SnakeMake: MissingRuleException

Question

[Alessandro]

Hi, I am trying to learn snakemake and I don't know why I'm getting this error: I set a Sankefile with the following lines:

rule overlapping:
    input:
        "../ApJa_bowtie_sorted.bam"
    output:
        "./ApJa_overlap_25_30_{sample}"
    shell:
        "python ../../overlapping_reads.py --input {input} --minquery 25 --maxquery 30 --mintarget 25 --maxtarget 30 --overlap {wildcards.sample} --output {output}"

But if I launch snakemake I get this error

$ snakemake  -s Snakefile --cores 20 ApJa_overlap_25_30_4 ApJa_overlap_25_30_5
Building DAG of jobs...
MissingRuleException:
No rule to produce ApJa_overlap_25_30_5 (if you use input functions make sure that they don't raise unexpected exceptions).

My goal would be to launch the python script with different settings in parallel:

python ../../overlapping_reads.py --input ../ApJa_bowtie_sorted.bam --minquery 25 --maxquery 30 --mintarget 25 --maxtarget 30 --overlap 4 --output ApJa_overlap_25_30_4

python ../../overlapping_reads.py --input ../ApJa_bowtie_sorted.bam --minquery 25 --maxquery 30 --mintarget 25 --maxtarget 30 --overlap 5 --output ApJa_overlap_25_30_5

Answer 1

[dariober]

I think

output:
        "./ApJa_overlap_25_30_{sample}"

should be:

output:
        "ApJa_overlap_25_30_{sample}"

so it matches the files you request on the command line.