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I'm wondering how Snakemake deals with output to stdout and stderr that is generated when running a rule with a shell: command.

I ran the following rule and only got informed that there was a non-zero exit code. However, I did not get a stack trace. To get access to the stack trace I had to run the shell command manually:

# Shortened for clarity
rule parse:
    input:
        sequences = rules.join_downloads.output
    output:
        sequences = "data/sequences.fasta"
    shell:
        """
        augur parse
        """

Why is that? And can I somehow make Snakemake output more detailed information when something goes wrong to help with debugging?

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You usually define a log file like below, and redirect the stdout and/or stderr to it. Stdout is >, stderr is 2> and both of them combined is &>.

rule parse:
    input:
        sequences = rules.join_downloads.output
    output:
        sequences = "data/sequences.fasta"
    log:
        my_output/my_log.log
    shell:
        """
        augur parse 2> {log}
        """
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