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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
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3-align output files are missing #50032

Open JWJ13164328557 opened 1 month ago

JWJ13164328557 commented 1 month ago

How to solve it：

Select jobs to execute...

[Wed Aug 14 14:31:51 2024] rule indexGraph: input: 2-processGraph/unitig-unrolled-hifi-resolved.gfa output: 3-align/graph.index, 3-align/diploid.index log: 3-align/index.err jobid: 100 reason: Missing output files: 3-align/graph.index, 3-align/diploid.index resources: tmpdir=/tmp, job_id=1, n_cpus=1, mem_gb=1, time_h=24

Waiting at most 2 seconds for missing files. MissingOutputException in rule indexGraph in file /home/liux/miniconda3/envs/Genomic/lib/verkko/Snakefiles/3-alignONT.sm, line 24: Job 100 completed successfully, but some output files are missing. Missing files after 2 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait: 3-align/graph.index 3-align/diploid.index Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-08-14T143150.185221.snakemake.log ERROR! Not running final consensus since no rukki paths provided!

martin-g commented 1 month ago

This repository contains several thousands of recipes! It would be helpful to mention the one either in the title or the description of the issue!

aliciaaevans commented 1 month ago

There's no "3-align" recipe in Bioconda. This looks like an error from Snakemake, so you should find the indexGraph rule in the Snakefile to see what code is actually being run and whether it is actually running a package from Bioconda. Also check those log files 3-align/index.err and .snakemake/log/2024-08-14T143150.185221.snakemake.log for messages.