snakemake MissingRuleException error!

Question

[yangliu326459]

When I use snakemake, I try to calculate md5 value for several files. The files are as below:

$ ls -l|cut -d" " -f1,2,5-
-rw-r--r-- 1   0 Oct 21 19:46 A.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 B.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 C.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 D.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 E.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 F.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 G.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 H.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 I.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 J.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 K.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 L.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 M.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 N.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 O.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 P.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 Q.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 R.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 S.fastq.gz
-rw-r--r-- 1 131 Oct 21 19:46 test.py
-rw-r--r-- 1   0 Oct 21 19:46 T.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 U.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 V.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 W.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 X.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 Y.fastq.gz
-rw-r--r-- 1   0 Oct 21 19:46 Z.fastq.gz

So I created a Snakefile file called test.py:

rule md5:
    input:
        "{sample}.fastq.gz"
    output:
        "{sample}.md5"
    shell:
        "md5sum {input} > {output}"

and then I run the code and got the error as below:

$ snakemake -c -s test.py *gz
Building DAG of jobs...
MissingRuleException:
No rule to produce I.fastq.gz (if you use input functions make sure that they don't raise unexpected exceptions).

I don't know why this error occurs and how to solve this.

I would be appreciated if anyone could help me figure out it.

Thanks a lot.

Answer 1

[hugo.avila]

Hello, you could pass the output instead of the input and let snakemake figure it out where the fastq file is located:

# -n is for a dryrun and -p is for snake to print the command line
snakemake -c -s test.py A.md5 -np

But this will work only for the A.fastq.gz, to run all you could do some shell string manipulation:

snakemake -c -s test.py $(ls *gz | sed -r 's:\..+::;s:$:.md5:')

This works but it is not very flexible, use glob_wildcards and a rule all. Edit the test.py file:

 from pathlib import Path

sample_dir = Path('.') # local dir 

SAMPLES, = glob_wildcards(sample_dir / '{sample}.fastq.gz') # Extract the name of the samples to create wildcards.

rule all:
    input:
        md5s_files=expand("{sample}.md5", sample=SAMPLES) # force the creation of the files 


rule md5:
    input:
        "{sample}.fastq.gz"
    output:
        "{sample}.md5"
    shell:
        "echo md5sum {input} > {output}"

then run:

snakemake -c -s test.py -np

You can further improve your code by passing the samples_dir variable as an argument inside a config.yaml file or through the command line.

[yangliu326459]

Many thanks!!!

I understand why I was wrong.

Thanks very much!