Snakemake "MissingRuleException" - Cannot Figure Out
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0
Entering edit mode
10 weeks ago
Aryan ▴ 20

Hello, I am looking for some help with Snakemake. I am getting a weird error which I am unable to figure out.

I have a Snakefile (at the bottom), and my directory looks like enter image description here.

When I execute a dry run with,

snakemake -np -s Snakefile.txt

I get no errors. However, when I run,

snakemake -n 1 -p -s Snakefile.txt,

I get the error,

enter image description here

My Snakefile:

import os

sra_codes = ["SRR502329", "SRR502327","SRR502228","SRR502225"]

# Go from SRA code to fastq
# Go from fastq to bam via alignment

rule all:
    input:
        expand("./bams/{name}.bam", name = sra_codes)

rule fastq:
    output:
        "./fastqs/{name}.fastq"
    log:
        stderr = "./logs/{name}.log"
    shell:
        """
        ml sra-tools
        fastq-dump -Z {wildcards.name} > {output}
        2> {log.stderr}
        """

rule bowtie:
    input:
        "./fastqs/{name}.fastq"
    output:
        "./sams/{name}.sam"
    log:
        stderr = "./logs/{name}_bt.log"
    shell:
        """
        ml bowtie2
        bowtie2 -q -p 4 -k 1 --local --no-unal -x hg19 {input} > {output}
        2> {log.stderr}
        """

rule filter:
    input:
        "./sams/{name}.sam"
    output:
        "./bams/{name}.bam"
    log:
        stderr = "./logs/{name}_filt.log"
    shell:
        """
        ml samtools
        ./process.sh {wildcards.name}
        2> {log.stderr}
        """

Everything was working fine till I tried to include the last rule, filter. Here is the process.sh script,

#!/bin/bash

sed '/chrM/d;/random/d;/chrUn/d' ./sams/$1.sam > ./filt_sams/$1_filtered.sam # This filters
# mitochondrial genes + unaligned genes.
ml samtools

samtools view -S -b ./filt_sams/$1_filtered.sam > ./bams/$1.bam
# This converts filtered sam file to bam file.

samtools view -c ./bams/$1.bam # Print count of reads.
ChIP-seq bash snakemake RNA-seq • 314 views
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1
Entering edit mode

-n is --dry-run so not sure why you would put an argument 1 after it

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1
Entering edit mode

I see what you're saying! I meant for it to be "-c 1" - I suppose that should work?

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0
Entering edit mode

right, Snakemake thinks you are trying to build a file called "1"

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