Snakemake version used is 7.32.3.

cademirch commented 10 months ago

@weirdo-onlooker Unfortunately I can't recreate this issue. Could you check that the env file: workflow/envs/cov_filter.yaml has mosdepth==0.3.3?

It's also possible the cov_filter conda env still has the broken mosdepth version installed. You can check this like so:

conda activate /ifs1/User/lengliang/yaozc/biosoft/snpArcher/.test/ecoli/.snakemake/conda/5cf955825d414ab876796f0a36009909_
mosdepth --version

Please try this check that the mosdepth version is 0.3.3.

Lastly, are there any logs produced?

weirdo-onlooker commented 10 months ago

@cademirch Thank you for your advice！ I changed 'mosdepth>=0.3.3' to 'mosdepth==0.3.3' in workflow/envs/cov_filter.yaml, and after trying again, it ran successfully！