Snakemake规则Shell命令为集群作业时的可行性及作业感知问题

Alright, let's break down your questions one by one—this is a super common pitfall when mixing Snakemake with external cluster job submissions, so I’ll walk you through the answers and a concrete solution.

Short answer: It depends on how you structure the command. By default, Snakemake marks a rule as "completed" the second its shell command exits. If your shell command only submits a cluster job (like running sbatch or qsub), that submission finishes in seconds—so Snakemake will think the work is done even though the actual cluster job is still running. This will almost certainly break downstream rules, which will try to use files that haven’t been generated yet.

To make this work correctly, you need to modify the shell command to block until the cluster job finishes. That way, Snakemake only moves on when the actual work is completed.

Not out of the box. If your script just submits the job and exits immediately, Snakemake only sees that the script ran successfully—it has no visibility into the cluster job’s state. But you can fix this by updating shell_script.sh to wait for the cluster job to finish, and pass back the job’s exit code to Snakemake. This lets Snakemake treat the cluster job’s success/failure like any other local command.

Since you’re running Snakemake locally (only the script submits cluster jobs), here’s how to set this up properly:

Step 1: Update shell_script.sh to wait for the cluster job #

Modify your script to track the cluster job ID, wait until it completes, and return the job’s exit status. The exact commands depend on your cluster scheduler—here’s an example for Slurm:

#!/bin/bash
# Submit the cluster job and capture the unique job ID
JOB_ID=$(sbatch --parsable job_that_creates_a.sh)

# Poll the cluster every 30 seconds until the job disappears from the queue
while squeue -j "$JOB_ID" > /dev/null 2>&1; do
    sleep 30
done

# Fetch the job's exit code to pass back to Snakemake
EXIT_CODE=$(sacct -j "$JOB_ID" --format=ExitCode -n | tail -n 1 | awk '{print $1}')

# Exit with the cluster job's code so Snakemake knows if it succeeded/failed
exit "$EXIT_CODE"

For PBS/Torque, replace sbatch with qsub and squeue with qstat to check job status.

Step 2: Adjust your Snakemake rules #

Your rules need to enforce the dependency between file a and file b. With your localrules setup, the code would look like this:

localrules: generate_a, generate_b

rule all:
    input:
        "file_b.txt"

rule generate_a:
    output:
        "file_a.txt"
    shell:
        "./shell_script.sh"  # This script blocks until file_a.txt is fully generated

rule generate_b:
    input:
        "file_a.txt"  # Snakemake will only run this after generate_a finishes successfully
    output:
        "file_b.txt"
    shell:
        "cat {input} > {output}"  # If this also needs a cluster job, apply the same waiting logic here

Key Notes: #

• Shared filesystem: Make sure the cluster job writes file_a.txt to a location your local Snakemake process can access (e.g., a networked shared drive).
• Native blocking: Some schedulers have built-in flags to block until a job finishes (like Slurm’s sbatch --wait). Use that if available—it simplifies the script and avoids polling.
• Error handling: By passing the cluster job’s exit code back, Snakemake will fail gracefully if the cluster job crashes, just like it would for a local command.

内容的提问来源于stack exchange，提问作者Manavalan Gajapathy