3-align output files are missing

[JWJ13164328557]

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]

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]

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.

[skoren]

This looks like it's related to verkko so the appropriate channel would be to ask on the verkko GitHub not here. However, based on the message it looks like your FS has some delay because the job completed but the output was missing so you can follow what snakemake suggest and increase the latency-wait.