Question: The errors reported when running snakemake file with log function
gravatar for wangdp123
4 months ago by
wangdp123120 wrote:

Hi there,

I am using snakemake to compile a pipeline and encounter an issue as follows:

The error reported is:

RuleException in line 284 of pipeline_1.snakemake: Wildcards in input, params, log or benchmark file of rule fastx_collapser cannot be determined from output files: 'PIPELINE_NAME'

The scripts in snakemake file is:

PIPELINE_NAME = "pipeline_1"

FOLDER = "/data/analysis/"

    rule test1:

        shell: """
               program -i {input} -o {output} 2> {log.err} 1> {log.out}

BTW, when the log function is not used, there is no problem. Therefore, I am just thinking about something wrong with the log file function.

Would you like to help me out about this problem?

Thank you very much,



snakemake • 357 views
ADD COMMENTlink modified 4 months ago by Devon Ryan85k • written 4 months ago by wangdp123120
gravatar for Devon Ryan
4 months ago by
Devon Ryan85k
Freiburg, Germany
Devon Ryan85k wrote:

The contents of wildcards is derived from what you have in the input: and output: directives. Since you've defined only FOLDER and smp there, only those wildcards exist. What you want to do is the following:

    out ="{{FOLDER}}/{}/logs/{{smp}}.log.stdout".format(PIPELINE_NAME),
    err ="{{FOLDER}}/{}/logs/{{smp}}.log.stderr".format(PIPELINE_NAME)

The {{...}} will keep things from getting filled in by format() right away.

ADD COMMENTlink written 4 months ago by Devon Ryan85k

Isn't it enough the double quotes?! as in documentation:

rule all:
  input: ["{dataset}/file.A.txt".format(dataset=dataset) for dataset in DATASETS]
ADD REPLYlink written 4 months ago by Medhat7.9k

There are two levels of .format() going on, only one of which is explicit and available when the Snakefile is first run. The second level is implicit and done for each sample that's processed through each rule.

ADD REPLYlink written 4 months ago by Devon Ryan85k

Going to high-jack this thread for some time. @Medhat you are now a moderator see: C: Inviting Biostars moderators to join Biostars slack channel

ADD REPLYlink written 3 months ago by genomax57k
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