Question: Snakemake logging error
1
gravatar for camerond
12 months ago by
camerond150
Cardiff
camerond150 wrote:

I'm building a Snakefile and getting an error I'm struggling to fix when trying to add the log parameter in my homer annotation rule.

Here is the Snakefile:

threshold="25 33 5 66 75".split()

rule all:
    input:
        expand("homer_files/annotation_files/ATAC24to31_fetal_hMG_consensusPeak.{THRESH}.homerann.txt", THRESH=threshold),

rule homer_annotation:
    input:
        "diffbind_files/ATAC24_31_fetalMG_.{THRESH}peakset.bed"
    output:
        "homer_files/annotation_files/ATAC24to31_fetal_hMG_consensusPeak.{THRESH}.homerann.txt"
    log:
            "logs/homer/annotation.ATAC24to31_fetal_hMG.consensusPeak.(THRESH}.log"
    shell:
        "annotatePeaks.pl {input} hg19 > {output}"

Now when I run this without the log parameter I get 5 separate files created as expected, however if I try to include it, I get the following error:

SyntaxError:
Not all output, log and benchmark files of rule homer_annotation contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
  File "/c8000xd3/big-c1477909/foetal_hMG_analysis/ATAC_24to31_foetal_hMG_May19/Snakefile", line 26, in <module>

I'm not sure what is going on here, and have never came across this before when running very similar rules. The way I'm reading this, a separate log file should be created for each iteration of the rule, but the error would suggest otherwise.

Any ideas on how to remedy this would be greatly appreciated.

I'm using Snakemake 5.2.2.

snakemake log • 763 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by camerond150
3
gravatar for camerond
12 months ago by
camerond150
Cardiff
camerond150 wrote:

It was a typo in the braces!

log:
    "logs/homer/annotation.ATAC24to31_fetal_hMG.consensusPeak.(THRESH}.log"
ADD COMMENTlink written 12 months ago by camerond150

Thanks for following up and sharing the solution :)

ADD REPLYlink written 12 months ago by ATpoint34k
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